Contacts of the strand formed by residues 53 - 60 (chain B) in PDB entry 1VWJ
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 ARG 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 6.0 1.4 - - - +
42B THR* 3.5 18.8 - - + -
43B TYR 3.3 2.9 - - - -
44B GLU* 3.5 42.7 + - + +
50B ALA* 3.1 46.6 + - - +
51B GLU* 3.2 3.4 + - - -
52B SER* 1.3 76.1 - - - +
54B TYR* 1.3 63.7 + - - +
81B ASN* 3.2 22.7 + - - +
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 3.3 8.7 - - - -
43B TYR* 2.9 35.6 + - + +
44B GLU* 5.3 0.2 - - - -
45B SER* 5.1 0.2 - - - -
51B GLU 4.9 1.4 + - - -
52B SER* 3.6 26.7 - - - -
53B ARG* 1.3 76.4 - - - +
55B VAL* 1.3 62.5 + - - +
77B VAL* 3.7 20.2 - - + -
78B ALA 4.4 1.8 - - - +
79B TRP* 3.8 24.2 - + - -
80B LYS* 3.7 37.5 - - - +
81B ASN* 3.6 24.5 + - + -
84B ARG* 3.9 22.9 - - + +
4M PRO* 3.6 35.5 - - + +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY 3.8 8.7 - - - +
42B THR* 4.7 2.9 - - + +
54B TYR* 1.3 76.1 - - - +
56B LEU* 1.3 71.7 + - - +
57B THR* 5.4 1.6 - - - -
76B THR 4.0 0.3 - - - +
77B VAL* 3.9 18.0 - - - +
78B ALA 4.5 2.5 + - - +
80B LYS 5.4 2.0 + - - -
59D ARG* 3.8 43.9 + - - +
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Residues in contact with LEU 56 (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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29B PHE* 3.4 42.8 - - + -
30B ILE 4.2 1.8 - - - +
31B VAL* 4.7 5.4 - - + -
39B LEU* 4.7 2.0 - - + -
40B THR* 3.6 12.7 - - - +
41B GLY* 3.1 35.1 + - - +
42B THR 3.5 28.3 - - - +
43B TYR* 4.0 5.6 - - + +
54B TYR 3.8 0.2 + - - -
55B VAL* 1.3 82.7 - - - +
57B THR* 1.3 68.2 + - - +
75B TRP* 4.1 18.4 - - + -
76B THR 3.2 14.1 - - - +
77B VAL* 3.6 11.7 - - + -
59D ARG* 4.9 0.7 - - - -
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Residues in contact with THR 57 (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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39B LEU 3.3 12.5 + - - -
40B THR* 4.7 6.2 - - - +
55B VAL* 5.4 1.8 - - - -
56B LEU* 1.3 76.8 - - - +
58B GLY* 1.3 59.8 + - - +
75B TRP* 3.2 4.5 - - - -
76B THR* 3.0 25.7 + - - -
38D ALA* 6.3 0.2 - - + -
57D THR* 2.7 28.2 + - - +
58D GLY* 3.1 40.2 - - - +
59D ARG* 3.7 13.7 - - + -
76D THR* 4.8 0.5 + - - -
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Residues in contact with GLY 58 (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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38B ALA* 3.8 0.9 - - - +
39B LEU* 2.9 36.0 + - - +
57B THR* 1.3 77.6 + - - +
59B ARG* 1.3 68.4 + - - -
74B GLY 3.1 15.0 - - - -
75B TRP* 3.7 3.4 - - - -
57D THR* 3.3 15.7 - - - +
76D THR* 4.4 3.4 - - - -
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Residues in contact with ARG 59 (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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36B ASP* 3.2 30.2 + - - +
37B GLY* 3.1 15.2 + - - -
38B ALA* 3.6 19.7 - - - +
39B LEU* 3.8 3.9 - - - +
58B GLY* 1.3 82.3 - - - -
60B TYR* 1.3 62.5 + - - +
73B LEU* 3.2 2.9 - - - +
74B GLY 3.0 29.4 + - - +
55D VAL* 3.9 45.0 + - - +
57D THR* 3.7 21.5 - - + -
76D THR* 3.9 23.3 - - + +
78D ALA* 3.7 29.1 + - + +
80D LYS 5.3 6.1 + - - -
89D ALA* 4.9 0.2 - - - +
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Residues in contact with TYR 60 (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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13B ALA* 5.1 2.2 - - - -
14B GLU* 3.5 23.0 + - + +
17B ILE* 4.0 22.4 - - + -
33B ALA* 3.7 13.7 - - + -
34B GLY 2.8 24.8 + - - -
35B ALA* 4.1 5.4 + - - -
37B GLY* 3.0 46.6 + - - +
38B ALA 3.6 6.1 - - - -
39B LEU* 3.7 18.8 - - + -
59B ARG* 1.3 76.7 + - - +
61B ASP* 1.3 64.5 - - - +
62B SER* 3.6 35.0 + - - -
71B THR* 4.2 4.9 - - + -
72B ALA 3.4 7.2 - - - +
73B LEU* 3.7 16.4 - - + +
78D ALA* 3.5 11.9 - - - +
80D LYS* 5.7 0.5 - - - +
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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