Contacts of the helix formed by residues 34 - 52 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A THR* 5.6 7.5 + - - +
30A ILE* 3.2 29.9 + - - +
31A GLY* 3.0 8.3 + - - +
32A ILE 3.6 0.4 - - - -
33A ASP* 1.3 72.7 - - - +
35A ALA* 1.3 65.3 + - - +
36A GLU* 3.7 9.5 + - - +
37A ALA* 3.3 31.1 + - + +
38A ALA 3.3 12.1 + - - -
152A VAL* 3.3 15.9 - - + +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP 3.4 7.5 + - - +
34A ASN* 1.3 71.8 - - - +
36A GLU* 1.3 66.1 + - - +
38A ALA* 3.1 3.6 + - - +
39A TYR* 3.0 34.7 + - + -
151A PHE* 3.9 29.2 - - + -
152A VAL* 4.2 3.8 - - - +
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.3 8.2 + - - +
35A ALA* 1.3 78.9 - - - +
37A ALA* 1.3 57.1 + - - +
39A TYR* 3.6 6.4 + - - +
40A ALA* 3.0 27.6 + - + +
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 5.7 2.2 - - - +
6A LEU* 4.1 24.6 - - + +
30A ILE* 4.4 11.0 - - + -
34A ASN* 3.3 32.6 + - + +
35A ALA 3.2 0.4 - - - -
36A GLU* 1.3 76.0 - - - +
38A ALA* 1.3 61.8 + - - +
40A ALA* 3.0 9.4 + - - +
41A ILE* 2.9 33.6 + - - +
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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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30A ILE* 4.5 6.0 - - + +
34A ASN 3.3 2.4 + - - -
35A ALA* 3.1 9.1 + - - +
37A ALA* 1.3 76.5 - - - +
39A TYR* 1.3 61.6 + - - +
41A ILE* 3.4 2.5 + - - +
42A GLN* 3.1 17.8 + - - +
152A VAL* 3.4 43.7 - - + +
155A VAL* 3.7 18.0 - - + +
156A ALA* 3.3 19.9 + - - +
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Residues in contact with TYR 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 ALA* 3.0 31.3 + - + +
36A GLU* 3.9 6.3 - - - +
38A ALA* 1.3 74.0 - - - +
40A ALA* 1.3 59.7 + - - +
42A GLN* 3.4 9.3 + - - +
43A HIS* 2.9 30.1 + - - +
77A PRO 4.3 4.3 + - - -
78A ASP* 3.8 11.1 + - - -
79A PHE* 3.2 72.1 + + - -
151A PHE* 4.5 15.7 - + - -
155A VAL* 3.4 24.8 - - + +
210A TRP* 4.3 4.3 - - - -
214A LYS* 4.2 18.9 + - - -
218A LEU* 6.0 2.5 - - + -
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Residues in contact with ALA 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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6A LEU* 4.0 21.3 - - + -
36A GLU* 3.0 15.1 + - + +
37A ALA* 3.0 10.0 + - - +
39A TYR* 1.3 78.1 - - - +
41A ILE* 1.3 56.5 + - - +
43A HIS* 3.3 8.5 + - - +
44A ILE* 2.8 38.9 + - + +
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Residues in contact with ILE 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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6A LEU* 4.0 23.3 - - + +
9A LEU* 3.9 31.2 - - + -
10A ALA* 3.8 17.3 - - - +
13A LEU* 3.8 27.6 - - + -
26A LEU* 5.1 1.6 - - + -
30A ILE* 4.2 17.9 - - + -
37A ALA 2.9 19.0 + - - +
38A ALA 3.6 6.3 - - - +
40A ALA* 1.3 71.8 - - - +
42A GLN* 1.3 66.0 + - - +
44A ILE* 3.3 9.4 + - - +
45A ASN* 3.2 22.4 + - - +
156A ALA* 3.8 18.6 - - + +
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 3.1 9.0 + - - +
39A TYR* 3.6 17.7 - - - +
41A ILE* 1.3 75.4 - - - +
43A HIS* 1.3 57.7 + - - +
45A ASN* 3.2 7.0 + - - +
46A VAL* 2.9 31.2 + - + +
79A PHE* 3.0 40.3 + - - -
81A THR* 3.1 24.4 + - - -
155A VAL* 3.1 26.4 + - - +
156A ALA 3.8 8.2 + - - -
158A ASN* 3.2 34.8 + - + +
159A ALA 4.0 0.2 - - - +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR 2.9 18.1 + - - +
40A ALA* 3.5 9.6 - - - +
42A GLN* 1.3 74.2 - - - +
44A ILE* 1.3 70.4 + - + +
46A VAL* 3.2 8.3 + - - +
47A GLN* 2.8 57.9 + - + +
220A GLU* 4.1 27.4 + - - -
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Residues in contact with ILE 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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3A LYS* 4.8 9.6 - - - -
6A LEU* 4.9 10.5 - - + +
7A GLU* 3.6 42.2 - - + +
10A ALA* 3.8 20.0 - - + -
14A ARG* 4.5 8.3 - - - +
40A ALA* 2.8 37.0 + - + +
41A ILE* 3.6 10.3 - - - +
43A HIS* 1.3 76.1 - - + +
45A ASN* 1.3 58.0 + - - +
47A GLN* 3.5 6.0 - - - +
48A HIS* 2.9 29.2 + - + +
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Residues in contact with ASN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 3.2 27.2 + - - +
13A LEU* 3.8 20.2 - - - +
14A ARG* 2.8 40.9 + - + +
41A ILE* 3.2 11.0 + - - +
42A GLN* 3.7 8.1 - - - +
43A HIS 3.2 0.4 - - - -
44A ILE* 1.3 77.7 - - - +
46A VAL* 1.3 64.3 + - + +
48A HIS* 3.7 2.9 - - - +
49A ASP* 3.1 30.8 + - - +
156A ALA 4.8 3.8 + - - +
158A ASN* 6.6 0.2 - - + -
1265A NA 4.6 7.4 - - - -
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Residues in contact with VAL 46 (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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42A GLN* 2.9 29.8 + - + +
43A HIS* 3.8 9.4 - - - +
45A ASN* 1.3 75.5 - - + +
47A GLN* 1.3 64.8 + - - +
49A ASP* 3.2 3.8 + - - +
50A VAL* 2.9 39.0 + - + +
56A VAL* 4.3 4.7 - - + -
59A ARG* 5.3 3.4 - - - +
81A THR* 3.7 38.6 - - + +
83A PHE* 4.0 23.8 - - + -
158A ASN* 4.7 3.6 - - - +
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Residues in contact with GLN 47 (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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43A HIS* 2.8 49.3 + - + +
44A ILE* 3.5 7.4 - - - +
46A VAL* 1.3 83.1 - - - +
48A HIS* 1.3 61.3 + - - +
50A VAL* 3.5 19.7 + - - +
51A ALA* 3.1 23.0 + - - +
220A GLU* 5.3 0.9 - - - +
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Residues in contact with HIS 48 (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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14A ARG* 3.7 43.3 + - - +
44A ILE* 2.9 18.2 + - + +
45A ASN* 3.7 8.7 - - - +
46A VAL 3.3 0.2 - - - -
47A GLN* 1.3 77.1 - - - +
49A ASP* 1.3 73.5 + - - +
51A ALA* 3.3 14.1 + - - +
52A GLN* 3.3 40.3 + - + +
1266A K 4.0 5.5 - - - -
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Residues in contact with ASP 49 (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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14A ARG* 4.7 0.5 - - - -
45A ASN 3.1 16.1 + - - +
46A VAL 3.2 3.6 + - - +
48A HIS* 1.3 87.7 - - - +
50A VAL* 1.3 66.3 + - - +
52A GLN* 3.0 27.6 + - - +
53A GLY 3.4 0.2 + - - -
54A ARG* 2.9 62.8 + - + +
83A PHE* 4.2 8.5 - - + -
1265A NA 3.1 20.3 - - - -
1266A K 3.9 5.7 - - - -
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Residues in contact with VAL 50 (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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46A VAL* 2.9 26.6 + - + +
47A GLN* 3.8 20.4 - - - +
48A HIS 3.4 0.2 - - - -
49A ASP* 1.3 75.4 - - - +
51A ALA* 1.3 58.4 + - - +
53A GLY* 2.8 20.8 + - - -
54A ARG 3.6 20.1 + - - +
56A VAL* 4.0 24.0 - - + +
83A PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 51 (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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47A GLN 3.1 13.6 + - - +
48A HIS* 3.5 12.6 - - - +
49A ASP 3.2 0.4 - - - -
50A VAL* 1.3 76.2 - - - +
52A GLN* 1.3 59.2 + - + +
53A GLY 3.3 0.8 + - - -
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Residues in contact with GLN 52 (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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48A HIS* 3.3 32.7 + - + +
49A ASP* 3.0 21.8 + - - +
51A ALA* 1.3 77.0 - - + +
53A GLY* 1.3 59.4 + - - +
54A ARG* 3.4 3.5 + - + +
1266A K 3.7 18.3 - - - -
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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
------------------------------------------------------------
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