Contacts of the helix formed by residues 35 - 45 (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 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A HIS* 6.2 2.5 - - + -
403A GLU* 6.3 3.1 - - + -
409A SER* 3.2 29.9 + - - -
413A GLU* 5.5 1.2 + - - -
36B LEU* 1.3 66.7 + - - +
37B PRO* 3.3 12.6 - - + -
38B GLU* 3.0 29.0 + - + +
39B LEU* 3.1 22.2 + - - +
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Residues in contact with LEU 36 (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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409A SER 4.5 1.8 - - - +
35B GLN* 1.3 71.0 + - - +
37B PRO* 1.3 73.6 - - + +
38B GLU 3.1 0.2 + - - -
39B LEU* 3.2 15.1 + - + +
40B ILE* 3.0 45.9 + - + +
56B GLY 5.2 0.7 - - - +
57B PHE* 3.7 33.4 - - + -
60B ALA* 3.6 31.0 - - + -
65B SER* 5.5 1.3 - - - +
66B ALA* 4.5 7.0 - - + +
70B GLN* 3.4 32.3 - - + +
74B MET* 4.8 0.2 - - + -
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Residues in contact with PRO 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASP 4.9 3.6 - - - +
204A VAL* 3.7 33.0 - - + +
206A ALA* 3.7 8.6 - - - +
402A HIS* 6.0 0.9 - - - +
408A ARG 4.6 3.1 - - - +
409A SER* 3.4 35.2 - - - +
35B GLN* 3.4 13.2 - - + -
36B LEU* 1.3 94.8 - - + +
38B GLU* 1.3 56.0 + - - +
40B ILE* 3.5 6.1 + - + +
41B ARG* 3.0 26.2 + - - +
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Residues in contact with GLU 38 (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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35B GLN* 3.0 21.9 + - + +
37B PRO* 1.3 75.3 - - - +
39B LEU* 1.3 68.4 + - - +
40B ILE 3.1 1.6 - - - -
41B ARG* 3.0 40.2 + - - +
42B MET* 2.9 45.4 + - + +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 3.1 22.1 + - - +
36B LEU* 3.2 20.2 + - + +
38B GLU* 1.3 76.9 - - - +
40B ILE* 1.3 64.0 - - + +
42B MET* 3.3 15.2 + - + +
43B LYS* 3.3 18.4 + - - +
49B LEU* 3.5 19.6 - - + +
53B ASP* 3.2 60.8 - - + +
56B GLY* 4.7 2.9 - - - -
57B PHE* 4.1 21.8 - - + +
74B MET* 4.5 5.6 - - + +
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A MET* 4.9 4.3 - - - -
204A VAL 4.1 12.3 - - - +
205A THR* 3.5 25.1 - - - +
206A ALA* 3.9 2.9 - - + -
36B LEU* 3.0 32.0 + - + +
37B PRO* 3.6 6.7 - - + +
39B LEU* 1.3 73.4 - - - +
41B ARG* 1.3 54.0 + - - +
43B LYS* 3.3 2.1 + - - +
44B ARG* 2.6 37.1 + - - +
70B GLN* 3.7 30.3 - - + +
73B ALA* 3.9 20.4 - - + +
74B MET* 3.7 27.1 - - + +
77B ALA* 4.4 4.6 - - + +
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Residues in contact with ARG 41 (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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206A ALA* 3.7 13.0 - - + +
399A LEU* 5.8 9.1 - - - +
37B PRO 3.0 13.4 + - - +
38B GLU* 3.0 47.9 + - - +
40B ILE* 1.3 75.8 - - - +
42B MET* 1.3 59.3 + - - +
44B ARG* 3.2 32.5 + - - +
45B ASP* 2.8 47.0 + - - +
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Residues in contact with MET 42 (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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35B GLN 6.3 0.2 - - - +
38B GLU* 2.9 37.8 + - + +
39B LEU* 3.3 50.0 - - + +
41B ARG* 1.3 84.1 - - - +
43B LYS* 1.3 55.7 + - - +
45B ASP* 3.2 6.6 + - - +
46B GLY 3.1 4.0 + - - -
47B GLY* 2.6 35.4 + - - -
48B ARG 4.9 9.6 - - - +
49B LEU* 4.3 9.4 - - + -
53B ASP* 4.4 15.9 - - - +
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Residues in contact with LYS 43 (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 3.3 10.4 + - - +
40B ILE 3.8 5.4 - - - +
42B MET* 1.3 76.5 - - - +
44B ARG* 1.3 67.0 + - - +
46B GLY* 3.0 12.4 + - - -
47B GLY 2.9 30.9 + - - +
48B ARG* 3.6 0.8 - - - +
49B LEU* 4.3 14.0 - - + +
74B MET* 4.1 9.4 - - - -
77B ALA* 3.9 4.0 - - + -
78B ILE* 3.5 47.6 - - + +
81B ARG* 3.3 21.5 - - - +
82B GLY 3.1 23.1 + - - +
83B MET* 4.0 4.5 - - + +
87B GLU* 3.1 35.0 + - - -
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Residues in contact with ARG 44 (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* 3.3 37.0 - - + -
79A ARG* 3.1 27.1 - - - +
80A LEU* 3.5 15.2 - - + +
206A ALA* 2.7 44.4 + - - +
209A ASP* 2.9 26.7 + - - -
40B ILE* 2.6 24.5 + - + +
41B ARG* 3.3 21.6 - - - +
43B LYS* 1.3 73.4 - - - +
45B ASP* 1.3 90.6 + - - +
77B ALA* 4.0 10.0 - - + +
81B ARG* 3.4 21.3 + - - +
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Residues in contact with ASP 45 (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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79A ARG* 4.3 4.2 + - - -
41B ARG* 2.8 28.1 + - - +
42B MET* 3.8 5.3 - - - +
43B LYS 3.1 0.4 - - - -
44B ARG* 1.3 113.2 + - - +
46B GLY* 1.3 58.5 + - - +
47B GLY 3.5 1.1 - - - +
81B ARG* 3.4 12.4 + - - +
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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