Contacts of the strand formed by residues 4 - 12 (chain B) in PDB entry 1VI9
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 ASN 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B MSE 4.0 9.0 + - - +
3B LYS* 1.3 73.3 - - - +
5B ILE* 1.3 61.3 + - - +
6B LEU 4.2 0.2 - - - -
32B ASN* 3.2 33.1 + - - +
34B TRP* 3.8 24.8 + - + -
75B THR* 2.9 41.4 + - - +
76B CYS* 3.9 1.5 - - - -
77B ASP* 2.8 38.6 + - - +
78B ALA 3.3 5.7 + - - +
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Residues in contact with ILE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS 5.5 0.2 - - - -
4B ASN* 1.3 78.2 - - - +
6B LEU* 1.3 69.3 + - - +
7B ALA* 3.4 3.8 + - + +
26B MSE 3.4 33.2 - - + -
31B ALA* 4.4 11.0 - - + -
32B ASN 2.9 13.4 + - - +
33B VAL* 3.3 3.6 - - - +
34B TRP* 2.6 36.4 + - - +
78B ALA 3.4 9.9 - - - +
80B LEU* 4.1 6.3 - - + -
231B LEU* 3.7 24.7 - - + -
232B VAL* 3.6 20.4 - - + -
235B LEU* 3.6 28.5 - - + -
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Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.8 22.0 - - + -
5B ILE* 1.3 70.8 - - - +
7B ALA* 1.3 57.6 + - - +
8B ILE* 3.8 24.9 + - + -
34B TRP* 3.6 38.8 - - + +
36B LEU* 3.9 14.1 - - + -
64B VAL* 4.1 11.0 - - + -
67B ILE* 4.7 5.4 - - + -
73B LEU* 5.4 2.5 - - + -
76B CYS* 4.0 12.7 - - - -
78B ALA 2.9 8.0 + - - +
79B VAL* 3.4 11.6 - - + +
80B LEU 2.8 26.7 + - - +
96B ILE* 3.8 19.3 - - + -
100B VAL* 4.5 7.0 - - + -
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.4 8.4 + - + -
6B LEU* 1.3 71.5 - - - +
8B ILE* 1.3 63.6 + - - +
9B GLN* 3.7 9.6 - - - +
19B ASN* 2.9 31.3 + - - +
26B MSE 5.1 6.3 - - + -
33B VAL* 3.8 21.5 - - + -
34B TRP 2.9 8.5 + - - -
36B LEU 2.9 24.8 + - - -
80B LEU* 3.6 10.3 - - + -
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Residues in contact with ILE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.8 25.8 - - + +
7B ALA* 1.3 73.3 - - - +
9B GLN* 1.3 60.1 + - - +
36B LEU* 3.3 30.5 - - + +
38B THR* 3.6 21.9 - - + +
60B LEU* 4.4 5.2 - - + -
79B VAL* 3.8 24.7 - - + -
80B LEU 2.7 14.5 + - - +
81B SER* 3.2 4.8 - - - -
82B GLY 3.0 23.6 + - - -
84B LEU* 4.6 2.1 - - - +
93B ILE* 3.7 27.4 - - + -
96B ILE* 4.0 18.2 - - + -
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ALA* 3.7 4.6 + - - +
8B ILE* 1.3 76.7 - - - +
10B SER* 1.3 62.9 + - - +
18B GLY* 3.6 21.7 + - - +
19B ASN* 3.0 39.5 + - - +
22B ALA* 4.1 14.3 - - - +
26B MSE 5.3 1.6 - - - -
36B LEU 3.4 3.4 + - - -
37B ASN* 3.2 8.0 - - - -
38B THR* 2.8 25.7 + - - +
80B LEU* 3.6 25.9 - - + +
82B GLY* 3.8 20.7 - - - -
83B TYR 3.6 12.3 + - - +
112B ASP* 5.4 1.0 - - - +
224B ASP* 3.8 15.9 + - - +
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Residues in contact with SER 10 (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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9B GLN* 1.3 76.5 - - - +
11B HIS* 1.4 60.8 + - - +
12B VAL* 4.3 4.9 - - - -
17B ALA* 3.8 6.3 - - - +
18B GLY* 3.2 22.2 + - - -
19B ASN* 2.8 33.1 + - - +
38B THR* 3.2 9.4 + - - +
39B VAL* 3.4 18.8 - - - -
41B PHE* 5.8 0.7 - - - -
83B TYR* 3.6 29.9 + - - +
300B BME 4.7 1.9 + - - -
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Residues in contact with HIS 11 (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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27A ARG* 6.0 0.4 - - - -
35A PRO* 2.8 46.5 + - + -
37A ASN* 3.8 9.8 + - - -
10B SER* 1.4 74.3 - - - +
12B VAL* 1.3 76.7 + - - +
13B VAL* 4.3 0.2 - - + -
19B ASN* 5.4 1.0 - - - +
20B SER* 2.8 25.1 + - - -
37B ASN* 3.4 32.3 + - + +
39B VAL* 3.1 16.1 + - - +
40B GLN* 3.3 32.6 + - + -
41B PHE 2.9 24.6 + - - -
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 4.6 1.0 - - - +
10B SER* 4.3 4.5 - - - -
11B HIS* 1.3 85.9 - - - +
13B VAL* 1.3 67.7 + - - +
14B TYR 3.4 18.6 - - - +
15B GLY 3.7 10.6 - - - +
16B HIS 3.9 1.3 - - - +
17B ALA* 3.6 35.4 + - + +
20B SER* 2.9 23.8 + - - -
41B PHE* 3.3 14.6 - - + +
43B ASN 3.6 28.0 - - - +
44B HIS* 3.8 12.8 - - + +
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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
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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