Contacts of the strand formed by residues 70 - 75 (chain B) in PDB entry 2W3B
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 3.9 4.4 - - - -
35B GLN* 4.0 9.3 + - - +
38B THR* 2.9 44.8 + - - +
39B THR* 3.2 23.8 + - - -
47B GLN* 3.7 8.1 + - - +
48B ASN* 3.4 12.8 - - + +
50B VAL* 4.0 20.6 - - + -
67B LEU* 3.3 23.5 - - - +
68B LYS* 2.9 44.3 + - - +
69B GLY* 1.3 81.7 + - - +
71B ILE* 1.3 60.0 + - - +
72B ASN* 2.9 20.9 + - - +
87B HIS* 3.6 8.8 - - - -
301B VG9 3.2 32.5 - - - +
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Residues in contact with ILE 71 (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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47B GLN* 3.7 22.9 - - + +
48B ASN 2.9 11.0 + - - +
49B LEU* 3.4 21.5 - - + +
50B VAL* 2.8 27.4 + - - +
70B ARG* 1.3 71.6 - - - +
72B ASN* 1.3 61.1 + - - +
87B HIS* 3.7 9.6 - - + +
88B PHE* 3.7 31.6 - - + -
105B LEU* 3.8 22.7 - - + -
108B LYS* 4.1 18.2 - - + +
109B VAL* 3.9 19.1 - - + -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 3.7 15.5 - - + +
52B MET* 3.9 6.5 - - + +
57B TRP* 3.6 23.6 - - + -
66B PRO* 3.5 13.5 - - + +
67B LEU* 2.8 46.2 + - - +
70B ARG 2.9 29.7 + - - -
71B ILE* 1.3 74.4 - - - +
73B LEU* 1.3 59.3 + - - +
86B ALA* 3.9 1.6 - - - +
87B HIS* 2.9 46.0 + - - +
88B PHE 3.2 7.1 + - - +
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Residues in contact with LEU 73 (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 LEU* 3.9 23.3 - - + -
50B VAL 2.9 16.9 + - - +
51B ILE* 3.4 9.9 - - + -
52B MET* 3.0 28.0 + - - +
71B ILE 3.9 0.2 + - - -
72B ASN* 1.3 74.7 - - - +
74B VAL* 1.3 77.7 + - - +
75B LEU* 3.9 9.6 - - + -
88B PHE* 3.3 28.7 - - + +
90B SER* 3.7 20.2 - - - +
96B ALA* 3.8 31.9 - - + +
99B LEU* 4.0 10.5 - - + -
105B LEU* 5.7 1.8 - - + -
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Residues in contact with VAL 74 (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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52B MET* 3.3 10.8 - - + +
53B GLY 4.3 0.2 - - - -
54B LYS* 4.0 20.4 - - + -
57B TRP* 3.9 39.3 - - + -
73B LEU* 1.3 81.2 - - - +
75B LEU* 1.3 72.2 + - - +
79B LEU* 4.9 1.6 - - + -
83B PRO* 4.0 24.0 - - + -
86B ALA* 3.9 14.6 - - + -
88B PHE 2.9 8.3 + - - +
89B LEU* 3.3 12.3 - - + +
90B SER 3.1 23.2 + - - -
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Residues in contact with LEU 75 (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 ILE* 3.9 17.5 - - + -
52B MET 2.8 13.8 + - - +
53B GLY* 4.6 0.7 - - - -
54B LYS 3.5 11.6 + - - -
73B LEU* 3.9 18.6 - - + -
74B VAL* 1.3 72.4 - - - +
76B SER* 1.3 63.2 + - - +
90B SER* 3.3 11.7 - - - +
92B SER 3.6 26.5 - - - +
93B LEU* 4.1 11.0 - - + +
96B ALA* 4.3 2.5 - - + -
120B VAL* 3.8 31.4 - - + -
201B NDP 3.2 55.0 - - + +
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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