Contacts of the helix formed by residues 33 - 45 (chain A) in PDB entry 1WXV
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 VAL 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLN* 3.5 20.3 + - - +
29A SER* 5.7 1.6 - - - -
31A GLU* 4.0 10.5 - - + +
32A PRO* 1.3 79.5 - - - +
34A VAL* 1.3 69.6 + - - +
35A GLN* 2.8 18.6 + - + -
36A ASP* 2.8 14.2 + - - +
37A LEU 3.5 5.4 + - - -
64A MET 3.2 16.2 - - - +
65A GLU* 4.1 11.4 - - - +
66A THR 3.4 9.9 - - - +
67A PRO* 3.8 19.5 - - + -
68A LEU* 3.5 11.0 - - - +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 1.3 70.5 - - - +
35A GLN* 1.3 63.4 + - - +
37A LEU* 2.8 23.2 + - + +
38A ALA* 2.9 12.6 + - + +
54A LEU* 5.6 2.7 - - + -
61A LEU* 5.0 7.4 - - + -
63A GLU 2.8 27.4 - - - +
64A MET* 3.5 22.0 - - + +
66A THR 3.0 19.7 + - - +
68A LEU* 3.4 21.3 - - + +
71A LEU* 2.9 38.1 - - + -
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Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 5.1 9.4 - - + +
33A VAL* 2.8 18.9 + - + -
34A VAL* 1.3 77.0 - - - +
36A ASP* 1.3 62.8 + - - +
38A ALA* 3.2 1.7 + - - +
39A GLN* 3.2 26.4 + - - +
49A GLN* 3.6 27.1 + - - +
64A MET* 2.8 44.3 + - + +
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.7 5.5 - - + +
24A THR* 2.5 41.9 + - - +
25A SER 3.4 11.3 - - - +
26A GLN* 3.5 23.9 + - - +
33A VAL 2.8 11.6 + - - +
35A GLN* 1.3 75.7 - - - +
37A LEU* 1.3 58.1 + - - +
39A GLN* 2.9 11.1 + - - +
40A VAL* 2.8 46.7 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 5.0 5.6 - - + -
12A VAL* 4.0 26.0 - - + -
21A LEU* 5.5 1.8 - - + -
23A VAL* 3.8 20.9 - - + +
33A VAL 3.5 2.0 + - - -
34A VAL* 2.8 21.8 + - + +
36A ASP* 1.3 74.9 - - - +
38A ALA* 1.3 62.3 + - - +
40A VAL* 3.5 5.3 + - + +
41A VAL* 3.3 22.6 + - + +
54A LEU* 4.0 28.0 - - + -
61A LEU* 4.5 2.0 - - + -
68A LEU* 3.4 34.5 - - + -
73A ILE* 4.4 14.1 - - + -
79A VAL* 4.9 5.6 - - + -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 2.9 6.1 + - + +
35A GLN 3.5 9.4 - - - +
37A LEU* 1.3 78.6 - - - +
39A GLN* 1.3 61.1 + - - +
41A VAL* 3.4 1.6 + - - -
42A GLU* 3.3 10.7 + - - +
49A GLN* 3.6 29.2 - - + +
52A GLN* 3.0 33.2 + - - +
54A LEU* 4.9 5.8 - - + -
64A MET* 3.7 22.0 - - + -
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLN* 3.2 19.0 + - - +
36A ASP* 2.9 14.1 + - - +
38A ALA* 1.3 76.1 - - - +
40A VAL* 1.3 57.1 + - + +
41A VAL 2.9 2.3 + - - -
42A GLU* 3.0 5.3 + - - +
43A GLU* 2.7 59.4 + - + +
49A GLN* 4.0 18.2 - - - +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.5 33.4 - - + -
22A HIS 3.9 23.6 - - - +
23A VAL* 4.2 8.7 - - + +
24A THR* 4.9 0.9 - - - +
36A ASP* 2.8 41.4 + - - +
37A LEU* 3.5 8.3 + - + +
39A GLN* 1.3 73.0 - - + +
41A VAL* 1.3 53.3 + - - +
43A GLU* 4.3 5.2 - - - -
44A VAL* 2.7 50.2 + - + +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.1 15.5 - - + -
21A LEU* 3.8 19.1 - - + -
37A LEU* 3.3 18.8 + - + +
38A ALA 3.5 1.1 - - - +
39A GLN 2.9 1.6 + - - -
40A VAL* 1.3 73.7 - - - +
42A GLU* 1.3 60.9 - - - +
43A GLU 2.9 4.0 - - - -
45A ILE* 2.5 63.2 + - + +
46A GLY 3.1 3.8 + - - -
47A VAL* 4.3 5.8 - - + +
52A GLN* 3.4 29.6 - - + +
54A LEU* 5.3 0.7 - - + -
81A LEU* 3.5 13.0 - - + -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA 3.3 8.1 + - - +
39A GLN* 3.0 8.7 + - - +
41A VAL* 1.3 78.8 - - - +
43A GLU* 1.3 67.8 + - + +
46A GLY* 3.7 13.6 - - - -
47A VAL 3.0 26.7 - - - +
48A PRO* 3.6 18.5 - - + +
49A GLN* 3.5 28.4 + - - +
52A GLN* 4.4 0.7 - - - +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 2.7 42.0 + - + +
40A VAL* 3.9 5.4 - - - +
42A GLU* 1.3 89.8 - - + +
44A VAL* 1.3 63.5 + - + +
46A GLY* 4.8 0.4 - - - -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 5.9 1.1 - - + -
20A ASP 5.2 0.2 - - - +
21A LEU* 3.1 29.8 - - + -
40A VAL* 2.7 44.0 + - + +
43A GLU* 1.3 80.1 - - + +
45A ILE* 1.3 67.5 + - + +
46A GLY* 4.6 0.2 - - - -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.8 20.2 - - + +
14A HIS* 4.2 14.6 - - + +
19A HIS* 4.9 12.6 - - + -
21A LEU* 4.2 14.6 - - + -
41A VAL* 2.5 48.0 + - + +
44A VAL* 1.3 75.7 - - + +
46A GLY* 1.3 58.2 + - - +
47A VAL* 4.2 13.5 - - + -
81A LEU* 3.6 16.2 - - + -
85A LYS* 3.8 33.5 - - + +
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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