Contacts of the helix formed by residues 67 - 76 (chain A) in PDB entry 1GTA
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 GLN 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A PHE* 6.0 4.8 - - + +
54A ASN* 4.0 15.6 - - - +
66A THR* 1.3 82.3 + - - +
68A SER* 1.3 62.3 + - - +
69A MET* 4.7 2.8 - - + +
70A ALA* 2.8 40.7 + - + +
71A ILE* 2.9 14.6 + - - +
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Residues in contact with SER 68 (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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13A LEU* 3.9 38.2 + - - +
14A VAL* 5.5 0.2 - - - -
17A THR* 4.4 4.3 + - - -
56A PRO* 4.0 25.6 - - - +
66A THR 3.8 3.2 + - - -
67A GLN* 1.3 73.6 + - - +
69A MET* 1.4 75.0 + - - +
71A ILE* 3.4 5.5 + - - +
72A ILE* 3.2 24.8 + - - +
104A TYR* 4.2 10.2 + - - -
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Residues in contact with MET 69 (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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13A LEU 5.6 2.7 - - - +
67A GLN* 3.3 3.3 - - + +
68A SER* 1.4 87.5 + - - +
70A ALA* 1.3 59.5 + - - +
72A ILE* 4.1 17.0 - - + -
73A ARG* 3.2 35.5 + - - +
96A GLU* 4.3 16.2 - - - +
100A LEU* 4.1 31.6 - - + -
104A TYR* 4.3 13.0 - - + +
154A MET* 4.0 23.1 - - + -
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Residues in contact with ALA 70 (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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65A LEU* 4.3 19.9 - - + +
66A THR 5.7 0.2 - - - +
67A GLN* 2.8 27.9 + - + +
69A MET* 1.3 72.0 - - - +
71A ILE* 1.3 64.2 + - - +
73A ARG* 4.1 4.5 - - - +
74A TYR* 3.1 25.3 + - - +
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Residues in contact with ILE 71 (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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5A LEU* 4.8 3.4 - - + -
14A VAL* 5.9 0.2 - - + -
17A THR* 4.1 24.9 - - + +
56A PRO* 3.9 32.8 - - + +
57A TYR 3.9 3.4 - - - +
58A TYR* 3.7 49.6 - - + +
65A LEU* 4.0 22.4 - - + +
66A THR 4.3 0.7 - - - -
67A GLN 2.9 16.1 + - - +
68A SER* 3.7 4.0 - - - +
70A ALA* 1.3 74.2 - - - +
72A ILE* 1.3 66.1 + - - +
74A TYR* 3.3 3.9 + - - +
75A ILE* 3.1 26.2 + - + +
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Residues in contact with ILE 72 (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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16A PRO* 4.0 34.3 - - + +
17A THR* 3.5 21.1 - - - +
20A LEU* 4.1 17.8 - - + +
68A SER 3.2 16.0 + - - +
69A MET* 3.9 25.6 - - + +
71A ILE* 1.3 75.2 - - - +
73A ARG* 1.3 65.4 + - + +
75A ILE* 3.6 6.0 + - - +
76A ALA* 3.3 22.3 + - - +
150A HIS* 3.8 37.8 - - + +
153A PHE* 5.7 0.2 - - + -
154A MET* 4.3 7.9 - - + -
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Residues in contact with ARG 73 (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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69A MET* 3.2 26.5 + - - +
70A ALA* 4.2 4.0 - - - +
71A ILE 3.3 0.2 - - - -
72A ILE* 1.3 74.8 - - + +
74A TYR* 1.3 54.5 + - - +
76A ALA* 3.5 2.1 + - - +
77A ASP* 2.6 37.9 + - - +
82A LEU* 3.5 42.1 + - + +
89A ARG* 4.9 8.5 + - - +
92A ILE* 4.4 4.9 - - - +
93A SER* 3.0 28.1 + - - +
96A GLU* 2.8 48.2 + - - +
150A HIS* 4.0 14.5 - - + +
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Residues in contact with TYR 74 (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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58A TYR* 3.8 20.2 - + - -
60A ASP* 2.8 28.6 + - - -
62A ASP* 4.1 9.2 + - - +
63A VAL* 3.8 30.5 - - + +
65A LEU* 4.1 15.9 - - + -
70A ALA 3.1 19.6 + - - +
71A ILE 3.5 3.1 - - - +
73A ARG* 1.3 74.4 - - - +
75A ILE* 1.3 69.6 + - + +
77A ASP* 3.4 9.9 - - + +
78A LYS* 3.0 51.6 + - + +
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Residues in contact with ILE 75 (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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17A THR* 3.8 28.5 - - + -
20A LEU* 3.5 22.4 - - + -
21A LEU* 3.9 31.2 - - + -
24A LEU* 4.0 11.2 - - + -
58A TYR* 4.0 28.0 - - + +
71A ILE* 3.1 24.5 + - + +
72A ILE* 3.6 5.1 + - - +
74A TYR* 1.3 81.5 - - + +
76A ALA* 1.3 54.6 + - - +
78A LYS* 3.5 8.9 - - - +
79A HIS* 2.7 37.8 + - + +
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Residues in contact with ALA 76 (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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20A LEU* 4.2 3.8 - - + +
72A ILE 3.3 16.9 + - - +
73A ARG 3.7 3.1 - - - +
75A ILE* 1.3 72.7 - - - +
77A ASP* 1.3 63.8 + - - +
79A HIS* 2.9 8.9 + - - -
81A MET* 2.9 49.9 + - + +
82A LEU* 3.8 7.2 - - + -
150A HIS* 3.8 28.7 - - + +
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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