Contacts of the strand formed by residues 62 - 67 (chain D) in PDB entry 3VXR
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 LEU 62 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.8 39.3 - - + +
48D LEU* 4.0 19.1 - - + -
58D THR* 3.2 5.9 - - - -
59D SER* 2.8 47.4 + - - +
60D GLY 3.9 2.4 - - - +
61D ARG* 1.3 83.6 - - + +
63D ASN* 1.3 61.4 + - - +
75D LEU* 4.3 8.3 - - + -
76D TYR 3.5 2.5 - - - +
77D ILE* 3.8 33.2 - - + -
84D ASP* 6.0 1.6 - - - +
88D TYR* 5.3 7.0 - - + +
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Residues in contact with ASN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLU* 3.5 16.1 + - - +
57D GLN 3.1 9.3 - - - +
58D THR* 3.1 27.5 - - + +
61D ARG 3.9 0.8 + - - -
62D LEU* 1.3 75.0 - - - +
64D ALA* 1.3 67.3 + - - +
65D SER* 4.4 4.2 - - - +
75D LEU* 3.5 3.2 - - - -
76D TYR* 2.7 79.9 + - + +
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Residues in contact with ALA 64 (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 TRP* 4.0 16.4 - - + -
48D LEU* 3.6 21.2 - - + +
50D ILE* 3.5 24.8 - - + +
56D GLU* 3.2 5.0 - - - +
57D GLN* 2.8 36.0 + - + +
63D ASN* 1.3 76.0 - - - +
65D SER* 1.3 60.7 + - - +
74D THR 3.2 9.9 - - - +
75D LEU* 4.2 2.5 - - + -
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Residues in contact with SER 65 (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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50D ILE* 4.0 1.9 - - - +
55D ARG 3.5 9.2 - - - -
56D GLU* 4.2 6.7 - - - +
63D ASN* 4.2 4.7 + - - +
64D ALA* 1.3 73.9 - - - +
66D LEU* 1.3 62.9 + - - +
72D ARG 5.6 0.2 + - - -
73D SER* 2.9 23.3 + - - -
74D THR* 2.9 31.7 + - - -
76D TYR* 4.2 15.9 + - - -
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Residues in contact with LEU 66 (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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25D PHE* 3.9 14.1 - - + -
30D ILE* 5.4 5.8 - - + -
32D ASN* 5.8 0.2 - - - -
33D LEU* 3.9 29.4 - - + +
50D ILE* 3.8 26.9 - - + +
51D GLN 3.8 25.6 - - - +
52D SER* 4.7 4.7 - - - +
54D GLN 4.0 5.6 - - - +
55D ARG* 2.9 38.1 + - - +
65D SER* 1.3 79.5 + - - +
67D ASP* 1.3 69.1 + - - +
68D LYS* 4.3 19.5 + - + +
72D ARG 3.7 9.6 - - - +
73D SER* 4.7 0.2 - - - +
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Residues in contact with ASP 67 (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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25D PHE* 4.5 0.5 - - - -
55D ARG* 5.1 10.3 + - - +
66D LEU* 1.3 75.3 - - - +
68D LYS* 1.3 58.4 + - - +
69D SER* 3.4 11.4 + - - -
70D SER* 2.9 37.0 + - - +
71D GLY 3.0 22.0 + - - -
72D ARG* 2.8 23.7 + - + +
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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