Contacts of the helix formed by residues 67 - 82 (chain B) in PDB entry 2WK6
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 GLN 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 3.8 9.4 - - - +
410A ARG* 3.1 25.6 - - + +
411A ALA* 2.6 61.3 + - - +
64B GLY 4.9 1.6 - - - +
65B SER 4.0 2.5 - - - +
66B ALA* 1.3 76.6 - - - +
68B GLY* 1.3 67.0 + - - +
69B ALA* 4.5 6.0 - - + +
70B GLN* 2.9 31.9 + - + +
71B ILE* 3.0 13.4 + - - +
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 3.9 6.3 - - - -
69A ALA* 3.0 24.1 - - - -
66B ALA 4.1 0.2 + - - -
67B GLN* 1.3 71.7 - - - +
69B ALA* 1.3 63.5 + - - +
71B ILE* 3.1 9.9 + - - +
72B GLY 3.0 18.5 + - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 3.1 25.3 - - - +
71A ILE* 4.7 1.6 - - + -
72A GLY* 3.2 14.6 - - - +
201A ALA* 4.0 21.3 - - + -
204A VAL* 5.9 1.1 - - + -
205A THR* 3.5 17.6 - - + +
67B GLN* 3.3 5.1 - - + +
68B GLY* 1.3 74.4 - - - +
70B GLN* 1.3 58.1 + - + +
73B ALA* 2.8 27.7 + - - +
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.2 42.1 + - + +
205A THR* 4.1 2.7 - - + -
409A SER 3.0 27.9 + - - +
410A ARG* 4.5 0.5 - - - +
36B LEU* 3.4 28.8 - - + +
37B PRO* 4.0 0.6 - - - +
40B ILE* 3.7 16.0 - - + +
57B PHE* 4.5 0.3 - - - -
65B SER 3.6 7.8 - - - +
66B ALA* 3.7 3.4 - - - -
67B GLN* 2.9 45.5 + - + +
69B ALA* 1.3 75.5 - - + +
71B ILE* 1.3 62.3 + - - +
74B MET* 2.9 31.0 + - - +
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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
----------------------------------------------------------
69A ALA* 4.9 1.3 - - + -
57B PHE* 3.8 11.4 - - + -
61B VAL* 3.0 39.5 - - + -
66B ALA* 3.2 26.0 - - + +
67B GLN 3.0 16.8 + - - +
68B GLY* 3.5 9.0 - - - +
70B GLN* 1.3 76.1 - - - +
72B GLY* 1.3 58.9 + - - +
74B MET* 3.5 1.7 + - - +
75B LEU* 3.0 52.1 + - + +
197B ILE* 5.0 10.5 - - + -
198B LEU* 4.0 14.1 - - + -
201B ALA* 4.1 15.3 - - + -
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 3.3 31.2 - - - +
73A ALA* 3.6 11.5 - - - +
68B GLY 3.0 10.3 + - - -
69B ALA 3.9 0.4 - - - -
71B ILE* 1.3 76.2 - - - +
73B ALA* 1.3 65.1 + - - +
75B LEU* 3.4 7.6 + - - +
76B MET* 2.9 25.8 + - - +
205B THR* 5.1 1.3 - - - -
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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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72A GLY 3.6 14.5 - - - +
76A MET* 3.7 11.3 - - + +
205A THR* 3.7 33.9 - - + +
207A THR* 5.5 0.2 - - + -
40B ILE* 3.9 11.2 - - + -
69B ALA 2.8 19.6 + - - +
70B GLN 3.4 4.2 + - - +
72B GLY* 1.3 77.3 - - - +
74B MET* 1.3 57.2 + - - +
77B ALA* 2.9 30.8 + - - +
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Residues in contact with MET 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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39B LEU* 4.5 3.8 - - + +
40B ILE* 3.7 28.9 - - + +
43B LYS* 4.1 19.5 - - - -
49B LEU* 3.3 28.0 - - + -
57B PHE* 3.3 50.7 - - + -
70B GLN 2.9 14.9 + - - +
71B ILE 3.7 1.1 - - - +
73B ALA* 1.3 77.6 - - - +
75B LEU* 1.3 56.6 + - - +
77B ALA* 3.2 3.7 + - - +
78B ILE* 2.9 65.4 + - + +
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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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57B PHE* 5.8 2.2 - - + -
71B ILE* 3.0 30.0 + - + +
72B GLY* 3.7 5.8 - - - +
74B MET* 1.3 77.9 - - + +
76B MET* 1.3 58.7 + - - +
78B ILE* 3.3 8.2 + - + +
79B ARG* 2.8 29.3 + - - +
198B LEU* 4.1 17.9 - - + +
201B ALA* 3.9 25.4 - - + -
202B ARG* 3.5 27.4 - - + +
205B THR* 4.5 2.5 - - - +
207B THR* 3.6 16.7 - - + +
213B LEU* 3.5 37.6 - - + +
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Residues in contact with MET 76 (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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40A ILE* 3.3 34.5 - - + -
44A ARG* 3.5 38.1 - - + -
73A ALA* 3.4 20.4 - - + +
76A MET* 3.7 21.1 - - + -
77A ALA* 3.8 9.9 - - + +
72B GLY 2.9 19.3 + - - +
75B LEU* 1.3 73.0 - - - +
77B ALA* 1.3 66.4 + - - +
79B ARG* 3.1 3.5 + - - +
80B LEU* 2.9 32.2 + - + +
205B THR 3.4 15.0 - - - +
207B THR* 3.6 10.7 - - + +
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Residues in contact with ALA 77 (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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76A MET* 3.7 14.9 - - + +
80A LEU* 4.3 6.7 - - - -
40B ILE* 4.4 4.5 - - + +
43B LYS* 3.9 18.4 - - + -
44B ARG* 4.0 21.1 - - - +
73B ALA 2.9 17.7 + - - +
74B MET* 3.5 7.9 - - - +
76B MET* 1.3 74.9 - - - +
78B ILE* 1.3 58.2 + - - +
80B LEU 3.1 1.4 + - - -
81B ARG* 2.8 35.0 + - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 3.5 28.0 - - + -
57B PHE* 5.6 2.5 - - + -
74B MET* 2.9 47.6 + - + +
75B LEU* 3.6 7.2 - - + +
77B ALA* 1.3 77.0 - - - +
79B ARG* 1.3 57.4 + - - +
82B GLY* 2.7 32.4 + - - +
83B MET* 3.9 33.2 - - + -
91B LEU* 5.6 2.7 - - + -
210B SER* 4.0 8.3 + - - +
212B PRO* 4.4 1.8 - - + -
213B LEU* 4.0 32.8 - - + -
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Residues in contact with ARG 79 (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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44A ARG* 3.2 42.4 - - + +
45A ASP* 4.5 3.4 + - - -
75B LEU 2.8 20.6 + - - +
76B MET* 3.1 6.3 + - - +
78B ILE* 1.3 74.0 - - - +
80B LEU* 1.3 69.9 + - - +
82B GLY* 4.7 1.0 + - - -
206B ALA 3.9 6.5 - - - +
207B THR* 3.8 15.7 - - + +
209B ASP* 2.8 62.5 + - - -
210B SER* 4.2 13.9 - - - +
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Residues in contact with LEU 80 (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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44A ARG* 3.6 33.9 - - + +
77A ALA* 4.4 9.2 - - - -
80A LEU* 3.8 40.2 - - + -
81A ARG* 4.1 17.9 - - + +
76B MET* 2.9 37.5 + - + +
79B ARG* 1.3 90.2 - - - +
81B ARG* 1.3 66.9 + - - +
82B GLY 3.6 0.4 - - - -
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Residues in contact with ARG 81 (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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80A LEU* 4.1 22.9 - - + +
43B LYS* 3.3 25.4 - - - +
44B ARG 3.4 14.9 + - - +
45B ASP* 3.4 22.4 + - - +
46B GLY* 3.8 17.4 - - - +
77B ALA 2.8 20.9 + - - +
80B LEU* 1.3 83.7 + - - +
82B GLY* 1.3 69.0 + - - +
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Residues in contact with GLY 82 (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 LYS* 3.1 24.8 + - - +
78B ILE 2.7 18.5 + - - -
79B ARG 4.5 1.2 + - - -
80B LEU 3.6 1.4 - - - -
81B ARG* 1.3 84.5 - - - +
83B MET* 1.3 62.8 + - - +
212B PRO* 4.7 7.9 - - - -
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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