Contacts of the helix formed by residues 149 - 163 (chain B) in PDB entry 3DVA
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 THR 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B MET* 4.1 6.2 - - - +
147B PRO* 3.7 0.6 - - - +
148B SER* 1.3 93.9 - - - +
150B PRO* 1.3 61.7 - - - +
151B TYR* 4.4 0.9 - - - +
152B ASP* 2.7 34.4 + - - +
153B ALA* 2.8 35.0 + - - +
179B PHE* 3.9 14.8 - - + -
181B GLN* 3.3 24.4 + - - +
198B LYS* 4.5 10.3 + - - -
213B VAL* 6.2 0.9 - - + -
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Residues in contact with PRO 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MET 3.3 26.7 - - - +
4B THR* 3.6 10.1 - - - +
5B MET* 3.6 29.8 - - + +
8B ALA* 3.2 11.4 - - + +
149B THR* 1.3 84.0 - - - +
151B TYR* 1.3 61.6 + - - +
153B ALA* 3.3 0.7 + - - +
154B LYS* 3.1 20.8 + - - +
179B PHE* 3.7 20.6 - - + +
181B GLN* 3.2 19.7 - - + +
183B VAL* 3.5 17.0 - - + +
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Residues in contact with TYR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 4.4 1.6 - - - +
150B PRO* 1.3 77.6 - - - +
152B ASP* 1.3 73.7 + - - +
155B GLY 3.3 8.0 + - - -
181B GLN* 2.9 27.6 + - - +
182B GLU 4.2 9.0 - - - +
183B VAL* 3.7 4.7 - - - +
184B PRO* 3.5 32.8 - - + -
188B TYR* 2.6 48.9 + + - -
190B ILE* 3.7 19.0 - - + +
236B ARG* 5.5 2.2 - - - -
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PRO* 4.3 7.6 - - + -
148B SER 4.6 0.2 - - - +
149B THR* 2.7 25.7 + - - +
151B TYR* 1.3 81.8 - - - +
153B ALA* 1.3 61.5 + - - +
155B GLY 3.4 0.2 + - - -
156B LEU* 2.8 50.1 + - + +
190B ILE* 3.6 11.0 - - - +
196B ASP* 4.7 0.5 - - - +
198B LYS* 2.8 24.7 + - - -
234B ASP* 4.1 3.3 - - - +
236B ARG* 2.9 37.0 + - - -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MET* 3.5 27.1 - - + +
8B ALA* 4.6 0.4 - - + -
9B ILE* 3.6 19.5 - - + -
147B PRO* 3.5 19.7 - - + +
149B THR 2.8 20.8 + - - +
150B PRO* 3.3 4.2 + - + +
152B ASP* 1.3 72.2 - - - +
154B LYS* 1.3 57.0 + - - +
157B LEU* 3.0 33.4 + - - +
169B PHE* 3.5 4.0 - - - -
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 3.8 22.6 - - + +
11B ASP* 2.5 31.3 + - + +
12B ALA* 3.7 15.1 - - + +
15B ILE* 3.7 12.7 - - - +
150B PRO 3.1 12.3 + - - +
153B ALA* 1.3 77.4 - - - +
155B GLY* 1.3 63.0 + - - +
158B ILE* 3.0 34.5 + - + +
183B VAL* 3.6 12.3 - - + +
184B PRO 2.7 23.7 + - - -
185B GLU* 3.8 0.4 - - - +
186B GLY 3.1 30.5 + - - +
188B TYR* 3.5 26.7 - - + +
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TYR 3.3 8.5 + - - -
154B LYS* 1.3 79.0 - - - +
156B LEU* 1.3 62.0 + - - +
158B ILE* 3.4 0.5 + - - +
159B SER* 3.1 25.5 + - - -
188B TYR* 3.5 32.7 + - - -
189B THR* 3.7 2.4 - - - -
190B ILE* 3.3 18.5 + - - -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 3.7 33.3 - - + +
147B PRO* 4.3 9.2 - - + -
152B ASP* 2.8 37.9 + - + +
155B GLY* 1.3 69.7 - - - -
157B LEU* 1.3 60.3 + - - +
159B SER* 3.4 1.9 + - - -
160B ALA* 2.8 28.9 + - - +
169B PHE* 4.0 6.6 - - + -
190B ILE* 3.6 37.7 - - + +
191B PRO 3.8 10.5 - - - +
192B ILE* 4.7 7.0 - - + +
194B LYS 5.4 0.2 - - - +
236B ARG* 3.7 29.6 - - + +
237B THR* 4.7 4.7 - - - +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.5 49.4 - - + +
12B ALA* 3.7 11.7 - - + -
13B LEU* 4.0 10.3 - - + -
77B VAL* 5.4 0.2 - - + -
113B THR* 4.2 15.5 - - + -
115B ARG* 4.4 10.1 - - + -
153B ALA 3.0 19.9 + - - +
154B LYS 3.7 2.9 - - - +
155B GLY 3.3 0.2 - - - -
156B LEU* 1.3 73.3 - - - +
158B ILE* 1.3 61.3 + - - +
160B ALA* 3.2 1.7 + - + -
161B ILE* 2.9 55.0 + - + +
169B PHE* 3.8 26.2 - - + -
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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
----------------------------------------------------------
12B ALA* 3.8 19.5 - - + +
15B ILE* 4.5 5.6 - - + -
16B GLU* 3.2 31.4 - - - +
154B LYS* 3.0 35.9 + - + +
155B GLY 3.8 4.5 - - - +
157B LEU* 1.3 76.6 - - - +
159B SER* 1.3 61.3 + - - +
161B ILE* 3.4 1.9 + - - +
162B ARG* 3.0 38.7 + - - +
187B GLU* 4.2 11.0 - - + -
188B TYR 3.4 29.6 - - - +
189B THR* 3.7 20.0 - - + -
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLY 3.1 5.9 + - - -
156B LEU 3.7 6.7 - - - -
158B ILE* 1.3 75.4 - - - +
160B ALA* 1.3 58.4 + - - +
162B ARG* 3.2 6.7 + - - +
163B ASP* 2.9 31.5 + - - +
189B THR* 3.1 25.7 - - - +
190B ILE 2.8 30.9 + - - -
191B PRO* 4.7 0.7 - - - +
192B ILE* 4.0 14.7 - - - +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 2.9 23.9 + - + -
145B VAL* 5.3 0.4 - - + -
156B LEU 2.8 18.8 + - - +
157B LEU* 3.4 9.4 - - - +
159B SER* 1.3 76.1 - - - +
161B ILE* 1.3 61.7 + - - +
163B ASP* 3.4 18.4 + - - +
165B ASP 4.9 0.3 - - - +
167B VAL* 3.7 28.8 - - + +
169B PHE* 4.6 7.6 - - + -
192B ILE* 3.9 11.8 - - + +
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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
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12B ALA 4.8 0.4 - - - +
13B LEU* 3.9 29.2 - - + -
16B GLU* 3.7 31.2 - - + +
23B VAL* 4.1 12.8 - - + -
75B ARG* 2.7 56.8 + - + +
77B VAL* 3.9 26.5 - - + -
111B PRO 4.9 1.2 - - - +
113B THR* 3.3 12.4 + - - +
157B LEU* 2.9 34.9 + - + +
158B ILE 4.0 3.4 - - - +
160B ALA* 1.3 76.6 - - - +
162B ARG* 1.3 51.2 + - - +
163B ASP 3.6 1.7 + - - +
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 4.0 24.3 + - - +
19B ASN* 4.8 8.9 - - - +
75B ARG* 3.0 16.6 + - - +
158B ILE* 3.0 27.0 + - - +
159B SER* 3.2 5.8 + - - +
161B ILE* 1.3 76.5 - - - +
163B ASP* 1.3 64.1 + - - +
164B ASN* 3.3 9.4 + - - +
187B GLU* 4.0 30.3 + - - +
189B THR* 4.1 22.5 - - - +
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A GLU* 6.0 0.5 - - - +
75B ARG* 3.6 6.8 + - - -
111B PRO* 4.0 6.2 - - - +
112B ILE 5.3 0.2 - - - +
143B LYS* 2.7 33.6 + - - +
159B SER 2.9 17.4 + - - +
160B ALA 3.6 12.0 - - - +
161B ILE 3.4 1.8 - - - +
162B ARG* 1.3 76.0 - - - +
164B ASN* 1.3 58.8 + - - +
165B ASP* 2.8 50.2 + - - +
167B VAL* 4.1 16.1 - - + +
192B ILE* 4.3 7.6 - - + +
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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
------------------------------------------------------------
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