Contacts of the strand formed by residues 65 - 70 (chain B) in PDB entry 2QKW
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 LYS 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B LYS* 4.2 22.2 - - - +
58B GLY 3.6 5.8 - - - +
59B VAL* 4.6 16.4 - - + +
63B GLY 3.3 17.9 + - - +
64B ALA* 1.3 75.2 - - - +
66B VAL* 1.3 59.7 + - - +
101B ILE* 5.4 0.9 - - - +
115B LYS* 4.2 5.5 - - - +
116B TYR* 3.5 29.7 + - + +
118B GLU* 5.3 4.0 - - - +
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Residues in contact with VAL 66 (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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40B ASN* 5.8 0.2 - - - +
56B TYR 3.9 0.2 - - - +
57B LYS* 3.6 5.9 - - - +
58B GLY 2.8 44.0 + - - +
60B LEU* 4.0 26.9 - - + -
64B ALA* 3.9 6.7 - - + +
65B LYS* 1.3 75.0 - - - +
67B ALA* 1.3 57.1 + - - +
68B LEU* 3.6 26.2 - - + -
101B ILE* 3.8 17.3 - - + -
113B ILE* 3.2 25.1 - - + -
114B TYR 3.2 18.4 - - - +
116B TYR* 3.9 9.3 - - - +
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Residues in contact with ALA 67 (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 ILE* 5.1 2.0 - - + -
55B VAL* 4.7 11.4 - - + -
56B TYR 3.6 6.1 - - - +
66B VAL* 1.3 75.2 - - - +
68B LEU* 1.3 63.0 + - - +
69B LYS 3.9 0.2 - - - -
112B LEU 3.5 5.4 - - - +
113B ILE* 3.5 0.3 - - - -
114B TYR* 2.7 49.7 + - + +
115B LYS 4.2 10.1 - - - +
116B TYR* 4.3 14.1 - - + -
117B MET 5.4 0.7 - - - +
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Residues in contact with LEU 68 (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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40B ASN* 5.6 7.4 - - + +
41B PHE* 5.0 11.7 - - + -
43B HIS* 5.9 4.5 - - + +
54B LYS 3.5 0.2 - - - +
55B VAL* 3.3 4.8 - - - +
56B TYR* 2.9 54.3 + - + +
57B LYS 4.4 1.8 - - - +
58B GLY* 4.2 13.2 - - - +
60B LEU* 5.7 3.6 - - + -
66B VAL* 3.6 24.2 - - + -
67B ALA* 1.3 69.7 - - - +
69B LYS* 1.3 59.9 + - - +
70B ARG* 3.1 7.7 + - + +
111B ILE* 3.9 14.8 - - + -
112B LEU 3.6 1.6 - - - -
113B ILE* 3.7 41.5 - - + -
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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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52B PHE 5.9 0.9 - - - +
53B GLY 6.0 1.3 - - - -
54B LYS 3.5 5.4 - - - +
55B VAL* 3.8 26.5 - - + -
67B ALA 3.7 1.8 + - - -
68B LEU* 1.3 67.8 - - - +
70B ARG* 1.3 61.2 + - - +
71B ARG* 3.4 38.8 + - + +
85B GLU* 3.3 22.4 + - - -
111B ILE* 3.6 4.1 - - - -
112B LEU* 2.9 33.3 + - + +
114B TYR* 3.6 29.3 + - + +
181B THR* 4.1 8.8 + - - +
182B ASP* 3.9 25.7 - - - +
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Residues in contact with ARG 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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43B HIS* 3.1 42.7 + - - +
53B GLY* 3.1 2.1 - - - -
54B LYS* 2.8 38.8 + - - +
56B TYR* 4.1 25.0 + - + +
68B LEU* 3.1 3.9 + - + +
69B LYS* 1.3 69.8 - - - +
71B ARG* 1.3 58.9 + - - +
72B THR* 3.4 28.6 - - - +
73B PRO* 3.5 9.7 - - + +
109B GLU* 3.1 30.9 + - - -
111B ILE* 4.0 24.0 - - + +
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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