Contacts of the helix formed by residues 156 - 168 (chain B) in PDB entry 2V3D
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 LEU 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASP* 5.3 3.6 - - + +
90B ALA* 4.1 14.1 - - + -
91B LEU* 3.8 33.7 - - + -
94B LEU* 3.9 23.1 - - + +
151B GLU* 3.1 13.4 + - + +
152B GLU* 3.4 24.0 - - + +
155B LYS* 1.3 93.7 - - + +
157B LYS* 1.3 67.0 + - + +
158B ILE 3.6 0.7 - - - -
159B PRO* 3.5 2.1 - - - +
160B LEU* 3.4 27.4 + - - +
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 3.6 40.2 - - + +
86B THR 4.4 0.7 - - - +
87B ASP* 3.3 27.6 + - - +
90B ALA* 4.3 11.0 - - + -
121B VAL* 3.7 11.0 - - - -
122B PRO* 2.8 31.4 + - - +
124B ALA 4.4 6.9 + - - -
133B TYR* 4.9 1.0 + - - -
135B TYR* 3.9 2.6 + - - -
152B GLU 2.9 22.5 + - - +
153B ASP* 3.4 17.5 + - - +
156B LEU* 1.3 70.0 - - - +
158B ILE* 1.3 60.9 + - - +
160B LEU* 3.2 2.9 + - - +
161B ILE* 2.8 38.6 + - + +
220B TYR* 3.7 18.2 - - - +
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.8 14.6 - - + -
153B ASP 2.9 28.2 + - - +
154B THR* 4.3 2.9 - - - +
157B LYS* 1.3 71.4 - - - +
159B PRO* 1.4 62.3 - - + +
161B ILE* 3.1 4.8 + - - +
162B HIS* 2.9 47.4 + - + +
220B TYR* 3.5 39.7 - - + -
223B HIS* 3.8 50.3 - - + +
225B LEU* 3.9 10.9 - - + +
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Residues in contact with PRO 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASP 3.7 2.7 - - - +
154B THR 3.4 23.1 - - - +
155B LYS* 3.5 16.2 - - - +
156B LEU 3.5 11.2 - - - +
158B ILE* 1.4 95.1 - - + +
160B LEU* 1.3 56.3 + - + +
162B HIS* 3.4 11.8 + - + +
163B ARG* 3.0 36.7 + - - +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 4.0 20.1 - - + +
90B ALA* 3.6 39.9 - - + +
93B ILE* 3.8 26.7 - - + -
94B LEU* 3.8 17.3 - - + -
105B LEU* 4.0 15.8 - - + +
156B LEU 3.4 17.1 + - - +
157B LYS 3.2 4.7 + - - +
159B PRO* 1.3 75.4 - - + +
161B ILE* 1.3 67.8 + - - +
163B ARG* 3.2 29.4 + - - +
164B ALA* 2.9 24.3 + - - +
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 4.1 19.1 - - + -
119B ILE* 4.3 12.8 - - + -
121B VAL* 3.7 31.0 - - + -
157B LYS* 2.8 28.5 + - + +
158B ILE 3.6 3.8 - - - +
160B LEU* 1.3 76.6 - - - +
162B HIS* 1.3 64.4 + - - +
164B ALA* 3.1 7.5 + - - +
165B LEU* 2.9 27.0 + - + +
174B LEU* 3.8 23.6 - - + -
220B TYR* 4.4 17.5 - - + -
225B LEU* 3.8 24.5 - - + -
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Residues in contact with HIS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE* 2.9 38.6 + - + +
159B PRO* 3.6 11.2 - - + +
161B ILE* 1.3 76.1 - - - +
163B ARG* 1.3 57.7 + - + +
165B LEU* 3.4 9.3 + - - +
166B GLN* 3.0 45.2 + - - +
223B HIS* 2.8 28.9 + - - +
224B LYS* 3.8 12.3 - - + -
225B LEU* 3.6 21.3 - - + +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.1 6.3 - - - +
98B PRO* 4.2 2.6 + - - +
101B GLN* 2.8 42.0 + - - +
102B ASN* 2.6 32.1 + - - +
105B LEU* 3.9 18.1 - - + +
159B PRO* 3.0 24.8 + - - +
160B LEU* 3.6 22.5 - - - +
161B ILE 3.2 0.2 - - - -
162B HIS* 1.3 73.8 - - + +
164B ALA* 1.3 64.6 + - - +
166B GLN* 3.2 23.4 + - - +
167B LEU* 3.0 32.0 + - + +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 5.4 1.3 - - + -
105B LEU* 4.6 7.7 - - + +
109B PHE* 3.6 43.0 - - + +
119B ILE* 3.9 15.9 - - + -
160B LEU 2.9 13.0 + - - +
161B ILE* 3.4 8.7 - - - +
163B ARG* 1.3 76.4 - - - +
165B LEU* 1.3 61.9 + - - +
167B LEU* 3.1 15.8 + - - +
168B ALA* 3.2 14.5 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 4.4 3.1 - - + -
161B ILE* 2.9 29.1 + - + +
162B HIS* 3.6 9.0 - - - +
164B ALA* 1.3 78.2 - - - +
166B GLN* 1.3 62.0 + - + +
168B ALA* 3.3 22.6 + - - +
172B VAL* 3.4 42.6 - - + +
174B LEU* 4.3 9.2 - - + -
224B LYS 5.8 0.7 - - - +
225B LEU* 3.8 26.0 - - + -
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Residues in contact with GLN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B HIS* 3.0 34.2 + - + +
163B ARG* 3.2 24.4 + - - +
165B LEU* 1.3 76.1 - - + +
167B LEU* 1.3 63.4 + - + +
168B ALA 3.6 3.8 + - - +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASN* 4.3 13.5 - - + +
105B LEU* 3.6 33.2 - - + +
106B LYS* 3.8 32.3 - - + +
109B PHE* 3.9 7.2 - - + -
110B SER* 3.4 27.8 - - - -
111B GLU 4.6 0.5 + - - -
163B ARG* 3.0 21.9 + - + +
164B ALA* 3.1 5.3 + - - +
166B GLN* 1.3 78.5 - - + +
168B ALA* 1.3 60.0 + - - +
169B GLN* 4.0 1.6 + - - +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.2 19.5 - - + +
116B TYR 5.0 2.5 - - - +
164B ALA 3.2 10.4 + - - +
165B LEU 3.5 12.3 - - - +
166B GLN 3.3 4.8 - - - +
167B LEU* 1.3 78.4 - - - +
169B GLN* 1.3 62.2 + - - +
170B ARG* 3.5 19.7 - - + +
172B VAL* 3.7 21.3 - - + -
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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
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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) + - + + + + + -
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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