Contacts of the helix formed by residues 52 - 62 (chain A) in PDB entry 1GQC
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 ASP 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.4 29.9 - - + +
50A THR* 3.2 14.7 + - - +
51A ASP* 1.3 85.0 - - - +
53A PRO* 1.4 70.7 - - - +
54A ARG* 2.8 65.4 + - - +
55A VAL* 3.0 12.2 + - + +
56A GLU 3.1 8.1 + - - -
68A MET* 4.0 3.6 - - - -
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Residues in contact with PRO 53 (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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51A ASP 4.1 2.2 - - - +
52A ASP* 1.4 88.1 - - - +
54A ARG* 1.3 61.3 + - + +
56A GLU* 3.3 19.5 - - + +
57A GLN* 2.8 38.4 + - + +
68A MET* 4.0 15.9 - - + -
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Residues in contact with ARG 54 (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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11A TYR* 3.3 44.0 + - + -
21A LEU* 4.1 17.1 - - + +
52A ASP* 2.8 34.2 + - - +
53A PRO* 1.3 78.7 - - + +
55A VAL* 1.3 64.8 + - - +
57A GLN* 3.7 4.9 + - - +
58A ALA* 3.3 21.1 + - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.0 18.2 - - + +
11A TYR* 4.0 21.8 - - + -
20A PRO* 3.7 32.1 - - + -
21A LEU* 4.1 10.5 - - + -
30A ILE* 5.2 1.8 - - + -
48A VAL* 4.7 1.1 - - + -
50A THR* 3.5 34.5 - - + +
52A ASP* 3.0 4.0 + - - +
54A ARG* 1.3 76.9 - - - +
56A GLU* 1.3 63.5 - - - +
58A ALA* 3.1 3.5 + - - +
59A VAL* 3.0 35.0 + - + +
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Residues in contact with GLU 56 (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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50A THR* 3.9 7.8 - - + +
52A ASP 3.1 7.0 + - - +
53A PRO* 3.2 22.6 + - + +
55A VAL* 1.3 79.1 - - - +
57A GLN* 1.3 78.7 + - - +
59A VAL* 3.3 2.4 + - - +
60A GLN* 3.1 47.0 + - - +
66A ALA* 4.3 20.3 - - + +
67A ILE 6.1 0.2 - - - -
68A MET* 3.4 30.7 + - + +
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Residues in contact with GLN 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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53A PRO* 2.8 25.7 + - + +
54A ARG* 4.1 5.2 - - - +
56A GLU* 1.3 95.8 + - - +
58A ALA* 1.3 58.0 + - - +
60A GLN* 3.1 22.1 + - - +
61A ALA* 2.8 31.7 + - - +
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Residues in contact with ALA 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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21A LEU* 3.4 31.2 - - + -
28A PRO* 5.1 6.8 - - + +
30A ILE* 5.0 6.3 - - + -
54A ARG 3.3 7.5 + - - +
55A VAL 3.1 9.8 + - - +
57A GLN* 1.3 80.2 - - - +
59A VAL* 1.3 60.7 + - - +
61A ALA* 3.5 13.5 + - - +
62A PHE* 3.3 19.4 + - - -
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Residues in contact with VAL 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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30A ILE* 4.1 17.5 - - + -
48A VAL* 3.8 29.6 - - + -
55A VAL* 3.0 23.4 + - + +
56A GLU 3.8 6.1 - - - +
57A GLN 3.2 0.2 - - - -
58A ALA* 1.3 73.1 - - - +
60A GLN* 1.3 63.7 + - - +
62A PHE* 3.2 23.9 + - + -
64A GLY* 2.8 50.7 + - - +
65A LYS 3.8 13.2 - - - +
66A ALA* 3.9 9.6 - - + -
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Residues in contact with GLN 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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56A GLU* 3.1 39.5 + - - +
57A GLN* 3.1 34.2 + - - +
59A VAL* 1.3 73.8 - - - +
61A ALA* 1.3 61.5 + - - +
63A GLY* 2.9 18.1 + - - -
64A GLY 4.0 14.8 - - - +
66A ALA* 4.6 12.0 + - + +
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Residues in contact with ALA 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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57A GLN 2.8 16.6 + - - +
58A ALA* 3.6 10.5 - - - +
60A GLN* 1.3 78.9 - - - +
62A PHE* 1.3 58.0 + - - +
63A GLY 3.1 2.1 + - - -
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Residues in contact with PHE 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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28A PRO* 4.2 4.9 - - + -
30A ILE* 3.8 16.6 - - + -
31A GLN* 3.5 53.8 - - + +
34A TYR* 3.6 45.3 - + + -
35A GLU* 5.9 0.9 - - + -
58A ALA 3.3 17.8 + - - +
59A VAL* 3.2 30.7 + - + -
60A GLN 3.2 0.4 - - - -
61A ALA* 1.3 78.4 - - - +
63A GLY* 1.3 56.9 + - - +
64A GLY* 3.7 13.0 - - - -
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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