Contacts of the helix formed by residues 119 - 141 (chain C) in PDB entry 4GTU
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 PHE 119 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C VAL* 3.2 37.2 - - + -
114C CYS* 4.0 6.7 - - - -
116C SER* 3.1 5.1 + - - +
117C PRO 3.0 6.2 + - - +
118C ASP* 1.3 75.3 - - - +
120C GLU* 1.3 76.2 + - + +
121C LYS 2.8 0.9 + - - -
122C LEU* 2.8 5.4 + - - -
123C LYS* 2.6 59.2 + - + +
169C PHE* 3.6 38.8 - + - -
213C VAL* 3.4 25.4 - - + -
214C TRP* 3.6 38.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PRO 4.9 7.0 - - - +
118C ASP 3.6 0.4 - - - -
119C PHE* 1.3 93.0 - - + +
121C LYS* 1.3 63.3 + - + +
123C LYS* 3.9 11.5 - - - +
124C PRO* 3.2 19.8 - - - +
213C VAL* 5.8 3.1 - - - +
----------------------------------------------------------
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 PRO 5.7 0.7 - - - -
118C ASP* 3.5 34.3 - - + +
119C PHE 2.8 1.6 + - - -
120C GLU* 1.3 85.3 + - + +
122C LEU* 1.3 66.4 + - + +
124C PRO* 3.1 22.5 - - - +
125C GLU* 4.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C VAL* 5.0 19.4 - - + +
116C SER* 5.2 11.4 - - - +
118C ASP* 2.9 40.2 + - + +
119C PHE* 2.8 4.7 + - - +
121C LYS* 1.3 82.3 - - + +
123C LYS* 1.3 66.5 + - - +
124C PRO 3.4 0.2 - - - -
125C GLU* 3.1 37.0 + - - +
126C TYR* 3.3 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C VAL* 5.8 1.8 - - - -
119C PHE* 2.6 50.3 + - + +
120C GLU* 3.9 9.7 - - - +
122C LEU* 1.3 73.0 - - - +
124C PRO* 1.3 70.6 - - + +
126C TYR* 3.3 8.8 + - - +
127C LEU* 3.1 47.0 + - + +
169C PHE* 3.9 33.9 - - + -
170C GLU* 5.7 1.1 - - - -
214C TRP* 5.4 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLU 3.2 15.0 - - - +
121C LYS* 3.1 20.2 - - - +
123C LYS* 1.3 91.3 - - + +
125C GLU* 1.3 63.9 + - + +
127C LEU* 3.1 16.8 + - + +
128C GLU* 3.0 27.1 + - - +
----------------------------------------------------------
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 5.1 1.3 - - - +
122C LEU* 3.1 31.7 + - - +
124C PRO* 1.3 81.2 - - - +
126C TYR* 1.3 61.5 + - - +
128C GLU* 3.0 36.7 - - + +
129C GLU* 3.3 18.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
106C VAL* 3.9 8.6 - - + +
109C GLN* 3.3 33.9 - - + -
110C LEU* 3.7 26.8 - - + +
113C VAL* 4.9 18.4 - - + -
122C LEU 3.3 6.3 + - - +
123C LYS* 3.3 8.8 + - - +
125C GLU* 1.3 79.2 - - - +
127C LEU* 1.3 54.2 + - + +
129C GLU* 3.3 11.1 + - + +
130C LEU* 2.8 55.0 + - + +
133C MET* 6.2 2.2 - - + -
166C HIS* 2.6 36.5 + + - -
169C PHE* 4.2 27.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LYS* 3.1 38.5 + - + +
124C PRO* 3.1 15.1 + - + +
126C TYR* 1.3 78.4 - - + +
128C GLU* 1.3 57.6 + - - +
130C LEU* 3.5 10.6 - - + +
131C PRO* 3.0 24.8 - - - +
169C PHE* 3.6 29.4 - - + -
170C GLU* 3.5 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PRO 3.0 11.0 + - - +
125C GLU* 3.0 36.9 - - + +
127C LEU* 1.3 77.2 - - - +
129C GLU* 1.3 69.0 + - + +
131C PRO* 3.5 12.2 - - - +
132C THR* 5.0 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLN* 6.2 0.2 - - - +
125C GLU* 3.3 23.8 + - + +
126C TYR* 3.3 16.1 + - + +
127C LEU 3.2 0.2 - - - -
128C GLU* 1.3 83.2 - - + +
130C LEU* 1.3 67.5 + - - +
132C THR* 2.9 35.9 + - + +
133C MET* 3.6 2.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 6.1 0.4 - - + -
126C TYR* 2.8 42.5 + - + +
127C LEU* 3.5 12.1 - - + +
129C GLU* 1.3 71.2 - - - +
131C PRO* 1.3 65.8 - - + +
133C MET* 3.1 11.3 + - + +
134C MET* 2.8 43.1 + - + +
166C HIS* 3.5 33.2 - - + -
169C PHE* 5.7 1.3 - - + -
170C GLU* 4.1 20.2 - - + -
173C CYS* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU 3.0 21.5 - - - +
128C GLU* 3.5 9.0 - - - +
129C GLU 3.5 3.6 - - - -
130C LEU* 1.3 89.5 - - + +
132C THR* 1.3 60.2 + - - +
134C MET* 4.7 5.2 - - + +
135C GLN* 3.3 21.5 + - - +
173C CYS* 5.9 5.4 - - + -
177C PHE* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU 5.0 0.8 + - - -
129C GLU* 2.9 31.5 + - + +
131C PRO* 1.3 72.4 - - - +
133C MET* 1.3 73.1 + - + +
135C GLN* 3.1 30.8 + - - +
136C HIS* 3.4 21.3 + - + -
50D PHE* 5.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 3.7 20.4 - - + +
105C ASP* 5.9 0.2 - - - +
106C VAL* 4.4 21.1 - - + -
109C GLN* 4.7 16.2 - - - +
126C TYR* 6.2 2.2 - - + -
129C GLU* 3.6 4.0 + - + +
130C LEU* 3.1 14.6 + - + +
132C THR* 1.3 83.7 - - + +
134C MET* 1.3 58.1 + - + +
136C HIS* 2.9 37.8 + - + +
137C PHE* 3.4 21.5 + - + -
56D PHE* 3.7 33.6 - - + -
57D PRO 6.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 6.2 0.2 - - + -
130C LEU* 2.8 22.4 + - + +
131C PRO* 4.7 1.1 - - + -
133C MET* 1.3 74.2 - - + +
135C GLN* 1.3 63.0 + - - +
136C HIS 3.2 0.2 - - - -
137C PHE* 3.4 23.6 + - + +
138C SER* 3.4 16.8 + - - -
163C LEU* 3.4 26.0 - - + -
166C HIS* 3.6 27.6 - - + -
173C CYS* 3.5 17.3 - - + +
174C LEU* 3.0 29.4 - - + -
177C PHE* 3.6 22.8 - - + -
180C LEU* 3.5 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C PRO 3.3 13.6 + - - +
132C THR* 3.1 27.9 + - - +
133C MET 3.0 0.2 - - - -
134C MET* 1.3 78.1 - - - +
136C HIS* 1.3 63.6 + - - +
138C SER* 3.6 3.3 + - - -
139C GLN* 2.9 45.4 + - - +
177C PHE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C THR* 3.4 27.7 + - + -
133C MET* 2.9 23.4 + - + +
135C GLN* 1.3 84.9 + - + +
137C PHE* 1.3 59.2 + - - +
139C GLN* 3.2 15.3 - - + +
140C PHE* 2.8 30.8 + - - +
49D LYS* 6.2 0.9 - - - -
50D PHE* 5.0 12.4 - + - -
54D LEU 4.9 0.7 - - - -
55D ASP 3.2 21.2 - - - +
56D PHE* 3.4 25.0 - + + -
57D PRO* 3.3 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 4.7 10.3 - - + -
102C GLN* 4.6 9.9 - - + -
103C ALA* 4.8 8.1 - - + -
106C VAL* 3.8 33.2 - - + -
133C MET* 3.4 19.5 + - + -
134C MET* 3.7 44.4 - - + +
135C GLN 3.3 0.4 - - - -
136C HIS* 1.3 77.1 - - - +
138C SER* 1.3 62.6 + - - +
140C PHE* 3.1 9.9 + - - +
141C LEU 3.2 10.2 + - - -
147C PHE* 3.4 24.5 - + + -
159C ALA* 6.0 4.0 - - + -
162C VAL* 4.2 9.6 - - + -
163C LEU* 3.8 12.8 - - + -
180C LEU* 4.0 16.2 - - + -
56D PHE* 3.7 25.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C MET 3.4 4.9 + - - -
135C GLN 4.1 4.9 - - - -
137C PHE* 1.3 78.5 - - - +
139C GLN* 1.3 58.3 + - - +
141C LEU* 4.6 1.3 - - - +
142C GLY* 3.0 27.7 + - - -
177C PHE* 3.5 31.8 - - - +
179C ASN* 2.9 36.1 + - - +
180C LEU* 3.7 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLN* 2.9 39.7 + - - +
136C HIS* 3.2 18.0 - - + +
137C PHE 3.1 0.2 - - - -
138C SER* 1.3 79.6 - - - +
140C PHE* 1.3 60.7 + - - +
142C GLY* 4.0 7.1 + - - -
144C ARG* 5.7 0.7 + - - -
54D LEU 6.1 0.2 - - - +
55D ASP* 4.7 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG* 2.8 68.8 + - + +
98C ILE* 4.0 15.9 - - + -
99C LEU* 3.7 27.1 - - + -
136C HIS 2.8 15.9 + - - +
137C PHE 3.1 5.4 + - - +
139C GLN* 1.3 76.2 - - - +
141C LEU* 1.3 53.9 + - - +
144C ARG* 2.6 34.0 + - - -
147C PHE* 3.6 18.4 - + + -
55D ASP* 3.5 37.7 - - + +
56D PHE* 3.6 22.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C PHE 3.2 9.4 + - - +
138C SER* 4.2 2.5 - - - +
140C PHE* 1.3 77.2 - - - +
142C GLY* 1.3 70.3 + - - +
144C ARG* 3.0 58.7 - - - +
145C PRO 3.2 14.6 - - - +
146C TRP 3.6 18.8 - - - +
147C PHE* 3.7 28.6 - - + +
179C ASN* 3.8 22.0 - - + +
180C LEU* 4.5 2.7 - - + +
183C PHE* 3.8 35.0 - - + -
186C ARG* 5.2 0.9 - - - +
----------------------------------------------------------
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