Contacts of the strand formed by residues 32 - 41 (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 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A HIS* 4.6 10.9 + - - -
267A GLN* 5.1 7.1 + - - +
269A VAL* 3.7 16.8 - - - +
2B MSE 3.5 34.7 - - - +
3B LYS 2.7 9.4 + - - +
4B ASN* 3.2 28.1 + - - +
5B ILE* 2.9 25.7 + - - +
27B ARG* 4.9 1.5 + - - -
31B ALA* 1.3 76.5 - - - +
33B VAL* 1.3 62.7 + - - +
34B TRP* 4.5 10.3 - - + +
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Residues in contact with VAL 33 (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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13A VAL 4.4 0.3 - - - +
5B ILE* 3.3 4.5 - - + +
7B ALA* 3.8 26.7 - - + -
19B ASN* 4.8 0.7 - - - +
23B GLU* 4.1 22.0 - - + +
26B MSE 3.6 43.5 - - + -
27B ARG* 2.9 43.2 + - + +
31B ALA* 3.9 1.3 + - + +
32B ASN* 1.3 79.7 - - - +
34B TRP* 1.3 70.4 + - - +
35B PRO* 3.2 11.8 - - + +
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Residues in contact with TRP 34 (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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13A VAL* 3.1 26.7 - - + +
14A TYR* 3.6 30.7 - + - -
15A GLY 5.0 3.1 - - - -
4B ASN* 3.8 31.0 + - + +
5B ILE 2.6 18.4 + - - +
6B LEU* 3.6 25.8 - - + +
7B ALA 2.9 24.0 + - - -
32B ASN* 4.5 6.4 - - + +
33B VAL* 1.3 79.6 - - - +
35B PRO* 1.3 61.1 - - - +
36B LEU 3.2 5.2 + - - -
67B ILE* 4.1 25.1 - - + -
72B LYS 3.5 21.1 - - - -
73B LEU* 4.4 7.4 - - + -
75B THR* 3.4 16.6 - - - -
76B CYS* 3.5 28.9 - - + -
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Residues in contact with PRO 35 (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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11A HIS* 2.7 49.1 + - + -
12A VAL 4.4 2.2 - - - +
13A VAL* 3.4 15.9 - - - +
40A GLN* 3.6 0.3 - - - +
7B ALA 3.7 5.8 - - - +
19B ASN* 3.8 19.5 - - + +
23B GLU* 4.5 10.5 - - + -
27B ARG* 3.8 15.7 - - - +
33B VAL* 3.2 21.5 - - + +
34B TRP* 1.3 80.3 - - - +
36B LEU* 1.3 60.8 - - - +
37B ASN* 3.4 8.0 + - - +
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Residues in contact with LEU 36 (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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13A VAL* 3.9 13.0 - - + -
40A GLN* 3.9 13.7 - - - +
6B LEU* 3.9 10.3 - - + -
7B ALA 2.9 11.6 + - - +
8B ILE* 3.3 49.2 - - + +
9B GLN 3.4 2.3 + - - -
34B TRP 3.2 1.8 + - - -
35B PRO* 1.3 69.3 - - - +
37B ASN* 1.3 63.1 + - - +
38B THR 3.6 0.3 + - - -
59B HIS* 4.5 0.2 - - - +
60B LEU* 3.7 46.7 - - + +
63B ILE* 3.8 36.1 - - + -
64B VAL* 4.2 10.3 - - + -
96B ILE* 4.4 0.2 - - + -
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Residues in contact with ASN 37 (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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11A HIS* 3.7 14.5 + - - -
37A ASN* 3.8 13.5 - - - +
40A GLN* 3.0 39.0 + - - +
9B GLN 3.2 4.0 - - - +
11B HIS* 3.4 39.6 + - + +
19B ASN* 3.0 30.5 + - - +
35B PRO* 3.9 7.4 - - - +
36B LEU* 1.3 70.8 - - - +
38B THR* 1.3 63.1 + - - +
39B VAL 3.4 6.7 - - - +
40B GLN* 5.1 2.6 + - + -
55B MSE 3.3 8.6 - - + +
60B LEU* 4.1 5.2 - - - +
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Residues in contact with THR 38 (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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8B ILE* 3.6 32.5 - - + +
9B GLN* 2.8 26.8 + - - +
10B SER* 3.2 5.2 + - - -
37B ASN* 1.3 74.5 - - - +
39B VAL* 1.3 64.8 + - - +
55B MSE 2.9 24.7 + - - +
60B LEU* 4.5 6.7 - - + -
83B TYR 3.0 21.8 + - - +
84B LEU* 4.4 5.4 - - + -
85B GLY 4.4 1.9 + - - -
89B GLN* 3.0 36.8 + - - +
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Residues in contact with VAL 39 (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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10B SER* 3.4 28.7 - - - -
11B HIS* 3.1 31.1 + - - +
37B ASN* 3.6 5.0 - - - +
38B THR* 1.3 83.3 - - - +
40B GLN* 1.3 63.0 + - - +
41B PHE* 3.5 43.1 - - + -
53B CSD 3.4 9.9 - - - +
54B VAL* 3.9 14.8 - - + -
55B MSE 4.2 5.8 - - - -
83B TYR* 4.3 4.0 - - + -
85B GLY* 4.1 15.9 - - - -
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Residues in contact with GLN 40 (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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36A LEU* 4.1 3.4 - - - +
37A ASN* 2.9 53.1 + - - +
55A MSE 3.2 19.8 - - + +
59A HIS* 3.0 28.5 + - - +
63A ILE* 3.7 0.4 - - + +
11B HIS* 3.3 23.9 - - + -
13B VAL* 4.0 16.8 - - + -
37B ASN* 5.1 3.3 + - + -
39B VAL* 1.3 73.8 - - - +
41B PHE* 1.3 62.0 + - - +
52B GLY* 3.2 7.1 - - - -
53B CSD 2.9 31.6 + - - -
55B MSE 4.9 4.5 - - - +
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Residues in contact with PHE 41 (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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63A ILE* 3.9 3.8 - - - -
10B SER* 5.8 0.7 - - - -
11B HIS 2.9 10.5 + - - +
12B VAL* 3.3 8.5 - - + -
13B VAL* 2.8 36.2 + - - +
39B VAL* 3.5 39.3 - - + -
40B GLN* 1.3 82.1 - - - +
42B SER* 1.3 55.8 + - - +
43B ASN 3.7 16.8 - - - +
44B HIS* 5.8 0.9 - - - -
45B THR* 4.9 6.5 - - + -
50B TRP* 3.7 38.4 - + + -
51B THR 3.3 7.4 - - - +
52B GLY 4.3 1.6 - - - -
53B CSD 3.8 19.3 - - - -
54B VAL* 4.3 9.0 - - + -
83B TYR* 4.1 22.2 - + - -
85B GLY* 6.0 0.2 - - - -
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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