Contacts of the strand formed by residues 83 - 89 (chain B) in PDB entry 2PQG
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 SER 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B GLU* 3.2 14.8 + - - +
77B LEU 3.1 16.2 - - - -
78B LYS* 3.4 28.4 + - - -
82B SER* 1.3 82.4 + - - +
84B ILE* 1.3 74.2 + - - +
101B PRO* 3.1 30.2 - - - +
153B VAL* 3.8 4.2 - - - +
157B ALA* 3.7 0.7 - - - +
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Residues in contact with ILE 84 (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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75B THR 3.8 0.9 - - - +
76B GLU* 3.5 2.5 - - - -
77B LEU* 2.9 32.2 + - + +
83B SER* 1.3 83.2 - - - +
85B THR* 1.3 64.2 + - - +
86B LEU* 3.5 28.0 - - + -
98B PHE* 4.5 12.1 - - + -
99B ARG 3.4 13.0 - - - +
100B THR* 4.9 0.2 - - - -
101B PRO* 4.8 0.9 - - + -
153B VAL* 3.6 34.3 - - + +
156B LEU* 4.3 15.9 - - + -
157B ALA* 3.8 17.5 - - + +
201B LEU* 3.8 22.7 - - + -
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Residues in contact with THR 85 (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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24B THR* 5.9 1.6 - - + -
74B TYR* 3.6 38.8 - - + -
75B THR 3.6 9.4 - - - +
76B GLU* 3.4 21.0 - - + +
84B ILE* 1.3 74.1 - - - +
86B LEU* 1.3 65.6 + - - +
87B ALA 3.8 0.5 + - - -
98B PHE* 3.0 6.2 - - - -
99B ARG* 2.8 54.6 + - - +
105B TRP* 4.0 4.7 - - + -
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Residues in contact with LEU 86 (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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73B LEU 3.1 8.0 - - - +
74B TYR* 3.3 3.3 - - - -
75B THR* 2.9 52.4 + - - +
77B LEU* 3.9 21.5 - - + -
84B ILE* 3.5 28.0 - - + -
85B THR* 1.3 73.7 - - - +
87B ALA* 1.3 60.2 + - - +
88B ILE* 3.6 6.4 + - + +
95B LEU* 3.8 25.6 - - + -
97B GLY 3.7 1.1 - - - -
98B PHE* 3.6 16.6 - - + -
198B LEU* 5.7 0.7 - - + -
201B LEU* 4.4 20.6 - - + +
205B VAL* 4.5 15.3 - - + -
206B CYS* 6.0 1.3 - - - -
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Residues in contact with ALA 87 (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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72B TRP* 4.2 11.2 - - + -
73B LEU 3.7 3.1 - - - -
74B TYR* 4.2 10.3 - - + -
85B THR 3.8 1.0 + - - -
86B LEU* 1.3 70.8 - - - +
88B ILE* 1.3 58.9 + - - +
95B LEU* 3.8 0.7 - - - +
96B VAL* 2.9 29.1 + - - +
97B GLY 2.9 13.9 + - - +
105B TRP* 3.5 28.7 - - + -
117B LEU* 3.9 21.3 - - + -
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Residues in contact with ILE 88 (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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72B TRP* 3.7 5.8 - - - -
73B LEU* 2.7 56.5 + - + +
75B THR* 4.1 20.6 - - + +
86B LEU* 4.3 7.2 - - + +
87B ALA* 1.3 75.8 - - - +
89B ARG* 1.3 65.2 + - - +
93B LEU* 3.2 42.2 - - + +
94B TYR 3.3 5.8 - - - +
95B LEU* 4.2 10.8 - - + -
205B VAL* 3.9 22.7 - - + -
206B CYS* 3.8 22.4 - - - -
209B LEU* 5.0 2.7 - - + -
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Residues in contact with ARG 89 (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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65B GLU* 3.8 9.3 - - - +
66B LYS 2.9 26.9 + - - -
67B LYS 4.3 5.7 + - - -
69B PRO* 3.8 19.7 - - + +
71B LEU 4.2 5.2 - - - -
72B TRP* 4.1 11.3 - - + -
88B ILE* 1.3 73.6 - - - +
90B MET* 1.3 58.5 + - - +
91B ASP* 2.9 36.1 + - - +
92B ASN* 3.5 26.6 - - - +
93B LEU* 2.8 29.6 + - - +
94B TYR* 2.9 11.9 + - - +
96B VAL* 3.3 26.7 - - + -
116B LEU* 3.6 24.4 - - - +
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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