Contacts of the helix formed by residues 34 - 52 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2O THR* 5.6 7.7 + - - +
30O ILE* 3.2 30.1 + - + +
31O GLY* 2.9 9.4 + - - +
32O ILE 3.6 0.4 - - - -
33O ASP* 1.3 73.7 - - - +
35O ALA* 1.3 64.5 + - - +
36O GLU* 3.7 9.9 + - - +
37O ALA* 3.3 29.0 + - + +
38O ALA 3.3 14.2 + - - -
152O VAL* 3.3 10.9 - - - +
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Residues in contact with ALA 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O ASP 3.4 7.5 + - - +
34O ASN* 1.3 74.0 - - - +
36O GLU* 1.3 63.9 + - - +
38O ALA* 3.2 3.6 + - - +
39O TYR* 3.0 36.1 + - + -
151O PHE* 3.9 25.6 - - + -
152O VAL* 4.2 7.8 - - - +
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Residues in contact with GLU 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O ASN* 3.3 8.6 + - - +
35O ALA* 1.3 79.5 - - - +
37O ALA* 1.3 56.6 + - - +
39O TYR* 3.5 6.1 + - - +
40O ALA* 3.0 27.8 + - + +
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Residues in contact with ALA 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O THR* 5.7 2.7 - - - +
6O LEU* 4.1 23.9 - - + +
30O ILE* 4.4 11.0 - - + -
34O ASN* 3.3 32.2 + - + +
35O ALA 3.2 0.8 - - - -
36O GLU* 1.3 76.0 - - - +
38O ALA* 1.3 62.0 + - - +
40O ALA* 3.1 9.3 + - - +
41O ILE* 2.9 34.1 + - - +
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Residues in contact with ALA 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O ILE* 4.5 6.1 - - + +
34O ASN 3.3 2.4 + - - -
35O ALA* 3.2 10.0 + - - +
37O ALA* 1.3 78.1 - - - +
39O TYR* 1.3 62.9 + - - +
41O ILE* 3.3 2.2 + - - +
42O GLN* 3.1 17.8 + - - +
152O VAL* 3.4 42.8 - - + +
155O VAL* 3.8 17.7 - - + -
156O ALA* 3.4 19.8 + - - -
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Residues in contact with TYR 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ALA* 3.0 30.7 + - + +
36O GLU* 3.9 5.8 - - - +
38O ALA* 1.3 73.3 - - - +
40O ALA* 1.3 60.8 + - - +
42O GLN* 3.4 10.6 + - - +
43O HIS* 2.9 29.5 + - - +
77O PRO 4.3 4.5 + - - -
78O ASP* 3.8 10.4 + - - -
79O PHE* 3.2 71.8 + + - -
151O PHE* 4.4 15.8 - + - -
155O VAL* 3.4 25.4 - - + +
210O TRP* 4.4 4.3 - - - -
214O LYS* 4.2 18.4 + - - -
218O LEU* 5.9 2.9 - - + -
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Residues in contact with ALA 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O LEU* 4.0 20.0 - - + -
36O GLU* 3.0 17.4 + - + +
37O ALA* 3.1 9.4 + - - +
39O TYR* 1.3 73.1 - - - +
41O ILE* 1.3 58.8 + - - +
43O HIS* 3.2 8.4 + - - +
44O ILE* 2.8 38.9 + - + +
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Residues in contact with ILE 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O LEU* 3.9 24.2 - - + +
9O LEU* 3.9 29.6 - - + -
10O ALA* 3.8 23.3 - - - +
13O LEU* 3.8 22.0 - - + -
26O LEU* 5.1 2.0 - - + -
30O ILE* 4.2 18.2 - - + -
37O ALA 2.9 18.6 + - - +
38O ALA 3.3 6.3 + - - +
40O ALA* 1.3 72.3 - - - +
42O GLN* 1.3 65.1 + - - +
44O ILE* 3.3 10.0 + - - +
45O ASN* 3.2 22.4 + - - +
156O ALA* 3.9 18.2 - - + +
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Residues in contact with GLN 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ALA 3.1 8.6 + - - +
39O TYR* 3.6 17.4 - - - +
40O ALA 3.4 0.2 - - - -
41O ILE* 1.3 75.5 - - - +
43O HIS* 1.3 58.4 + - - +
45O ASN* 3.3 6.3 + - - +
46O VAL* 2.9 31.8 + - + +
59O ARG* 4.9 0.2 + - - -
79O PHE* 3.0 41.8 + - - -
81O THR* 3.1 23.6 + - - -
155O VAL 3.1 26.4 + - - +
156O ALA 3.9 7.8 + - - -
158O ASN* 3.3 34.4 + - + +
159O ALA 4.0 0.2 - - - +
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Residues in contact with HIS 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O TYR 2.9 18.4 + - - +
40O ALA* 3.4 9.4 - - - +
41O ILE 3.2 0.2 - - - -
42O GLN* 1.3 76.0 - - - +
44O ILE* 1.3 70.4 + - + +
46O VAL* 3.2 8.8 + - + +
47O GLN* 2.9 57.4 + - + +
220O GLU* 4.1 27.7 + - - -
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Residues in contact with ILE 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O LYS* 4.8 10.5 - - + -
6O LEU* 4.9 10.8 - - + +
7O GLU* 3.6 42.6 - - + +
10O ALA* 3.8 20.2 - - + -
14O ARG* 4.5 7.6 - - - +
40O ALA* 2.8 37.0 + - + +
41O ILE* 3.3 10.1 + - - +
43O HIS* 1.3 77.3 - - + +
45O ASN* 1.3 57.4 + - - +
47O GLN* 3.3 6.3 + - - +
48O HIS* 2.9 28.3 + - + +
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Residues in contact with ASN 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O ALA* 3.2 29.3 + - - +
13O LEU* 3.8 18.2 - - - +
14O ARG* 2.8 41.9 + - + +
41O ILE* 3.2 10.4 + - - +
42O GLN* 3.7 7.9 - - - +
43O HIS 3.2 0.6 - - - -
44O ILE* 1.3 77.9 - - - +
46O VAL* 1.3 65.2 + - + +
48O HIS* 3.5 4.1 + - - +
49O ASP* 3.1 32.1 + - - +
156O ALA 4.8 3.6 + - - -
158O ASN* 6.6 0.2 - - + -
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Residues in contact with VAL 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O GLN* 2.9 29.7 + - + +
43O HIS* 3.2 9.4 + - - +
45O ASN* 1.3 75.6 - - + +
47O GLN* 1.3 65.4 + - - +
49O ASP* 3.2 3.5 + - - +
50O VAL* 2.9 39.2 + - + +
56O VAL* 4.4 4.5 - - + -
59O ARG* 5.3 3.6 - - - +
81O THR* 3.6 39.0 - - + +
83O PHE* 4.1 23.5 - - + -
158O ASN* 4.7 3.8 - - - +
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Residues in contact with GLN 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O HIS* 2.9 49.1 + - + +
44O ILE* 3.5 6.7 - - - +
46O VAL* 1.3 83.2 - - - +
48O HIS* 1.3 61.3 + - - +
50O VAL* 3.4 19.7 + - - +
51O ALA* 3.1 23.0 + - - +
220O GLU* 5.3 1.0 - - - +
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Residues in contact with HIS 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O ARG* 3.7 43.2 + - - +
44O ILE* 2.9 17.8 + - + +
45O ASN* 3.6 9.2 - - - +
47O GLN* 1.3 76.1 - - - +
49O ASP* 1.3 75.2 + - - +
51O ALA* 3.3 15.6 + - - +
52O GLN* 3.3 37.0 + - + +
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Residues in contact with ASP 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O ARG* 4.7 3.3 - - - -
45O ASN 3.1 17.0 + - - +
46O VAL 3.7 4.0 - - - +
48O HIS* 1.3 88.0 - - - +
50O VAL* 1.3 66.1 + - - +
52O GLN* 3.0 27.8 + - - +
53O GLY 3.4 0.3 + - - -
54O ARG* 3.0 62.5 + - + +
83O PHE* 4.1 9.2 - - + -
1316O NA 3.4 18.4 - - - -
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Residues in contact with VAL 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O VAL* 2.9 26.1 + - + +
47O GLN* 3.8 20.6 - - - +
48O HIS 3.3 0.2 - - - -
49O ASP* 1.3 75.4 - - - +
51O ALA* 1.3 57.9 + - - +
53O GLY* 2.8 21.3 + - - -
54O ARG 3.7 18.6 - - - +
56O VAL* 3.9 24.7 - - + -
83O PHE* 4.3 2.7 - - + -
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Residues in contact with ALA 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O GLN 3.1 13.0 + - - +
48O HIS* 3.4 13.2 - - - +
49O ASP 3.2 0.4 - - - -
50O VAL* 1.3 75.8 - - - +
52O GLN* 1.3 59.0 + - + +
53O GLY 3.3 1.2 + - - -
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Residues in contact with GLN 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O HIS* 3.3 33.9 + - + +
49O ASP* 3.0 27.1 + - - +
51O ALA* 1.3 78.0 - - + +
53O GLY* 1.3 59.2 + - - +
54O ARG* 3.4 3.2 + - + +
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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