Contacts of the helix formed by residues 24 - 33 (chain X) in PDB entry 2Q4G
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 THR 24 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93W ASN* 4.5 25.1 - - - +
22X SER* 2.9 15.7 + - - +
23X SER* 1.3 87.7 - - - +
25X TYR* 1.3 57.6 + - - +
26X CYS 3.5 1.1 - - - -
27X ASN* 3.2 7.9 + - - +
28X GLN* 2.6 48.2 + - - +
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Residues in contact with TYR 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X ASP* 2.5 31.0 + - - +
17X SER* 3.3 22.9 - - - -
18X SER 5.2 0.2 - - - -
21X SER* 3.7 30.1 - - - -
22X SER* 3.1 18.9 + - - +
24X THR* 1.3 78.1 + - - +
26X CYS* 1.3 62.3 + - - +
28X GLN* 2.8 11.7 + - - -
29X MET* 2.5 52.5 + - + +
46X PHE* 3.7 28.5 - + - +
48X HIS* 3.2 19.8 - + - -
82X THR* 4.0 16.8 - - + -
99X THR* 4.0 1.3 - - + -
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Residues in contact with CYS 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X TYR* 1.3 79.7 - - - +
27X ASN* 1.3 66.3 + - - +
29X MET* 4.4 0.9 - - - +
30X MET* 2.8 31.5 + - - +
82X THR* 4.1 4.3 - - - -
83X ASP 3.7 2.7 - - - -
84X CYS* 2.0 60.6 - - + -
97X TYR* 3.7 14.8 - - + -
99X THR* 3.0 41.3 + - - +
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Residues in contact with ASN 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63W ARG* 5.6 5.5 - - - +
121W ASP* 5.5 4.6 + - - -
23X SER 4.9 7.4 + - - +
24X THR* 3.2 13.0 + - - +
26X CYS* 1.3 76.2 - - - +
28X GLN* 1.3 61.4 + - - +
30X MET* 4.7 0.5 - - - +
31X ARG* 3.5 21.5 + - - +
95X CYS 4.7 4.6 + - - -
96X ALA* 4.3 12.5 - - - +
97X TYR* 2.8 47.8 + - - +
99X THR* 4.6 0.4 + - - -
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Residues in contact with GLN 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36W ASP* 4.0 7.1 + - - +
93W ASN* 6.2 1.6 - - - +
24X THR* 2.6 32.3 + - - +
25X TYR* 2.8 10.1 + - - +
27X ASN* 1.3 72.6 - - - +
29X MET* 1.3 81.4 + - - +
31X ARG* 3.2 7.4 + - - +
32X ARG* 3.0 75.6 + - - +
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Residues in contact with MET 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X ASP* 4.2 14.8 - - - +
25X TYR* 2.5 50.2 + - + +
26X CYS 4.4 0.2 - - - +
28X GLN* 1.3 91.4 - - - +
30X MET* 1.3 59.7 + - - +
31X ARG 3.0 2.0 - - - -
32X ARG* 4.3 14.8 - - + +
33X ARG* 2.8 75.6 + - + +
46X PHE* 3.8 22.2 - - + -
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Residues in contact with MET 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X CYS 2.8 29.6 + - - +
27X ASN 4.7 0.7 - - - +
29X MET* 1.3 74.3 - - - +
31X ARG* 1.3 58.1 + - - +
34X ASN 3.7 1.0 + - - -
35X MET* 3.1 42.8 + - + +
36X THR* 3.8 7.5 + - + -
41X LYS* 3.5 24.7 - - + +
44X ASN* 3.4 44.6 - - + +
46X PHE* 3.9 6.7 - - + -
84X CYS* 4.2 12.3 - - - -
97X TYR* 3.5 49.4 - - + +
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Residues in contact with ARG 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W GLN* 2.8 57.8 + - - +
11W CYS* 3.7 19.0 - - - +
33W ARG* 5.6 3.6 - - - +
35W ASP* 4.0 28.0 + - - -
36W ASP* 5.6 3.1 - - - -
63W ARG* 6.0 3.0 - - - +
64W SER* 6.5 0.4 - - - -
27X ASN 3.5 14.6 + - - +
28X GLN* 3.2 10.5 + - - +
29X MET 3.0 0.6 - - - -
30X MET* 1.3 77.7 - - - +
32X ARG* 1.3 65.9 + - - +
34X ASN* 3.2 17.7 + - - +
36X THR* 4.0 18.5 + - + +
37X GLN* 5.6 0.5 + - - +
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Residues in contact with ARG 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W CYS* 3.8 27.4 - - + +
36W ASP* 2.9 35.4 + - - +
28X GLN* 3.0 56.0 + - - +
29X MET* 3.3 21.1 + - + +
31X ARG* 1.3 74.6 - - - +
33X ARG* 1.3 63.7 + - + +
34X ASN* 3.3 12.8 + - - +
1Y SER 4.4 5.9 + - - -
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Residues in contact with ARG 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X GLN 3.1 8.3 + - - -
10X ARG* 2.8 86.3 + - + +
13X MET 2.7 30.7 + - - -
14X ASP* 3.8 16.8 + - - +
29X MET* 2.8 44.9 + - + +
31X ARG 3.2 0.4 - - - -
32X ARG* 1.3 82.6 - - - +
34X ASN* 1.3 62.9 + - - +
35X MET* 3.4 16.9 + - + +
46X PHE* 4.0 10.2 - - + -
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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