Contacts of the helix formed by residues 133 - 159 (chain C) in PDB entry 3V5I
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 ALA 133 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C GLY 3.8 1.0 + - - -
132C GLN* 1.3 71.4 - - - +
134C THR* 1.3 58.7 + - - +
136C ILE* 3.2 12.5 + - - +
137C GLU* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLN* 4.3 3.1 - - - +
133C ALA* 1.3 76.7 - - - +
135C GLU* 1.3 58.1 + - - +
137C GLU* 3.3 15.7 + - - +
138C ILE* 3.1 35.7 + - + +
171D ARG* 3.6 43.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
129C ALA* 5.4 0.4 - - - -
130C GLN 4.0 11.0 - - - +
131C GLY* 3.5 9.0 - - - -
132C GLN* 2.9 39.8 + - + +
134C THR* 1.3 74.3 - - - +
136C ILE* 1.3 65.4 + - - +
138C ILE* 3.3 11.0 + - + +
139C ALA* 3.1 22.0 + - - +
171D ARG* 3.5 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA* 4.0 29.8 - - + +
130C GLN* 4.4 1.3 - - - -
131C GLY 3.4 32.8 - - - +
132C GLN 2.9 13.2 + - - +
133C ALA* 3.6 10.3 - - - +
135C GLU* 1.3 74.6 - - - +
137C GLU* 1.3 53.2 + - - +
139C ALA* 3.2 3.6 + - - +
140C ALA* 2.8 37.7 + - + +
----------------------------------------------------------
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 ALA 2.9 12.5 + - - +
134C THR* 3.4 19.9 + - - +
136C ILE* 1.3 77.6 - - - +
138C ILE* 1.3 66.3 + - + +
140C ALA* 3.3 7.2 + - + +
141C ASN* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C THR* 3.1 27.9 + - + +
135C GLU* 3.7 10.1 - - + +
136C ILE 3.3 0.4 - - - -
137C GLU* 1.3 78.9 - - + +
139C ALA* 1.3 58.9 + - - +
141C ASN* 3.4 8.4 + - - +
142C HIS* 3.0 27.2 + - - +
171D ARG* 3.6 32.8 - - + -
172D ASP* 3.5 35.0 - - + +
174D PHE* 4.3 12.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLY 4.3 8.3 - - - +
129C ALA* 3.6 26.0 - - + -
135C GLU 3.1 10.5 + - - +
136C ILE 3.5 6.7 - - - +
138C ILE* 1.3 75.3 - - - +
140C ALA* 1.3 65.9 + - - +
142C HIS* 3.2 8.0 + - - +
143C ILE* 3.0 26.7 + - - +
174D PHE* 5.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ILE* 2.8 25.3 + - + +
137C GLU* 3.6 7.6 - - - +
139C ALA* 1.3 73.4 - - - +
141C ASN* 1.3 63.6 + - - +
143C ILE* 3.3 10.5 + - - +
144C LEU* 3.0 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLU* 2.9 40.1 + - - +
138C ILE* 3.7 7.4 - - - +
140C ALA* 1.3 75.4 - - - +
142C HIS* 1.3 58.1 + - - +
144C LEU* 3.8 10.7 - - - +
145C LYS* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE 3.0 17.3 + - - +
139C ALA* 3.2 7.9 + - - +
141C ASN* 1.3 76.4 - - - +
143C ILE* 1.3 62.3 + - - +
145C LYS* 3.4 8.6 + - + +
146C THR* 3.0 41.2 + - - -
95D MET* 4.7 3.4 - - + -
119D GLU* 3.0 33.7 + - - -
174D PHE* 3.4 59.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PRO* 3.9 25.1 - - + +
126C LEU 3.7 9.9 - - - +
127C GLY* 3.6 34.1 - - - +
128C GLY 5.3 0.2 - - - +
139C ALA 3.0 16.0 + - - +
140C ALA* 3.3 15.3 - - - +
142C HIS* 1.3 76.6 - - - +
144C LEU* 1.3 74.0 + - + +
146C THR* 3.3 7.9 + - + -
147C ARG* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C GLN* 6.3 0.9 - - - +
140C ALA* 3.0 30.0 + - + +
141C ASN* 3.8 10.8 - - - +
143C ILE* 1.3 83.2 - - + +
145C LYS* 1.3 61.7 + - - +
147C ARG* 3.1 17.3 + - + +
148C GLU* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASN 2.9 18.1 + - - +
142C HIS* 3.7 9.6 - - + +
143C ILE 3.2 0.2 - - - -
144C LEU* 1.3 75.6 - - - +
146C THR* 1.3 64.1 + - - +
148C GLU* 3.3 18.4 + - + +
149C LYS* 3.0 21.9 + - - +
174D PHE 5.8 0.8 + - - -
176D THR* 3.8 22.6 - - + +
179D GLU* 3.7 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 3.8 33.2 - - + -
75C PHE* 5.2 3.1 - - + -
125C PRO* 5.0 5.4 - - + -
142C HIS* 3.0 30.5 + - - -
143C ILE* 3.6 11.2 - - + -
144C LEU 3.2 0.2 - - - -
145C LYS* 1.3 76.8 - - - +
147C ARG* 1.3 58.2 + - - +
149C LYS* 3.2 9.2 + - + +
150C LEU* 2.9 36.4 + - + +
119D GLU* 3.8 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C GLN* 3.4 37.6 + - - +
125C PRO* 3.7 23.1 - - + +
143C ILE 3.0 13.9 + - - +
144C LEU* 3.1 19.2 + - + +
146C THR* 1.3 77.4 - - - +
148C GLU* 1.3 56.8 + - + +
150C LEU* 3.2 3.9 + - + +
151C ASN* 2.8 47.4 + - - +
166C GLN* 3.0 61.3 + - - +
169C THR* 3.1 29.3 + - - -
170C ASP* 3.6 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 3.1 17.0 + - - +
145C LYS* 3.3 20.7 + - + +
147C ARG* 1.3 74.7 - - - +
149C LYS* 1.3 58.1 + - - +
151C ASN* 3.9 5.6 - - - +
152C ARG* 2.9 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 3.5 36.0 - - + -
145C LYS* 3.0 13.6 + - + +
146C THR* 3.5 12.3 - - - +
148C GLU* 1.3 76.0 - - - +
150C LEU* 1.3 62.0 + - - +
152C ARG* 3.7 27.7 - - - +
153C ILE* 3.2 28.5 + - + +
117D ASN* 2.9 41.7 + - - +
118D ALA 4.7 0.8 + - - -
119D GLU* 3.4 29.6 + - - +
176D THR* 6.0 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 4.3 5.6 - - + -
75C PHE* 3.6 30.5 - - + -
99C MET* 3.7 33.0 - - + -
102C PHE* 3.7 25.6 - - + -
125C PRO* 4.1 28.0 - - + -
146C THR* 2.9 28.6 + - + +
147C ARG* 3.7 3.8 - - + +
149C LYS* 1.3 77.3 - - - +
151C ASN* 1.3 61.4 + - - +
153C ILE 3.4 0.5 + - - -
154C LEU* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ARG* 2.8 36.7 + - - +
148C GLU* 3.9 5.3 - - - +
150C LEU* 1.3 72.6 - - - +
152C ARG* 1.3 54.6 + - - +
154C LEU* 3.2 3.5 + - - +
155C SER* 2.7 37.6 + - - -
162C ILE* 4.4 15.4 + - + +
165C ILE* 3.5 30.0 - - + +
166C GLN* 2.8 44.3 + - - +
169C THR* 4.3 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C GLU* 2.9 24.9 + - - +
149C LYS* 3.7 43.7 - - - +
151C ASN* 1.3 71.9 - - - +
153C ILE* 1.3 72.9 + - - +
155C SER* 3.3 3.3 + - - -
156C GLU* 3.2 39.1 + - + +
162C ILE* 4.2 24.1 - - + +
117D ASN* 4.1 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 3.8 19.1 - - + -
78C TYR* 3.3 33.9 - - + +
102C PHE* 3.7 16.8 - - + -
149C LYS* 3.2 19.4 + - + +
150C LEU 4.0 0.2 - - - +
152C ARG* 1.3 85.0 - - - +
154C LEU* 1.3 65.5 + - - +
156C GLU* 3.3 18.9 + - - +
157C ARG* 3.2 26.5 + - + +
117D ASN* 3.5 36.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C SER 5.8 0.2 - - - -
102C PHE* 4.0 26.6 - - + -
105C ALA* 4.3 15.3 - - + -
122C ILE* 5.1 15.3 - - + -
150C LEU* 2.9 19.1 + - + +
151C ASN* 3.5 6.7 - - - +
153C ILE* 1.3 78.8 - - - +
155C SER* 1.3 55.6 + - - +
157C ARG* 3.1 4.5 + - + +
158C THR* 2.8 44.8 + - + +
165C ILE* 4.0 27.8 - - + -
169C THR* 5.2 5.8 - - + -
183C TYR* 5.7 0.7 - - + -
185C LEU* 4.2 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ASN 2.7 20.5 + - - -
152C ARG 3.3 7.2 - - - -
154C LEU* 1.3 74.2 - - - +
156C GLU* 1.3 56.7 + - - +
158C THR* 3.9 2.2 - - - -
159C GLY* 2.9 32.2 + - - -
160C GLN 2.6 24.7 + - - +
161C SER* 3.8 2.1 - - - -
162C ILE* 3.5 29.0 + - - +
165C ILE* 4.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 5.3 2.1 + - - -
109C LYS* 3.7 11.4 + - - -
152C ARG* 3.2 33.6 + - + +
153C ILE* 3.5 23.5 - - - +
154C LEU 3.3 0.2 - - - -
155C SER* 1.3 76.6 - - - +
157C ARG* 1.3 64.0 + - + +
159C GLY* 4.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 3.3 29.0 + - - -
82C GLN* 3.6 32.9 - - - +
102C PHE* 5.8 0.7 - - - -
105C ALA* 3.5 36.3 + - + +
106C ALA* 4.1 8.6 + - - +
107C GLY 3.7 15.4 + - - -
108C ALA* 5.7 0.2 - - - +
109C LYS* 3.8 34.0 + - - +
112C ARG* 3.1 24.9 + - - +
153C ILE* 3.2 18.4 - - + +
154C LEU* 3.1 6.9 + - + +
156C GLU* 1.3 82.1 - - + +
158C THR* 1.3 62.8 + - + +
184C GLY 3.4 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ALA* 5.0 1.6 - - + -
154C LEU* 2.8 32.6 + - + +
155C SER* 3.6 0.9 + - - -
157C ARG* 1.3 79.5 - - - +
159C GLY* 1.3 62.4 + - - +
160C GLN* 3.2 22.7 + - - +
165C ILE* 4.0 2.6 - - - +
183C TYR* 3.5 28.3 - - + +
184C GLY* 3.4 28.2 - - - +
185C LEU* 3.8 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C SER 2.9 12.4 + - - -
156C GLU 4.3 4.1 + - - -
157C ARG 3.6 1.2 - - - -
158C THR* 1.3 77.6 - - - +
160C GLN* 1.3 63.6 + - - +
161C SER 4.0 0.2 + - - -
----------------------------------------------------------
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