Contacts of the helix formed by residues 34 - 52 (chain B) in PDB entry 2WQT
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 ASN 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B THR* 5.6 8.1 + - - +
30B ILE* 3.2 29.9 + - - +
31B GLY* 3.0 9.0 + - - +
32B ILE 3.6 0.4 - - - -
33B ASP* 1.3 74.2 - - - +
35B ALA* 1.3 65.2 + - - +
36B GLU* 3.7 9.7 + - - +
37B ALA* 3.2 29.1 + - + +
38B ALA 3.3 12.3 + - - -
152B VAL* 3.3 14.9 - - + +
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP 3.4 7.4 + - - +
34B ASN* 1.3 74.2 - - - +
36B GLU* 1.3 64.2 + - - +
38B ALA* 3.2 3.3 + - - +
39B TYR* 3.0 35.5 + - + -
151B PHE* 3.9 26.5 - - + -
152B VAL* 4.2 7.4 - - - +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASN* 3.3 7.3 - - - +
35B ALA* 1.3 78.0 - - - +
37B ALA* 1.3 56.8 + - - +
39B TYR* 3.5 6.7 + - - +
40B ALA* 3.0 27.2 + - + +
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B THR* 5.7 2.5 - - - +
6B LEU* 4.1 25.0 - - + +
30B ILE* 4.4 9.6 - - + -
34B ASN* 3.2 33.6 + - + +
36B GLU* 1.3 76.3 - - - +
38B ALA* 1.3 65.6 + - - +
40B ALA* 3.0 9.2 + - - +
41B ILE* 2.9 28.4 + - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.5 5.7 - - + +
34B ASN 3.3 2.6 + - - -
35B ALA* 3.2 9.9 + - - +
37B ALA* 1.3 76.3 - - - +
39B TYR* 1.3 61.5 + - - +
41B ILE* 3.3 2.3 + - - +
42B GLN* 3.1 17.7 + - - +
152B VAL* 3.4 43.5 - - + +
155B VAL* 3.7 18.0 - - + +
156B ALA* 3.3 20.0 + - - -
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 3.0 31.5 + - + +
36B GLU* 3.9 6.1 - - - +
38B ALA* 1.3 73.8 - - - +
40B ALA* 1.3 60.2 + - - +
42B GLN* 3.4 10.3 + - - +
43B HIS* 2.9 29.2 + - - +
77B PRO 4.3 4.3 + - - -
78B ASP* 3.8 10.9 + - - -
79B PHE* 3.2 72.1 + + - -
151B PHE* 4.4 15.8 - + - -
155B VAL* 3.4 24.6 - - + +
210B TRP* 4.4 4.2 - - - -
214B LYS* 4.2 18.6 + - - -
218B LEU* 6.0 2.2 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.1 20.6 - - + -
36B GLU* 3.0 16.2 + - + +
37B ALA* 3.0 10.6 + - - +
39B TYR* 1.3 74.7 - - - +
41B ILE* 1.3 58.8 + - - +
43B HIS* 3.3 8.7 + - - +
44B ILE* 2.8 38.9 + - + +
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Residues in contact with ILE 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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6B LEU* 3.9 24.7 - - + +
9B LEU* 3.9 31.0 - - + -
10B ALA* 3.8 17.7 - - - +
13B LEU* 3.8 27.1 - - + -
26B LEU* 5.1 1.6 - - + -
30B ILE* 4.2 22.7 - - + -
37B ALA 2.9 18.0 + - - +
38B ALA 3.6 6.7 - - - +
40B ALA* 1.3 72.8 - - - +
42B GLN* 1.3 65.0 + - - +
44B ILE* 3.3 8.8 + - - +
45B ASN* 3.2 23.1 + - - +
156B ALA* 3.9 12.8 - - + +
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA 3.1 8.8 + - - +
39B TYR* 3.6 13.2 - - - +
41B ILE* 1.3 75.5 - - - +
43B HIS* 1.3 57.5 + - - +
45B ASN* 3.2 6.5 + - - +
46B VAL* 2.9 31.9 + - + +
79B PHE* 2.9 41.6 + - - -
81B THR* 3.1 24.1 + - - -
155B VAL* 3.1 30.3 + - - +
156B ALA 3.8 8.0 + - - +
158B ASN* 3.2 36.0 + - + +
159B ALA 4.0 0.4 - - - +
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR 2.9 19.0 + - - +
40B ALA* 3.4 8.3 - - - +
42B GLN* 1.3 74.0 - - - +
44B ILE* 1.3 71.0 + - + +
46B VAL* 3.2 9.4 + - + +
47B GLN* 2.9 56.9 + - + +
220B GLU* 4.1 27.6 + - - -
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Residues in contact with ILE 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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3B LYS* 4.9 10.1 - - + -
6B LEU* 4.9 11.2 - - + +
7B GLU* 3.6 42.4 - - + +
10B ALA* 3.8 19.3 - - + -
14B ARG* 4.5 8.1 - - - +
40B ALA* 2.8 37.9 + - + +
41B ILE* 3.6 9.6 - - - +
43B HIS* 1.3 77.2 - - + +
45B ASN* 1.3 58.3 + - - +
47B GLN* 3.3 6.5 + - - +
48B HIS* 2.9 28.3 + - + +
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Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 3.3 27.7 + - - +
13B LEU* 3.9 20.0 - - - +
14B ARG* 2.8 42.0 + - + +
41B ILE* 3.2 10.9 + - - +
42B GLN* 3.7 8.7 - - - +
43B HIS 3.2 0.4 - - - -
44B ILE* 1.3 77.9 - - - +
46B VAL* 1.3 65.0 + - + +
48B HIS* 3.5 4.1 + - - +
49B ASP* 3.1 30.7 + - - +
156B ALA 4.8 3.4 + - - -
158B ASN* 6.5 0.4 - - + -
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLN* 2.9 29.2 + - + +
43B HIS* 3.7 9.9 - - + +
45B ASN* 1.3 75.1 - - + +
47B GLN* 1.3 65.5 + - - +
49B ASP* 3.2 3.8 + - - +
50B VAL* 2.9 39.0 + - + +
56B VAL* 4.4 4.5 - - + -
59B ARG* 5.3 3.4 - - - +
81B THR* 3.6 39.7 - - + +
83B PHE* 4.1 22.8 - - + -
158B ASN* 4.6 3.8 - - - +
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Residues in contact with GLN 47 (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* 2.9 48.2 + - + +
44B ILE* 3.5 7.0 - - - +
46B VAL* 1.3 84.6 - - - +
48B HIS* 1.3 61.4 + - - +
50B VAL* 3.4 20.5 + - - +
51B ALA* 3.1 22.7 + - - +
220B GLU* 5.3 1.2 - - - +
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.7 43.6 + - - +
44B ILE* 2.9 17.7 + - + +
45B ASN* 3.7 9.0 - - - +
47B GLN* 1.3 77.4 - - - +
49B ASP* 1.3 75.4 + - - +
51B ALA* 3.3 16.4 + - - +
52B GLN* 3.3 38.0 + - + +
1264B K 4.0 6.1 - - - -
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Residues in contact with ASP 49 (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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14B ARG* 4.8 4.0 - - - -
45B ASN* 3.1 19.9 + - - +
46B VAL 3.2 3.3 + - - +
48B HIS* 1.3 87.6 - - - +
50B VAL* 1.3 66.4 + - - +
52B GLN* 3.0 27.4 + - - +
53B GLY 3.3 0.2 + - - -
54B ARG* 2.9 62.7 + - + +
83B PHE* 4.1 9.4 - - + -
1264B K 4.1 6.2 - - - -
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Residues in contact with VAL 50 (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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46B VAL* 2.9 25.7 + - + +
47B GLN* 3.8 21.5 - - - +
48B HIS 3.4 0.2 - - - -
49B ASP* 1.3 75.6 - - - +
51B ALA* 1.3 57.3 + - - +
53B GLY* 2.8 21.3 + - - -
54B ARG 3.6 19.5 - - - +
56B VAL* 3.9 24.9 - - + +
83B PHE* 4.3 2.2 - - + -
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Residues in contact with ALA 51 (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 GLN 3.1 13.2 + - - +
48B HIS* 3.5 13.2 - - - +
49B ASP 3.2 0.4 - - - -
50B VAL* 1.3 75.6 - - - +
52B GLN* 1.3 59.2 + - + +
53B GLY 3.3 1.6 + - - -
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Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 3.3 33.1 + - + +
49B ASP* 3.0 23.0 + - - +
51B ALA* 1.3 76.9 - - + +
53B GLY* 1.3 60.1 + - - +
54B ARG* 3.4 3.4 + - + +
1264B K 3.8 18.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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