Contacts of the helix formed by residues 108 - 137 (chain C) in PDB entry 3EAB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 108 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY* 1.3 60.3 + - - +
110C SER* 2.8 29.1 + - - -
111C MET* 2.9 40.2 + - + +
112C GLU* 3.9 14.7 + - + +
165C THR* 5.6 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C MET* 1.3 82.5 - - - +
110C SER* 1.3 55.8 + - - +
111C MET 3.5 0.4 - - - -
112C GLU* 3.3 28.8 + - - +
113C ALA* 3.2 22.9 + - - +
164C VAL* 4.4 6.4 - - - +
165C THR 3.9 12.9 + - - -
171C CYS* 4.9 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C MET 2.8 17.4 + - - -
109C GLY* 1.3 69.4 - - - -
111C MET* 1.3 57.1 + - - +
112C GLU 3.1 1.1 - - - -
113C ALA* 3.3 6.4 + - - +
114C GLU* 2.8 36.5 + - - +
117C ARG* 4.4 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C MET* 2.9 26.3 + - - +
110C SER* 1.3 77.4 - - - +
112C GLU* 1.3 58.4 + - + +
114C GLU* 3.2 8.5 - - - +
115C ARG* 2.9 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C MET* 4.3 13.7 - - + +
109C GLY* 3.3 23.5 - - - +
110C SER 3.1 0.6 - - - -
111C MET* 1.3 75.8 - - + +
113C ALA* 1.3 67.1 + - - +
115C ARG* 3.0 25.4 + - - +
116C VAL* 3.0 17.8 + - - +
162C VAL* 3.9 11.9 - - + +
163C ILE* 3.2 22.8 - - - +
164C VAL* 3.7 5.5 - - - -
165C THR* 2.9 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY 3.2 12.9 + - - +
110C SER* 3.8 8.3 - - - +
112C GLU* 1.3 77.9 - - - +
114C GLU* 1.3 62.7 + - - +
116C VAL* 3.2 11.7 + - - +
117C ARG* 3.1 44.1 + - - +
164C VAL* 4.6 4.3 - - + +
170C GLN 5.7 0.4 - - - +
171C CYS* 6.3 0.7 - - - -
174C ALA* 3.9 26.2 - - + -
177C LEU* 5.7 0.2 - - - +
178I THR* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C SER 2.8 14.6 + - - +
111C MET* 3.2 14.1 - - + +
113C ALA* 1.3 76.6 - - - +
115C ARG* 1.3 64.3 + - + +
117C ARG* 2.3 62.1 + - - +
118C VAL* 3.0 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C MET* 2.9 22.8 + - + +
112C GLU* 3.0 17.2 + - - +
114C GLU* 1.3 74.0 - - + +
116C VAL* 1.3 59.6 + - - +
118C VAL* 2.9 32.2 - - + +
119C PHE* 3.2 26.1 + - + -
162C VAL* 3.6 37.5 - - + +
163C ILE 5.1 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLU 3.0 12.5 + - - +
113C ALA* 3.4 9.2 - - - +
114C GLU 3.0 0.4 - - - -
115C ARG* 1.3 78.7 - - - +
117C ARG* 1.3 56.3 + - - +
119C PHE* 3.4 10.0 + - - +
120C HIS* 2.9 24.3 + - - +
159C GLY* 3.8 8.1 - - - +
162C VAL* 3.6 24.7 - - + -
164C VAL* 3.9 11.7 - - + -
174C ALA* 5.1 2.7 - - + +
177C LEU* 4.0 18.2 - - + -
178C GLN* 3.9 18.6 - - + +
181C MET* 3.8 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C SER* 4.4 5.5 + - - +
113C ALA* 3.1 26.6 + - - +
114C GLU* 2.3 49.8 + - - +
116C VAL* 1.3 74.3 - - - +
118C VAL* 1.3 61.5 + - - +
120C HIS* 3.0 12.0 + - + +
121C LYS* 2.9 28.6 + - - +
177C LEU* 4.4 15.5 - - + -
174I GLY* 3.4 29.2 + - - +
177I GLY* 3.3 36.4 - - - +
178I THR* 2.8 29.8 + - - +
181I ALA* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 3.0 31.8 + - + +
115C ARG* 2.9 21.1 - - - +
117C ARG* 1.3 74.3 - - - +
119C PHE* 1.3 83.6 + - + +
121C LYS* 3.1 21.8 + - - +
122C GLN* 3.2 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ARG* 3.2 32.8 + - + -
116C VAL 3.7 5.4 - - - +
118C VAL* 1.3 89.2 - - + +
120C HIS* 1.3 62.7 + - - +
121C LYS 3.3 0.2 + - - -
122C GLN* 3.4 3.7 + - + +
123C ALA* 3.0 23.4 + - - +
155C GLU* 3.3 35.7 - - - +
158C LYS* 3.5 57.2 - - + -
159C GLY* 3.5 13.2 - - - -
162C VAL* 3.8 15.3 - - + -
181C MET* 4.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C VAL 2.9 12.3 + - - +
117C ARG* 3.0 14.1 + - + +
119C PHE* 1.3 77.9 - - - +
121C LYS* 1.3 63.4 + - + +
123C ALA* 3.5 2.4 + - - +
124C PHE* 2.8 40.4 + + + +
177C LEU* 5.0 2.7 - - + -
181C MET* 3.4 20.8 - - + +
180I VAL* 5.8 0.7 - - + -
181I ALA* 3.5 40.7 + - + -
184I GLU* 2.7 38.9 + - + +
185I GLN* 3.2 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ARG 2.9 11.8 + - - +
118C VAL* 3.1 14.3 + - - +
120C HIS* 1.3 83.5 - - + +
122C GLN* 1.3 78.8 + - - +
124C PHE* 3.2 5.9 + - + +
125C GLU* 3.0 23.6 + - - +
158I ASP* 5.2 16.2 - - - +
163I ASP* 5.2 8.1 + - - -
184I GLU* 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL 3.2 11.3 + - - +
119C PHE* 3.7 3.1 - - + +
121C LYS* 1.3 93.2 - - - +
123C ALA* 1.3 68.0 + - - +
125C GLU* 3.0 16.2 + - - +
126C TYR* 3.0 43.8 + - + -
155C GLU* 3.4 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE 3.0 17.2 + - - +
120C HIS* 3.6 6.1 - - - +
122C GLN* 1.3 76.4 - - - +
124C PHE* 1.3 64.1 + - - +
126C TYR* 3.1 0.3 + - - -
127C ILE* 2.8 33.0 + - + +
152C GLY* 4.1 7.6 - - - +
155C GLU* 3.6 18.4 - - + +
156C LEU* 3.7 33.9 - - + +
185I GLN* 5.0 1.8 - - - +
188I LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C HIS* 2.8 29.7 + + + +
121C LYS* 3.7 5.6 - - + +
122C GLN 3.2 0.2 - - - -
123C ALA* 1.3 76.6 - - - +
125C GLU* 1.3 61.9 + - - +
128C SER* 2.6 46.0 + - - -
155I GLU 5.2 0.7 - - - -
158I ASP* 3.6 23.8 - - + -
159I GLU* 3.4 38.1 - - + -
184I GLU* 3.7 39.5 - - + -
187I GLU* 3.8 17.7 - - + -
188I LEU* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LYS 3.0 11.9 + - - +
122C GLN* 3.0 13.0 + - - +
124C PHE* 1.3 79.5 - - - +
126C TYR* 1.3 74.0 + - + +
128C SER* 3.1 6.3 + - - -
129C ILE* 2.9 52.0 + - + +
158I ASP* 3.9 17.5 - - - +
159I GLU 6.0 0.7 - - - -
161I GLY* 3.9 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLN* 3.0 44.5 + - + +
123C ALA 3.8 0.2 - - - +
125C GLU* 1.3 84.6 - - + +
127C ILE* 1.3 58.2 + - - +
129C ILE* 3.1 5.2 + - - +
130C ALA 2.8 24.1 + - - -
148C TRP* 3.6 44.4 - + + +
151C LYS* 3.7 41.9 - - + +
152C GLY* 3.6 18.4 - - - +
155C GLU* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ALA* 2.8 25.5 + - + +
126C TYR* 1.3 74.3 - - - +
128C SER* 1.3 58.1 + - - +
130C ALA* 3.7 5.3 - - - +
131C LEU* 2.9 46.0 + - + +
148C TRP 5.0 0.9 - - - +
149C TYR* 4.4 17.7 - - + +
152C GLY* 3.7 20.2 - - - -
153C ILE 4.7 1.1 - - - +
156C LEU* 3.8 33.4 - - + -
184C ASN* 5.6 1.6 - - + -
188C ALA* 5.3 6.7 - - + -
188I LEU* 3.9 28.7 - - + -
192I LEU* 4.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 2.6 49.0 + - - -
125C GLU* 3.4 7.4 - - - -
127C ILE* 1.3 75.3 - - - +
129C ILE* 1.3 66.4 + - - +
131C LEU* 3.4 10.5 + - - +
132C ARG* 3.1 24.0 + - - +
158I ASP 5.5 1.1 - - - -
159I GLU* 4.1 20.9 + - - -
187I GLU* 5.1 0.7 + - - -
188I LEU* 4.2 3.5 - - - +
191I ARG* 5.0 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLU* 2.9 45.0 + - + +
126C TYR* 3.5 6.1 - - + +
128C SER* 1.3 73.7 - - - +
130C ALA* 1.3 68.6 + - - +
132C ARG* 2.8 17.0 + - + +
133C ILE* 2.9 27.7 + - + +
148C TRP* 3.8 48.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR 2.8 11.9 + - - +
127C ILE 3.7 5.4 - - - +
129C ILE* 1.3 74.1 - - - +
131C LEU* 1.3 54.2 + - - +
133C ILE* 4.6 0.4 - - - -
134C ASP* 2.7 37.7 + - - +
145C ALA* 3.5 9.9 - - - +
148C TRP* 3.6 11.3 - - + +
149C TYR* 3.4 55.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ILE* 2.9 39.8 + - + +
128C SER* 3.8 4.5 - - - +
129C ILE 3.1 0.2 - - - -
130C ALA* 1.3 77.3 - - - +
132C ARG* 1.3 57.6 + - - +
134C ASP* 3.4 1.7 - - - +
135C GLU* 2.9 43.7 + - - +
149C TYR* 3.4 20.4 - - - +
188I LEU* 4.1 12.3 - - + -
191I ARG* 3.7 40.2 - - + +
192I LEU* 3.6 30.1 - - + +
195I LEU* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C SER 3.1 12.6 + - - +
129C ILE* 2.8 13.1 + - + +
131C LEU* 1.3 76.0 - - - +
133C ILE* 1.3 68.9 + - + +
135C GLU* 3.0 16.4 + - - +
136C ASP* 3.0 33.2 + - - +
159I GLU 5.9 0.8 + - - -
160I ALA* 5.2 9.5 + - - +
191I ARG* 4.6 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ILE* 2.9 29.4 + - + +
130C ALA 3.8 3.8 - - - +
132C ARG* 1.3 76.1 - - + +
134C ASP* 1.3 69.3 + - - +
136C ASP* 2.9 14.5 + - - -
137C GLU* 3.1 26.8 + - + +
142C LYS 5.0 0.9 - - - +
144C GLN* 3.6 35.4 - - + +
145C ALA* 3.7 12.1 - - + +
148C TRP* 4.4 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ALA 2.7 23.7 + - - +
131C LEU* 3.4 5.6 - - - +
133C ILE* 1.3 76.8 - - - +
135C GLU* 1.3 56.3 + - - +
136C ASP 3.1 0.3 + - - -
137C GLU 3.8 0.9 + - - +
142C LYS* 2.6 46.1 + - - +
145C ALA* 3.8 9.2 - - + +
149C TYR* 2.6 30.6 + - - +
191C ARG* 2.8 41.3 + - - -
195C LEU* 3.9 6.5 - - - +
195I LEU* 3.5 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU* 2.9 28.8 + - - +
132C ARG* 3.0 7.4 + - - +
134C ASP* 1.3 77.3 - - - +
136C ASP* 1.3 67.4 + - - +
137C GLU 3.9 4.2 - - - +
142C LYS* 4.4 2.8 + - - +
191I ARG* 3.0 42.1 + - - -
194I ARG* 6.2 2.7 - - - -
195I LEU* 4.4 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ARG* 3.0 30.6 + - - +
133C ILE* 2.9 5.6 + - - +
135C GLU* 1.3 83.5 - - - +
137C GLU* 1.3 70.4 + - + +
138C LYS* 4.5 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 3.1 28.1 + - + +
135C GLU 3.9 3.1 - - - +
136C ASP* 1.3 84.7 - - + +
138C LYS* 1.3 72.0 + - - +
141C GLN* 3.5 44.7 - - + +
142C LYS* 2.9 18.2 + - + +
144C GLN* 2.6 30.0 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il