Contacts of the helix formed by residues 34 - 52 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J THR* 5.6 8.1 + - - +
30J ILE* 3.2 29.5 + - + +
31J GLY* 2.9 8.1 + - - +
32J ILE 3.6 0.6 - - - -
33J ASP* 1.3 73.5 - - - +
35J ALA* 1.3 63.9 + - - +
36J GLU* 3.7 9.2 + - - +
37J ALA* 3.3 29.8 + - + +
38J ALA 3.3 12.0 + - - -
152J VAL* 3.3 15.9 - - + +
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Residues in contact with ALA 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ASP 3.4 7.6 + - - +
34J ASN* 1.3 73.7 + - - +
36J GLU* 1.3 64.6 + - - +
38J ALA* 3.2 3.8 + - - +
39J TYR* 3.0 35.3 + - + -
151J PHE* 4.0 28.7 - - + -
152J VAL* 4.2 3.8 - - - +
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Residues in contact with GLU 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J ASN* 3.3 8.2 + - - +
35J ALA* 1.3 79.0 - - - +
37J ALA* 1.3 57.6 + - - +
39J TYR* 3.6 6.2 + - - +
40J ALA* 3.0 26.9 + - + +
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Residues in contact with ALA 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J THR* 5.7 2.5 - - - +
6J LEU* 4.2 23.2 - - + +
30J ILE* 4.4 10.5 - - + -
34J ASN* 3.3 32.8 + - + +
35J ALA 3.2 0.6 - - - -
36J GLU* 1.3 75.6 - - - +
38J ALA* 1.3 67.1 + - - +
40J ALA* 3.0 9.4 + - - +
41J ILE* 2.9 28.7 + - - +
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Residues in contact with ALA 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ILE* 4.5 6.8 - - + +
34J ASN 3.3 2.6 + - - -
35J ALA* 3.2 10.2 + - - +
37J ALA* 1.3 78.1 - - - +
39J TYR* 1.3 59.9 + - - +
41J ILE* 3.3 3.0 + - - +
42J GLN* 3.1 18.2 + - - +
152J VAL* 3.4 42.6 - - + +
155J VAL* 3.7 17.9 - - + -
156J ALA* 3.4 18.9 + - - +
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Residues in contact with TYR 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ALA* 3.0 30.9 + - + +
36J GLU* 3.9 6.3 - - - +
38J ALA* 1.3 73.8 - - - +
40J ALA* 1.3 60.5 + - - +
42J GLN* 3.4 10.6 + - - +
43J HIS* 2.9 29.1 + - - +
77J PRO 4.3 4.9 + - - -
78J ASP* 3.8 10.7 + - - -
79J PHE* 3.2 72.2 + + - -
151J PHE* 4.4 15.5 - + - -
155J VAL* 3.4 25.6 - - + +
210J TRP* 4.4 4.0 - - - -
214J LYS* 4.2 18.5 + - - -
218J LEU* 5.9 2.7 - - + -
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Residues in contact with ALA 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU* 4.0 20.9 - - + -
36J GLU* 3.0 15.5 + - + +
37J ALA* 3.0 10.6 + - - +
39J TYR* 1.3 75.6 - - - +
41J ILE* 1.3 59.2 + - - +
43J HIS* 3.3 7.6 + - - +
44J ILE* 2.8 38.3 + - + +
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Residues in contact with ILE 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU* 4.0 24.5 - - + +
9J LEU* 4.0 31.0 - - + -
10J ALA* 3.8 16.6 - - - -
13J LEU* 3.8 27.1 - - + -
26J LEU* 5.0 1.3 - - + -
30J ILE* 4.2 22.7 - - + -
37J ALA 2.9 18.3 + - - +
38J ALA 3.3 6.3 + - - +
40J ALA* 1.3 73.2 - - - +
42J GLN* 1.3 65.0 + - - +
44J ILE* 3.3 10.6 + - - +
45J ASN* 3.2 22.4 + - - +
156J ALA* 3.9 14.4 - - + +
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Residues in contact with GLN 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ALA 3.1 8.6 + - - +
39J TYR* 3.6 17.7 - - - +
40J ALA 3.4 0.2 - - - -
41J ILE* 1.3 75.1 - - - +
43J HIS* 1.3 58.9 + - - +
45J ASN* 3.2 6.5 + - - +
46J VAL* 2.9 30.9 + - + +
79J PHE* 3.0 41.1 + - - -
81J THR* 3.0 23.9 + - - -
155J VAL 3.1 26.3 + - - +
156J ALA 3.8 8.0 + - - -
158J ASN* 3.2 34.6 + - + +
159J ALA 4.0 0.4 - - - +
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Residues in contact with HIS 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J TYR 2.9 19.0 + - - +
40J ALA* 3.5 9.0 - - - +
41J ILE 3.2 0.2 - - - -
42J GLN* 1.3 74.2 - - - +
44J ILE* 1.3 70.8 + - + +
46J VAL* 3.3 9.5 + - + +
47J GLN* 2.9 57.4 + - + +
220J GLU* 4.1 27.2 + - - -
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Residues in contact with ILE 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J LYS* 4.8 10.1 - - + -
6J LEU* 4.9 11.0 - - + +
7J GLU* 3.6 43.1 - - + +
10J ALA* 3.9 19.5 - - + -
14J ARG* 4.5 8.5 - - - +
40J ALA* 2.8 37.9 + - + +
41J ILE* 3.3 9.4 + - - +
43J HIS* 1.3 77.2 - - + +
45J ASN* 1.3 58.6 + - - +
47J GLN* 3.3 6.2 + - - +
48J HIS* 2.9 28.7 + - + +
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Residues in contact with ASN 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J ALA* 3.2 27.7 + - - +
13J LEU* 3.8 19.6 - - - +
14J ARG* 2.8 44.6 + - + +
41J ILE* 3.2 9.2 + - - +
42J GLN* 3.2 9.8 + - - +
43J HIS 3.2 0.6 - - - -
44J ILE* 1.3 78.0 - - - +
46J VAL* 1.3 62.5 + - - +
48J HIS* 3.5 3.6 + - - +
49J ASP* 3.2 31.9 + - - +
156J ALA 4.8 4.0 + - - +
158J ASN* 6.6 0.2 - - + -
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Residues in contact with VAL 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J GLN* 2.9 29.7 + - + +
43J HIS* 3.8 8.7 - - - +
45J ASN* 1.3 74.6 - - - +
47J GLN* 1.3 65.2 + - - +
49J ASP* 3.2 4.2 + - - +
50J VAL* 2.9 38.7 + - + +
56J VAL* 4.4 5.4 - - + -
59J ARG* 5.3 2.9 - - - +
81J THR* 3.6 38.6 - - + +
83J PHE* 4.1 23.5 - - + -
158J ASN* 4.6 4.0 - - - +
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Residues in contact with GLN 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J HIS* 2.9 48.8 + - + +
44J ILE* 3.5 6.5 - - - +
46J VAL* 1.3 84.1 - - - +
48J HIS* 1.3 61.5 + - - +
50J VAL* 3.4 20.3 + - - +
51J ALA* 3.1 22.9 + - - +
220J GLU* 5.4 0.9 - - - +
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Residues in contact with HIS 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ARG* 3.7 44.4 + - - +
18J GLU* 6.0 0.6 + - - -
44J ILE* 2.9 17.7 + - + +
45J ASN* 3.7 9.9 - - - +
46J VAL 3.2 0.2 - - - -
47J GLN* 1.3 76.8 - - - +
49J ASP* 1.3 74.9 + - - +
51J ALA* 3.3 16.7 + - - +
52J GLN* 3.4 37.8 + - + +
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Residues in contact with ASP 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ARG* 4.8 4.9 - - - -
45J ASN* 3.2 17.8 + - - +
46J VAL 3.2 3.6 + - - +
48J HIS* 1.3 88.5 - - - +
50J VAL* 1.3 65.0 + - - +
52J GLN* 3.0 26.7 + - - +
53J GLY 3.4 0.2 + - - -
54J ARG* 3.0 64.0 + - + +
83J PHE* 4.1 8.6 - - + -
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Residues in contact with VAL 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J VAL* 2.9 25.2 + - + +
47J GLN* 3.8 20.9 - - - +
49J ASP* 1.3 75.2 - - - +
51J ALA* 1.3 58.3 + - - +
53J GLY* 2.8 22.2 + - - -
54J ARG 3.6 19.0 - - - +
56J VAL* 4.0 25.4 - - + +
83J PHE* 4.3 2.7 - - + -
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Residues in contact with ALA 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J GLN 3.1 13.2 + - - +
48J HIS* 3.4 12.8 - - - +
49J ASP 3.2 0.4 - - - -
50J VAL* 1.3 76.6 - - - +
52J GLN* 1.3 59.4 + - + +
53J GLY 3.3 1.2 + - - -
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Residues in contact with GLN 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J HIS* 3.4 34.0 + - + +
49J ASP* 3.0 27.2 + - - +
51J ALA* 1.3 77.4 - - + +
53J GLY* 1.3 59.3 + - - +
54J ARG* 3.4 3.4 + - + +
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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