Contacts of the strand formed by residues 54 - 59 (chain D) in PDB entry 2XVA
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 ASP 54 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLY 3.0 14.7 + - - +
33D LYS* 3.5 28.1 - - + +
34D THR 2.7 30.8 + - - +
52D GLY 4.0 1.5 + - - +
53D TYR* 1.3 68.4 - - - +
55D VAL* 1.3 60.2 + - - +
79D ASN* 3.8 31.8 - - - +
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D THR* 3.4 13.0 - - + +
36D ASP* 4.5 5.4 - - + -
45D SER* 3.5 28.5 - - - +
48D LEU* 3.9 14.1 - - + -
49D ALA* 3.7 20.6 - - - +
53D TYR* 3.6 20.4 - - + +
54D ASP* 1.3 75.3 + - - +
56D ASP* 1.3 71.6 + - - +
79D ASN 2.9 14.0 + - - +
80D LEU* 3.4 16.9 + - + -
81D HIS* 2.8 31.9 + - - +
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Residues in contact with ASP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LYS* 3.9 9.9 - - - -
34D THR 2.8 12.6 + - - +
35D LEU* 3.4 11.3 - - + +
36D ASP 2.8 26.7 + - - -
55D VAL* 1.3 77.2 - - - +
57D ALA* 1.3 59.5 + - - +
58D TRP* 3.7 16.8 - - - +
81D HIS* 3.5 21.2 - - - +
94D ARG* 3.6 23.8 + - - -
96D TYR* 2.7 30.0 + - - +
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ASP 3.9 4.3 - - - -
39D CYS* 3.7 14.1 - - - -
45D SER* 3.2 26.2 - - - +
55D VAL 4.0 0.2 - - - -
56D ASP* 1.3 72.1 - - - +
58D TRP* 1.3 61.7 + - - +
65D ILE* 3.7 5.7 - - - +
68D VAL* 5.1 1.8 - - + -
80D LEU* 3.9 18.8 - - + -
81D HIS 2.8 11.8 + - - +
82D THR* 3.3 11.6 - - + -
83D ARG 3.1 21.3 + - - +
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Residues in contact with TRP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 3.6 31.0 - - + -
36D ASP 3.1 10.1 + - - +
37D LEU* 3.8 13.9 - - + -
38D GLY 2.8 26.7 + - - +
39D CYS* 2.9 8.5 + - - -
56D ASP* 3.7 13.3 - - + +
57D ALA* 1.3 86.5 - - - +
59D ASP* 1.3 60.9 + - - +
81D HIS* 5.0 2.0 + - - -
82D THR 4.6 0.2 - - - -
83D ARG* 3.3 51.7 - - + +
85D VAL* 3.7 21.5 - - + -
87D LEU* 5.6 0.2 - - + -
90D LEU* 3.8 28.7 - - + -
92D PHE* 3.7 33.7 - + + -
94D ARG* 4.0 14.1 - - - +
96D TYR* 3.8 15.3 - - - -
1198D SFG 5.6 0.2 - - - -
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Residues in contact with ASP 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLY* 3.2 12.1 - - - -
39D CYS* 3.9 5.6 - - - -
40D GLY* 2.8 20.4 + - - +
58D TRP* 1.3 73.8 - - - +
60D LYS* 1.3 63.0 + - - +
61D ASN* 2.8 24.6 + - - +
64D SER* 5.0 0.2 - - - -
65D ILE* 3.8 19.9 - - + +
83D ARG 3.2 5.9 + - - +
84D VAL* 3.2 11.1 - - - +
85D VAL* 3.1 21.3 + - - +
1198D SFG 2.6 56.3 + - - -
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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
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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