Contacts of the strand formed by residues 64 - 68 (chain E) in PDB entry 4NQD
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 TYR 64 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E ARG* 2.9 26.0 + - - -
46E ILE* 3.5 24.7 - - + -
47E TYR* 3.4 13.3 + - + -
60E VAL* 3.4 27.1 - - + -
61E PRO 3.1 14.6 + - - +
62E ASN 3.5 16.4 - - - -
63E GLY* 1.3 80.0 + - - +
65E ASN* 1.3 68.0 + - - +
76E LEU* 4.0 13.9 - - + -
77E ARG 3.3 6.3 - - - +
78E LEU* 3.8 20.4 - - + -
79E GLU 5.7 0.2 - - - +
85E GLN* 3.4 26.0 - - + +
89E TYR* 2.7 44.0 + + - -
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Residues in contact with ASN 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E TYR* 4.0 18.2 + - - -
64E TYR* 1.3 79.4 + - - +
66E VAL* 1.3 81.2 + - - +
76E LEU* 3.6 0.9 - - - +
77E ARG* 2.7 45.7 + - + +
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Residues in contact with VAL 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E TRP* 3.9 5.4 - - + -
47E TYR* 3.5 45.1 - - + -
55E THR* 4.3 18.3 + - + +
65E ASN* 1.3 91.5 + - - +
67E SER* 1.3 66.7 + - - +
74E PHE* 3.4 27.8 - - + -
75E SER 3.2 16.4 - - - +
76E LEU* 3.7 17.7 - - + -
77E ARG* 5.7 0.4 - - - -
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Residues in contact with SER 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E THR* 5.3 0.4 - - - -
66E VAL* 1.3 78.2 + - - +
68E ARG* 1.3 60.2 + - - +
69E LEU* 3.1 25.4 + - - +
74E PHE* 3.3 6.5 - - - -
75E SER* 3.1 39.8 + - - -
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Residues in contact with ARG 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E HIS 3.9 3.8 + - - -
30E ASN* 2.8 36.7 + - - +
32E MET* 3.7 14.6 - - - +
49E SER* 2.8 49.8 + - - +
51E SER 3.5 5.1 - - - -
52E GLU* 3.9 20.8 - - + +
53E GLY* 4.3 9.1 + - - +
54E THR 4.6 1.6 - - - +
55E THR* 3.8 19.0 - - + +
67E SER* 1.3 67.7 - - - +
69E LEU* 1.3 65.9 + - - +
70E ASN* 3.0 21.4 + - - +
71E LYS* 2.8 31.7 + - - +
73E GLU 3.6 7.2 - - - -
74E PHE* 3.9 13.3 - - + -
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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