Contacts of the strand formed by residues 68 - 75 (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 ALA 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLY 5.2 0.2 - - - -
64B LYS 3.8 0.9 - - - -
65B GLY 3.0 31.1 + - - +
66B ASN 3.1 3.4 + - - +
67B PHE* 1.3 81.4 - - - +
69B LYS* 1.3 62.9 + - - +
70B VAL* 5.9 2.5 - - + -
85B LYS* 5.8 3.6 - - + +
86B ILE 3.3 9.6 - - - +
87B ILE* 4.4 11.0 - - + -
203B PHE* 4.0 23.6 - - - +
204B THR* 4.3 14.9 - - - +
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Residues in contact with LYS 69 (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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61B THR* 3.3 31.5 + - + +
63B GLY 3.5 10.5 - - - +
64B LYS* 4.6 9.9 - - + +
68B ALA* 1.3 75.8 - - - +
70B VAL* 1.3 70.4 + - - +
71B LYS* 3.7 25.1 - - - +
85B LYS* 3.7 0.7 - - - -
86B ILE* 2.9 46.4 + - + +
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Residues in contact with VAL 70 (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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61B THR* 3.6 4.0 - - - +
62B ILE* 3.0 46.3 + - + -
63B GLY* 2.8 27.6 + - - +
68B ALA* 5.8 2.9 - - + -
69B LYS* 1.3 77.6 - - - +
71B LYS* 1.3 69.2 + - - +
83B ALA* 4.2 13.2 - - + -
84B ILE 3.3 10.3 - - - +
85B LYS* 4.3 22.2 - - + +
204B THR 6.1 0.9 - - - +
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Residues in contact with LYS 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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58B LEU* 4.1 36.3 - - + +
60B LYS 3.4 12.3 - - - +
61B THR* 3.4 24.5 + - - +
62B ILE* 4.2 3.8 - - - -
69B LYS* 3.7 24.8 - - + +
70B VAL* 1.3 78.4 - - - +
72B LEU* 1.3 68.2 + - - +
73B ALA 3.7 0.3 + - - -
83B ALA* 3.5 2.3 - - - -
84B ILE* 2.7 36.3 + - + +
86B ILE* 3.7 30.1 - - + -
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Residues in contact with LEU 72 (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* 3.8 1.2 - - - -
59B LEU* 2.7 44.8 + - + -
60B LYS* 3.0 39.3 + - + +
62B ILE* 3.9 12.8 - - + +
71B LYS* 1.3 74.9 - - - +
73B ALA* 1.3 61.1 + - - +
81B GLU* 4.4 16.8 - - + +
82B VAL 3.4 15.9 - - - +
83B ALA* 4.7 0.7 - - - +
134B TYR* 3.6 49.6 - - + +
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Residues in contact with ALA 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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56B TYR* 4.2 4.5 - - + -
57B ARG 2.9 20.4 - - - +
58B LEU* 4.1 4.0 - - + -
59B LEU* 4.2 7.0 - - - -
71B LYS 3.7 0.4 + - - +
72B LEU* 1.3 75.6 - - - +
74B ARG* 1.3 58.0 + - - +
81B GLU* 3.2 8.1 - - - +
82B VAL* 2.8 38.1 + - + -
84B ILE* 3.4 33.9 - - + -
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Residues in contact with ARG 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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56B TYR* 3.4 4.5 - - - -
57B ARG* 2.8 48.6 + - + +
59B LEU* 4.3 16.5 - - + +
73B ALA* 1.3 73.5 - - - +
75B HIS* 1.3 70.4 + - - +
76B ILE* 3.4 25.2 + - - +
79B GLY* 3.2 42.2 + - - +
80B ARG 3.4 3.8 - - - +
81B GLU* 4.4 5.6 - - + +
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Residues in contact with HIS 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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55B ASN* 3.4 29.0 + - + -
56B TYR* 3.2 44.2 - + + -
74B ARG* 1.3 71.5 + - - +
76B ILE* 1.3 60.7 + - - +
77B LEU* 3.6 11.2 - - + +
78B THR* 3.0 44.6 - - + -
79B GLY* 2.7 32.7 + - - -
80B ARG 2.8 17.0 + - - +
82B VAL* 5.0 1.1 - - + +
120B GLU* 4.6 3.4 - - - -
356B GLU 5.0 0.2 - - - -
360B THR* 3.1 29.8 + - - -
363B LEU* 3.8 12.5 - - + +
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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
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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