Contacts of the helix formed by residues 56 - 66 (chain A) in PDB entry 2GDA
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 ALA 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.6 11.8 - - + -
37A LEU* 3.5 26.0 - - - +
38A CYS* 3.4 29.6 - - + +
54A CYS* 3.4 6.2 - - - -
55A PRO* 1.4 75.8 - - + +
57A CYS* 1.4 63.3 + - - +
58A ARG 3.3 1.3 - - - -
59A TYR* 3.2 18.5 + - - +
60A ARG* 3.2 19.9 + - - +
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Residues in contact with CYS 57 (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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38A CYS* 3.8 8.5 - - - -
42A ASN* 4.7 13.5 - - - -
43A ASP 5.1 0.4 - - - -
44A CYS* 3.4 23.8 - - - +
46A ILE* 3.5 24.2 - - + -
54A CYS* 3.7 0.8 - - - -
56A ALA* 1.4 78.4 - - - +
58A ARG* 1.3 51.5 + - - +
60A ARG* 3.3 13.7 + - + +
61A LYS* 2.8 37.4 + - - +
74A ZN 2.3 35.2 - - - -
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Residues in contact with ARG 58 (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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4A VAL* 3.1 26.4 - - + +
5A CYS* 4.7 5.9 - - + -
21A SER* 3.7 23.0 + - - -
22A CYS* 3.7 20.7 - - - -
25A PHE* 3.5 43.3 - - + +
46A ILE* 3.6 23.7 - - + +
51A ARG* 3.5 51.6 + - - +
52A LYS* 5.6 0.2 - - - +
54A CYS 3.6 12.8 - - - +
55A PRO* 3.6 17.5 - - + +
57A CYS* 1.3 74.5 - - - +
59A TYR* 1.4 60.6 + - - +
61A LYS 3.9 0.4 - - - -
62A CYS* 3.3 12.0 + - - -
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Residues in contact with TYR 59 (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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25A PHE* 3.8 19.7 - + + -
26A PHE* 4.0 10.9 - + - -
29A ALA* 3.5 32.1 + - + -
30A VAL* 3.5 31.8 - - + +
36A TYR* 3.3 41.7 - + + -
55A PRO 4.2 0.2 - - - +
56A ALA 3.2 13.2 + - - +
58A ARG* 1.4 77.8 - - - +
60A ARG* 1.4 62.9 + - + +
62A CYS* 3.3 17.9 - - - -
63A LEU* 3.4 34.8 - - + +
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Residues in contact with ARG 60 (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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38A CYS 4.2 18.1 + - - +
39A ALA* 4.9 15.3 - - - +
42A ASN* 3.4 30.0 - - - +
56A ALA* 3.2 9.8 + - - +
57A CYS* 3.4 27.1 - - - +
59A TYR* 1.4 80.2 - - + +
61A LYS* 1.4 57.0 + - + +
62A CYS 3.6 0.2 - - - -
63A LEU* 3.7 10.9 + - + +
64A GLN* 3.2 31.7 + - - +
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Residues in contact with LYS 61 (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 LEU 4.5 4.6 - - - +
4A VAL* 3.5 41.3 - - + +
46A ILE* 4.2 10.1 - - + +
57A CYS 2.8 18.8 + - - +
58A ARG* 3.9 1.8 - - - -
59A TYR 3.3 0.2 - - - -
60A ARG* 1.4 75.4 - - + +
62A CYS* 1.4 57.6 + - - +
64A GLN* 3.2 37.6 + - - +
65A ALA* 3.1 25.6 + - - +
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Residues in contact with CYS 62 (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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4A VAL* 3.4 30.1 - - + -
18A THR* 5.0 0.4 - - + -
22A CYS* 5.5 3.4 - - + -
25A PHE* 4.9 4.3 - - - -
26A PHE* 3.5 38.4 - - - -
58A ARG 3.3 14.1 + - - +
59A TYR* 3.3 24.9 - - - -
61A LYS* 1.4 76.4 - - - +
63A LEU* 1.4 60.5 + - - +
65A ALA* 3.2 10.2 - - - +
67A MET* 3.0 36.3 + - + +
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Residues in contact with LEU 63 (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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26A PHE* 3.6 29.8 - - + -
30A VAL* 5.7 0.4 - - + -
59A TYR* 3.4 46.7 + - + +
60A ARG* 3.7 11.2 - - - +
61A LYS 3.3 0.4 - - - -
62A CYS* 1.4 73.5 - - - +
64A GLN* 1.4 61.7 + - - +
66A GLY* 3.3 13.9 + - - -
67A MET 4.0 15.5 + - - +
68A ASN* 6.4 0.2 - - - +
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Residues in contact with GLN 64 (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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60A ARG* 3.2 20.1 + - - +
61A LYS* 3.2 41.4 + - - +
63A LEU* 1.4 74.3 - - - +
65A ALA* 1.4 59.4 + - - +
66A GLY* 3.6 0.7 + - - -
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Residues in contact with ALA 65 (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 LEU* 4.5 17.0 - - + +
4A VAL* 5.0 1.6 - - + -
16A VAL* 3.7 30.0 - - + +
61A LYS 3.1 10.3 + - - +
62A CYS* 3.2 17.7 - - - +
63A LEU 3.2 0.4 - - - -
64A GLN* 1.4 77.5 - - - +
66A GLY* 1.4 53.8 + - - +
67A MET* 4.9 0.4 - - + -
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Residues in contact with GLY 66 (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 TYR 4.0 2.9 - - - +
15A GLY* 5.0 2.6 - - - -
16A VAL* 3.3 11.6 - - - +
63A LEU 3.3 9.7 + - - -
64A GLN 4.5 1.1 - - - -
65A ALA* 1.4 78.4 - - - +
67A MET* 1.4 67.2 + - - +
68A ASN* 3.8 4.0 + - - +
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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