Contacts of the helix formed by residues 34 - 52 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T THR* 5.6 8.1 + - - +
30T ILE* 3.2 30.4 + - + +
31T GLY* 2.9 8.7 + - - +
32T ILE 3.6 0.2 - - - -
33T ASP* 1.3 72.7 - - - +
35T ALA* 1.3 64.8 + - - +
36T GLU* 3.7 9.5 + - - +
37T ALA* 3.2 28.9 + - + +
38T ALA 3.3 12.5 + - - -
152T VAL* 3.3 15.8 - - + +
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Residues in contact with ALA 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T ASP* 3.4 7.5 + - - +
34T ASN* 1.3 74.0 - - - +
36T GLU* 1.3 64.4 + - - +
38T ALA* 3.2 4.3 + - - +
39T TYR* 3.1 35.9 + - + -
151T PHE* 4.0 24.2 - - + -
152T VAL* 4.2 7.2 - - - +
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Residues in contact with GLU 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T ASN* 3.3 9.3 + - - +
35T ALA* 1.3 78.8 - - - +
37T ALA* 1.3 56.4 + - - +
39T TYR* 3.6 6.4 + - - +
40T ALA* 3.0 27.3 + - + +
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Residues in contact with ALA 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2T THR* 5.7 2.5 - - - +
6T LEU* 4.1 23.9 - - + +
30T ILE* 4.4 11.2 - - + -
34T ASN* 3.2 32.9 + - + +
35T ALA 3.2 0.4 - - - -
36T GLU* 1.3 76.6 - - - +
38T ALA* 1.3 60.7 + - - +
40T ALA* 3.0 9.1 + - - +
41T ILE* 2.9 33.9 + - - +
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Residues in contact with ALA 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T ILE* 4.5 6.2 - - + +
34T ASN 3.3 2.2 + - - -
35T ALA* 3.2 9.9 + - - +
37T ALA* 1.3 75.8 - - - +
39T TYR* 1.3 63.0 + - - +
41T ILE* 3.3 2.1 + - - -
42T GLN* 3.1 17.7 + - - +
152T VAL* 3.4 42.4 - - + +
155T VAL* 3.7 17.9 - - + -
156T ALA* 3.4 20.0 + - - +
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Residues in contact with TYR 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35T ALA* 3.1 29.6 + - + +
36T GLU* 3.9 5.8 - - - +
38T ALA* 1.3 74.0 - - - +
40T ALA* 1.3 60.6 + - - +
42T GLN* 3.4 9.6 + - - +
43T HIS* 2.9 28.9 + - - +
77T PRO 4.3 4.5 + - - -
78T ASP* 3.8 10.4 + - - -
79T PHE* 3.2 73.0 + + - -
151T PHE* 4.5 15.1 - + - -
155T VAL* 3.4 25.5 - - + +
210T TRP* 4.4 4.2 - - - -
214T LYS* 4.2 18.2 + - - -
218T LEU* 5.9 2.5 - - + -
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Residues in contact with ALA 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6T LEU* 4.1 19.5 - - + -
36T GLU* 3.0 15.9 + - + +
37T ALA* 3.0 11.5 + - - +
39T TYR* 1.3 74.7 - - - +
41T ILE* 1.3 59.3 + - - +
43T HIS* 3.2 8.4 + - - +
44T ILE* 2.8 38.1 + - + +
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Residues in contact with ILE 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6T LEU* 4.0 24.0 - - + +
9T LEU* 3.9 32.1 - - + -
10T ALA* 3.9 16.4 - - - +
13T LEU* 3.8 27.8 - - + -
26T LEU* 5.0 1.6 - - + -
30T ILE* 4.2 17.0 - - + -
37T ALA 2.9 18.2 + - - +
38T ALA 3.3 6.7 + - - +
40T ALA* 1.3 72.8 - - - +
42T GLN* 1.3 64.8 + - - +
44T ILE* 3.2 10.0 + - - +
45T ASN* 3.2 22.6 + - - +
156T ALA* 3.8 17.9 - - + +
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Residues in contact with GLN 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T ALA 3.1 8.6 + - - +
39T TYR* 3.6 18.3 - - - +
40T ALA 3.4 0.2 - - - -
41T ILE* 1.3 75.1 - - - +
43T HIS* 1.3 58.0 - - - +
45T ASN* 3.3 6.7 + - - +
46T VAL* 2.9 30.5 + - + +
79T PHE* 3.0 40.4 + - - -
81T THR* 3.1 23.7 + - - -
155T VAL 3.1 25.6 + - - +
156T ALA 3.8 7.8 + - - +
158T ASN* 3.3 34.7 + - + +
159T ALA 4.0 0.6 - - - +
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Residues in contact with HIS 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T TYR 2.9 19.2 + - - +
40T ALA* 3.4 9.9 - - - +
42T GLN* 1.3 74.3 - - - +
44T ILE* 1.3 71.4 + - + +
46T VAL* 3.2 9.3 + - + +
47T GLN* 2.9 57.9 + - + +
220T GLU* 4.1 27.8 + - - -
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Residues in contact with ILE 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3T LYS* 4.8 10.3 - - + -
6T LEU* 4.9 10.8 - - + +
7T GLU* 3.6 42.2 - - + +
10T ALA* 3.8 20.9 - - + -
14T ARG* 4.5 7.0 - - - +
40T ALA* 2.8 37.2 + - + +
41T ILE* 3.2 9.8 + - - +
43T HIS* 1.3 77.4 - - + +
45T ASN* 1.3 58.9 + - - +
47T GLN* 3.3 6.4 + - - +
48T HIS* 2.9 28.0 + - + +
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Residues in contact with ASN 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T ALA* 3.2 26.8 + - - +
13T LEU* 3.8 20.2 - - - +
14T ARG* 2.8 42.5 + - + +
41T ILE* 3.2 10.6 + - - +
42T GLN* 3.7 8.1 - - - +
43T HIS 3.2 0.4 - - - -
44T ILE* 1.3 77.2 - - - +
46T VAL* 1.3 64.0 + - + +
48T HIS* 3.5 4.6 + - - +
49T ASP* 3.1 31.9 + - - +
156T ALA 4.8 3.6 + - - -
158T ASN* 6.5 0.4 - - + -
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Residues in contact with VAL 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T GLN* 2.9 29.4 + - + +
43T HIS* 3.8 8.7 - - + +
45T ASN* 1.3 74.8 - - + +
47T GLN* 1.3 64.7 + - - +
49T ASP* 3.2 3.5 + - - +
50T VAL* 2.9 39.2 + - + +
56T VAL* 4.4 4.3 - - + -
59T ARG* 5.3 3.1 - - - +
81T THR* 3.6 38.8 - - + +
83T PHE* 4.1 22.7 - - + -
158T ASN* 4.6 4.3 - - + +
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Residues in contact with GLN 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T HIS* 2.9 49.5 + - + +
44T ILE* 3.5 7.0 - - - +
46T VAL* 1.3 82.5 - - - +
48T HIS* 1.3 61.7 + - - +
50T VAL* 3.4 18.7 + - - +
51T ALA* 3.1 23.6 + - - +
220T GLU* 5.3 1.0 - - - +
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Residues in contact with HIS 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T ARG* 3.7 43.5 + - - +
44T ILE* 2.9 17.7 + - + +
45T ASN* 3.7 9.4 - - - +
46T VAL 3.3 0.2 - - - -
47T GLN* 1.3 75.9 - - - +
49T ASP* 1.3 75.2 + - - +
51T ALA* 3.3 13.9 + - - +
52T GLN* 3.3 39.4 + - + +
1263T K 4.0 5.3 - - - -
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Residues in contact with ASP 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ARG* 4.8 1.6 - - - -
45T ASN 3.1 17.2 + - - +
46T VAL 3.7 3.8 - - - +
48T HIS* 1.3 88.1 - - - +
50T VAL* 1.3 65.4 + - - +
52T GLN* 3.0 28.2 + - - +
53T GLY 3.4 0.2 + - - -
54T ARG* 3.0 63.5 + - + +
83T PHE* 4.1 8.2 - - + -
1263T K 3.9 6.8 - - - -
1303T NA 3.4 18.0 - - - -
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Residues in contact with VAL 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46T VAL* 2.9 26.1 + - + +
47T GLN* 3.7 20.6 - - - +
48T HIS 3.4 0.2 - - - -
49T ASP* 1.3 76.1 - - - +
51T ALA* 1.3 57.0 + - - +
53T GLY* 2.8 21.3 + - - -
54T ARG 3.6 18.8 - - - +
56T VAL* 4.0 24.7 - - + -
83T PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T GLN 3.1 12.6 + - - +
48T HIS* 3.4 13.0 - - - +
49T ASP 3.2 0.2 - - - -
50T VAL* 1.3 76.4 - - - +
52T GLN* 1.3 59.4 + - + +
53T GLY 3.3 1.0 + - - -
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Residues in contact with GLN 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48T HIS* 3.3 33.6 + - + +
49T ASP* 3.0 22.0 + - - +
51T ALA* 1.3 77.4 - - + +
53T GLY* 1.3 58.6 + - - +
54T ARG* 3.4 3.5 + - + +
1263T K 3.6 19.6 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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