Contacts of the helix formed by residues 68 - 79 (chain A) in PDB entry 1GQT
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 SER 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP* 1.3 74.0 - - - +
69A ILE* 1.3 69.3 + - - +
71A GLU* 2.8 19.4 + - - +
72A SER* 3.0 16.2 + - - -
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Residues in contact with ILE 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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15A ALA* 4.1 27.4 - - + -
38A VAL* 5.5 9.2 - - + -
40A PHE* 4.1 20.9 - - + -
67A ASP* 3.5 12.7 - - - +
68A SER* 1.3 76.0 - - - +
70A GLY* 1.3 66.0 + - - +
72A SER* 3.0 7.9 + - - +
73A VAL* 3.0 23.2 + - + +
95A THR* 3.5 29.4 - - + +
97A VAL* 6.3 1.8 - - + -
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Residues in contact with GLY 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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64A THR* 4.0 8.5 - - - -
65A GLY 4.2 1.6 - - - -
67A ASP* 3.0 16.6 + - - -
68A SER 3.1 0.4 - - - -
69A ILE* 1.3 77.3 - - - +
71A GLU* 1.3 62.5 + - - +
73A VAL* 3.4 9.7 - - - +
74A ARG* 3.2 36.7 + - - +
95A THR* 3.2 19.7 - - - -
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Residues in contact with GLU 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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67A ASP 3.2 11.3 + - - +
68A SER* 2.8 16.3 + - - +
70A GLY* 1.3 75.6 - - - +
72A SER* 1.3 63.1 + - - +
74A ARG* 3.4 29.9 + - - +
75A GLN* 2.7 46.7 + - - +
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Residues in contact with SER 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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40A PHE* 3.8 16.4 - - - -
68A SER* 3.0 12.7 + - - -
69A ILE* 3.0 11.7 + - - -
71A GLU* 1.3 76.9 - - - +
73A VAL* 1.3 63.2 + - - +
75A GLN* 3.1 15.7 + - - +
76A GLN* 3.0 22.5 + - - +
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Residues in contact with VAL 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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13A ILE* 3.8 32.8 - - + -
40A PHE* 3.4 45.5 - - + -
45A ALA* 5.7 1.8 - - + -
64A THR* 3.9 13.2 - - + -
69A ILE* 3.0 13.3 + - + +
70A GLY* 3.4 14.6 - - - +
72A SER* 1.3 75.7 - - - +
74A ARG* 1.3 67.8 + - + +
76A GLN* 3.1 1.6 + - + +
77A LEU* 2.8 44.8 + - + +
95A THR* 5.0 3.1 - - + -
292A GLN* 4.9 1.3 - - - +
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Residues in contact with ARG 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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64A THR* 3.1 30.2 + - + -
65A GLY 4.7 3.0 + - - -
66A ASP* 5.9 1.0 - - - +
67A ASP 5.2 1.2 + - - -
70A GLY 3.2 14.8 + - - +
71A GLU* 3.5 38.9 + - - +
72A SER 3.3 0.2 - - - -
73A VAL* 1.3 77.8 - - + +
75A GLN* 1.3 61.8 + - - +
77A LEU* 3.2 14.5 + - + +
78A ALA* 3.2 9.0 + - - +
84A ILE* 3.5 25.9 - - + +
87A VAL* 3.8 28.7 - - + -
89A VAL* 3.3 30.5 - - - +
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Residues in contact with GLN 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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71A GLU* 2.7 53.8 + - - +
72A SER* 3.1 14.1 + - - +
74A ARG* 1.3 76.2 - - - +
76A GLN* 1.3 65.1 + - - +
78A ALA* 3.4 10.9 + - - +
79A THR* 3.4 19.3 + - - +
84A ILE* 5.6 0.2 - - - -
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Residues in contact with GLN 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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40A PHE* 4.0 28.3 - - + -
53A ARG* 3.8 11.3 - - - +
72A SER 3.0 12.6 + - - +
73A VAL 3.6 6.5 - - - +
75A GLN* 1.3 77.2 - - - +
77A LEU* 1.3 69.5 + - + +
79A THR* 2.9 33.1 + - - -
80A ASP* 3.0 37.1 + - - +
292A GLN* 5.2 5.8 - - + +
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Residues in contact with LEU 77 (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 ILE* 4.0 28.3 - - + -
45A ALA* 4.6 8.3 - - + +
49A VAL* 3.7 28.5 - - + -
60A PHE* 4.0 18.4 - - + -
73A VAL* 2.8 31.7 + - + +
74A ARG* 3.2 4.9 + - - +
76A GLN* 1.3 78.2 - - + +
78A ALA* 1.3 63.9 + - - +
80A ASP* 3.0 18.6 + - - +
82A ILE* 3.5 22.8 - - + +
84A ILE* 3.6 21.5 - - + -
87A VAL* 5.1 3.1 - - + -
292A GLN* 4.0 12.6 - - - +
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Residues in contact with ALA 78 (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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74A ARG 3.2 5.7 + - - +
75A GLN* 3.9 9.9 - - - +
76A GLN 3.0 1.4 - - - -
77A LEU* 1.3 77.2 - - - +
79A THR* 1.3 62.4 + - + +
80A ASP 3.3 1.0 + - - -
81A ASN* 3.7 8.0 + - - -
82A ILE 4.0 14.7 + - - +
84A ILE* 3.9 24.2 - - + +
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Residues in contact with THR 79 (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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75A GLN 3.4 15.7 - - - +
76A GLN* 2.9 30.3 + - - -
78A ALA* 1.3 79.1 - - + +
80A ASP* 1.3 56.6 + - - +
81A ASN 3.3 4.9 + - - -
297A TRP* 3.7 16.1 - - - -
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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