Contacts of the strand formed by residues 62 - 66 (chain B) in PDB entry 2NS2
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ASN* 5.2 2.1 - - - -
28B ILE* 4.2 32.8 + - + +
51B VAL* 3.9 22.2 - - + -
53B ASP 2.9 14.4 - - - +
54B GLN* 3.4 40.1 + - + -
59B PRO 3.9 1.5 + - - -
60B SER* 3.8 23.6 - - - -
61B LEU* 1.3 76.1 - - - +
63B LEU* 1.3 64.1 + - - +
64B ILE* 3.7 4.8 - - + +
73B TYR 3.4 1.0 - - - +
74B GLY* 3.3 4.3 - - - -
75B LEU 2.9 38.7 + - - +
77B LEU* 4.1 25.6 - - + -
78B ASN* 3.9 20.6 + - - -
79B LYS* 5.9 0.2 + - - -
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Residues in contact with LEU 63 (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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51B VAL* 3.9 0.9 - - - +
52B LEU* 2.9 27.8 + - + +
53B ASP* 2.8 40.1 + - + +
55B VAL* 4.5 9.2 - - + -
61B LEU* 5.0 2.0 - - + -
62B TYR* 1.3 78.4 - - - +
64B ILE* 1.3 63.0 + - - +
72B VAL* 4.0 13.0 - - + -
73B TYR 3.2 2.0 - - - +
74B GLY* 4.0 4.5 - - - -
142B TYR* 4.1 17.9 - - + +
151B LEU* 4.8 6.7 - - + -
208B ILE* 4.4 10.8 - - + -
209B HIS* 4.4 16.2 - - + -
219B PHE* 5.0 2.9 - - + -
228B ILE* 3.6 37.2 - - + -
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Residues in contact with ILE 64 (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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33B ILE* 4.8 3.6 - - + -
49B GLY 4.2 2.0 - - - -
50B THR 3.8 16.6 - - - +
51B VAL* 4.2 16.8 - - + +
52B LEU* 4.3 4.7 - - - -
62B TYR* 3.7 19.5 - - + +
63B LEU* 1.3 78.8 - - - +
65B LYS* 1.3 71.8 + - - +
66B TYR* 3.6 51.0 + - + +
71B CYS 4.4 0.5 - - - +
72B VAL* 3.6 5.6 - - - +
73B TYR* 2.7 43.9 + - - +
75B LEU* 4.1 11.4 - - + -
77B LEU* 4.1 22.0 - - + -
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Residues in contact with LYS 65 (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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49B GLY* 3.0 1.6 - - - -
50B THR* 3.0 28.2 + - - +
52B LEU* 3.9 16.0 - - + +
64B ILE* 1.3 74.9 - - - +
66B TYR* 1.3 79.5 + - - +
67B ASP* 4.7 2.1 - - - +
68B GLY 4.4 3.8 - - - +
69B PHE 2.7 30.0 + - - +
70B ASP* 5.0 1.5 + - - +
71B CYS 5.1 4.9 - - - +
72B VAL* 5.2 0.7 - - - +
137B MET* 3.4 24.0 - - + +
140B TRP* 4.2 29.4 - - - -
153B MET* 3.1 43.7 - - + -
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Residues in contact with TYR 66 (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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191A LYS* 5.3 1.6 - - - +
33B ILE* 3.8 13.4 - - + +
35B HIS* 2.8 34.4 + + - -
47B TRP* 3.7 32.3 - + + -
48B LYS 3.3 23.3 - - - +
49B GLY* 3.6 3.6 - - - -
64B ILE* 3.6 36.1 + - + +
65B LYS* 1.3 97.8 + - - +
67B ASP* 1.3 66.3 - - - +
69B PHE* 3.2 36.1 + + + +
71B CYS 5.3 1.0 + - - -
73B TYR* 3.8 23.3 - + + -
75B LEU* 3.4 15.6 - - + +
77B LEU* 3.9 1.2 - - - +
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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