Contacts of the helix formed by residues 68 - 79 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B ASP* 1.3 70.2 - - - +
69B ILE* 1.3 67.8 + - - +
70B GLY 3.1 2.2 - - - -
71B GLU* 3.3 8.2 + - - +
72B SER* 2.9 27.9 + - - -
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN 5.7 0.4 - - - +
15B ALA* 4.2 22.4 - - + +
40B PHE* 3.2 34.5 - - + -
67B ASP* 3.2 33.2 - - + +
68B SER* 1.3 75.0 - - - +
70B GLY* 1.3 55.0 + - - +
72B SER* 3.1 5.4 + - - -
73B VAL* 2.9 27.1 + - + +
95B THR* 4.1 17.3 - - + +
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Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B THR* 4.0 6.2 - - - +
65B GLY 4.2 0.4 - - - -
67B ASP* 3.1 16.1 + - - -
68B SER 3.1 0.4 - - - -
69B ILE* 1.3 77.7 - - - +
71B GLU* 1.3 60.5 + - - +
73B VAL* 3.1 15.9 - - - +
74B ARG* 3.1 33.3 - - - +
95B THR* 3.4 18.4 - - - -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP 3.4 6.5 + - - +
68B SER* 3.3 9.7 + - - +
70B GLY* 1.3 75.9 - - - +
72B SER* 1.3 65.3 + - - +
74B ARG* 2.5 46.8 + - - +
75B GLN* 3.1 35.5 + - + +
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 3.8 15.2 - - - -
68B SER* 2.9 16.4 + - - -
69B ILE* 3.1 10.4 + - - -
71B GLU* 1.3 80.5 - - - +
73B VAL* 1.3 61.7 + - - +
75B GLN* 3.4 6.5 + - - +
76B GLN* 3.0 23.0 + - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.8 23.1 - - + -
40B PHE* 3.5 37.4 - - + -
45B ALA* 5.5 2.0 - - + -
64B THR* 3.9 15.7 - - + -
69B ILE* 2.9 22.0 + - + +
70B GLY* 3.1 24.7 - - - +
72B SER* 1.3 72.7 - - - +
74B ARG* 1.3 58.3 + - - +
76B GLN* 3.2 1.4 + - - +
77B LEU* 2.8 52.2 + - + +
95B THR* 4.9 1.3 - - + -
292B GLN* 5.1 0.9 - - - +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B THR* 3.0 29.8 + - + -
65B GLY 3.4 17.8 + - - -
66B ASP* 4.4 2.8 - - - +
67B ASP 4.0 5.1 + - - -
70B GLY 3.1 10.3 + - - +
71B GLU* 2.5 60.0 + - - +
72B SER 3.3 0.2 - - - -
73B VAL* 1.3 76.7 - - - +
75B GLN* 1.3 62.4 + - - +
77B LEU* 3.4 7.6 + - + +
78B ALA* 3.1 18.5 + - - +
84B ILE* 3.5 25.7 - - + +
87B VAL* 4.2 17.0 - - + -
89B VAL* 3.5 32.5 - - - +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 3.1 29.9 + - - +
72B SER* 3.8 6.1 - - - +
74B ARG* 1.3 76.8 - - - +
76B GLN* 1.3 64.0 + - - +
78B ALA* 3.5 10.4 + - + +
79B THR* 3.3 24.9 + - + +
84B ILE* 5.6 0.4 - - - -
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 3.7 29.8 - - + -
53B ARG* 3.8 11.8 - - - +
72B SER 3.0 17.2 + - - +
73B VAL 3.2 3.8 + - - +
75B GLN* 1.3 77.2 - - - +
77B LEU* 1.3 63.6 + - + +
79B THR* 2.8 35.8 + - - -
80B ASP* 3.1 36.1 + - - +
292B GLN* 5.0 5.8 - - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.3 9.0 - - + -
45B ALA* 4.6 7.2 - - + +
49B VAL* 3.4 32.1 - - + -
60B PHE* 4.0 27.1 - - + -
73B VAL* 2.8 43.0 + - + +
74B ARG* 3.9 4.0 - - + +
76B GLN* 1.3 73.2 - - + +
78B ALA* 1.3 63.4 + - - +
80B ASP* 2.9 21.7 + - - +
82B ILE* 3.6 21.0 - - + +
84B ILE* 3.7 20.0 - - + -
87B VAL* 5.2 2.7 - - + -
292B GLN* 3.8 13.9 - - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG 3.1 13.1 + - - +
75B GLN* 3.7 12.3 - - + +
76B GLN 3.3 0.2 - - - -
77B LEU* 1.3 76.5 - - - +
79B THR* 1.3 61.1 + - + +
80B ASP 3.4 0.7 + - - -
81B ASN* 3.7 8.7 + - - -
82B ILE 4.0 14.0 + - - +
84B ILE* 4.0 19.8 - - + +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLN* 3.3 22.7 - - + +
76B GLN* 2.8 33.5 + - - -
78B ALA* 1.3 75.6 - - + +
80B ASP* 1.3 57.0 + - - +
81B ASN 3.3 5.7 + - - -
297B TRP* 3.4 19.1 - - - -
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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