Contacts of the strand formed by residues 32 - 37 (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 ARG 32 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLY 5.8 0.4 - - - +
31B CYS* 1.3 73.4 - - - +
33B ILE* 1.3 63.0 + - - +
48B LYS* 4.4 10.5 - - - +
49B GLY* 3.6 15.3 - - - -
50B THR* 3.3 33.9 - - + +
67B ASP* 2.4 46.0 + - - -
88B VAL* 3.2 6.8 - - - +
89B LEU* 2.5 71.0 + - + +
90B PRO 4.1 16.2 - - - +
91B ASP* 4.8 6.3 + - - +
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.8 28.7 - - + -
32B ARG* 1.3 80.5 - - - +
34B GLN* 1.3 61.1 + - - +
35B HIS* 3.3 33.2 - - + -
48B LYS* 3.4 5.0 - - - +
49B GLY 2.8 42.7 + - - +
51B VAL* 3.8 13.9 - - + -
64B ILE* 4.8 2.9 - - + -
66B TYR* 3.8 20.6 - - + +
77B LEU* 4.4 10.1 - - + -
86B LEU* 3.6 16.6 - - + -
87B GLU 3.1 14.4 - - - +
88B VAL* 4.5 2.5 - - + +
89B LEU* 4.3 7.8 - - - +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLN* 5.8 1.4 + - - -
33B ILE* 1.3 78.1 - - - +
35B HIS* 1.3 66.1 + - - +
46B GLN* 2.9 36.2 - - + +
47B TRP 3.1 17.5 - - - +
48B LYS* 2.9 35.6 + - + +
85B ALA 3.6 2.4 - - - +
86B LEU* 3.4 1.4 - - - +
87B GLU* 3.0 40.6 + - + +
89B LEU* 3.9 16.6 - - + +
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Residues in contact with HIS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.3 29.2 - - + -
34B GLN* 1.3 78.6 - - - +
36B GLY* 1.3 79.5 + - - +
37B TRP* 4.2 11.9 - + - -
46B GLN* 3.4 10.2 + - - +
47B TRP* 2.8 54.6 + + + -
66B TYR* 2.8 31.5 + + - -
77B LEU* 4.4 2.1 - - + +
83B VAL* 3.6 22.8 - - + +
84B SER 3.1 18.4 - - - +
85B ALA 3.8 1.8 - - - -
86B LEU* 3.7 15.3 - - + -
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B HIS* 1.3 91.5 + - - +
37B TRP* 1.3 59.5 + - - -
44B VAL* 3.5 13.2 - - - -
45B THR 3.4 10.3 - - - -
46B GLN* 3.6 11.2 - - - +
82B ARG 3.4 1.4 - - - +
84B SER* 2.9 35.3 + - - -
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Residues in contact with TRP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 4.3 4.8 - - + +
188A LEU* 6.1 1.6 - - + -
35B HIS* 4.2 9.6 - + - -
36B GLY* 1.3 73.6 - - - -
38B LYS* 1.3 60.2 + - - +
39B GLU* 3.0 29.1 + - + +
43B PRO 4.1 3.3 - - - +
44B VAL* 3.4 5.6 - - - +
45B THR* 3.0 28.8 + - - +
47B TRP* 3.3 56.6 - + + +
75B LEU* 4.1 18.8 - - + -
80B ASP* 4.6 0.7 - - - -
82B ARG* 3.2 63.7 - - + -
83B VAL* 4.1 14.6 - - + -
226B PHE* 3.8 28.5 - + - -
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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
------------------------------------------------------------
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