Contacts of the strand formed by residues 81 - 88 (chain B) in PDB entry 2QNJ
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 GLU 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 4.5 16.7 - - + +
72B LEU* 4.4 13.4 - - + +
73B ALA 3.2 11.2 - - - +
74B ARG* 5.0 5.4 - - + -
79B GLY 3.5 4.0 + - - +
80B ARG* 1.3 78.0 - - - +
82B VAL* 1.3 66.5 + - - +
119B PHE* 5.9 0.5 - - - -
134B TYR* 3.8 38.9 + - + +
363B LEU* 5.5 0.2 - - - +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 3.7 32.1 - - + -
72B LEU* 3.4 9.5 - - - +
73B ALA* 2.8 44.6 + - + +
75B HIS* 5.5 0.2 - - + -
80B ARG 4.7 4.7 - - - +
81B GLU* 1.3 80.2 - - - +
83B ALA* 1.3 61.5 + - - +
84B ILE* 3.9 4.3 - - + -
119B PHE* 4.2 5.6 - - + -
131B ILE* 3.8 20.9 - - + -
132B MET 3.4 13.0 - - - +
133B GLU* 5.4 0.2 - - - -
134B TYR* 3.8 8.3 - - - +
363B LEU* 4.0 25.6 - - + -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 4.8 3.6 - - + -
70B VAL* 4.2 18.2 - - + -
71B LYS 3.5 4.5 - - - +
82B VAL* 1.3 73.9 - - - +
84B ILE* 1.3 61.9 + - - +
85B LYS* 5.8 0.2 - - - -
130B LEU 3.5 0.9 - - - +
132B MET* 2.8 47.6 + - + +
133B GLU 4.2 7.9 - - - +
134B TYR* 3.8 24.4 - - + +
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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
----------------------------------------------------------
53B ILE* 4.2 4.7 - - + -
56B TYR* 3.7 26.0 - - + -
58B LEU* 3.8 14.6 - - + -
70B VAL* 3.3 5.7 - - - -
71B LYS* 2.7 37.5 + - + +
73B ALA* 3.4 31.6 - - + -
82B VAL* 3.9 9.0 - - + -
83B ALA* 1.3 75.8 - - - +
85B LYS* 1.3 74.3 + - - +
86B ILE* 3.5 7.2 + - + +
129B TYR* 4.1 17.3 - - + -
130B LEU 3.4 2.0 - - - +
131B ILE* 3.9 27.4 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 6.0 0.9 - - + -
69B LYS 3.7 5.4 - - - +
70B VAL* 4.3 18.2 - - + +
83B ALA 3.8 0.8 + - - -
84B ILE* 1.3 73.2 - - - +
86B ILE* 1.3 61.3 + - - +
87B ILE* 4.1 8.6 - - + +
107B MET* 5.2 2.5 - - - -
116B VAL* 6.5 0.2 - - - -
128B LEU 3.2 1.6 - - - +
129B TYR* 3.2 8.0 - - - -
130B LEU* 2.9 56.7 + - + +
132B MET* 3.6 36.6 - - + -
196B ASP* 3.3 26.4 + - - -
199B PHE* 3.3 27.6 - - + -
203B PHE 3.6 11.1 + - - -
204B THR* 4.6 3.4 - - - +
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Residues in contact with ILE 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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58B LEU* 5.0 5.6 - - + -
67B PHE 3.9 0.3 - - - +
68B ALA* 3.3 5.9 - - - -
69B LYS* 2.9 51.2 + - + +
71B LYS* 3.7 45.3 - - + +
84B ILE* 3.8 10.5 - - + +
85B LYS* 1.3 78.2 - - - +
87B ILE* 1.3 65.2 + - - +
88B ASP* 4.2 0.4 + - + -
127B THR* 3.6 21.3 - - + -
128B LEU 3.5 2.5 - - - -
129B TYR* 3.8 26.2 - - + +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 3.7 12.3 - - + +
68B ALA* 4.4 9.2 - - + -
85B LYS* 4.6 6.5 - - + -
86B ILE* 1.3 82.7 - - - +
88B ASP* 1.3 62.0 + - - +
89B LYS* 3.3 5.1 + - - +
92B LEU* 4.2 14.6 - - + -
100B LEU* 3.7 42.0 - - + -
127B THR* 3.3 6.1 - - - +
128B LEU* 2.9 44.6 + - + +
130B LEU* 4.1 19.3 - - + -
199B PHE* 4.4 4.3 - - + -
203B PHE* 4.3 23.1 - - + +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 3.2 18.6 + - - +
86B ILE* 4.2 1.4 + - + +
87B ILE* 1.3 72.7 - - - +
89B LYS* 1.3 62.2 + - - +
90B THR* 2.7 42.0 + - - +
91B GLN* 3.3 23.1 + - + +
92B LEU* 3.7 12.5 - - - +
126B LYS* 3.4 6.7 - - - +
127B THR* 4.8 4.4 + - - +
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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