Contacts of the helix formed by residues 75 - 85 (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 SER 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A HIS* 3.5 2.7 - - - +
74A GLU* 1.3 80.6 - - - +
76A GLY* 1.3 65.7 + - - +
77A THR* 3.5 2.3 + - - -
78A ASP* 2.8 33.3 + - - +
79A ARG* 3.0 21.7 + - - +
186A TYR* 4.1 1.7 + - - -
195A GLU* 5.5 1.6 - - - -
201A GLU* 3.4 33.8 + - - +
204A ARG* 4.5 1.7 + - - -
1244A CMK 3.7 16.4 + - - -
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Residues in contact with GLY 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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8A PRO* 4.2 10.3 - - - -
75A SER* 1.3 74.7 - - - +
77A THR* 1.3 56.7 + - - +
79A ARG* 3.0 6.0 + - - +
80A LEU* 2.9 30.7 + - - +
94A ASN* 4.0 9.0 - - - -
201A GLU* 3.3 6.6 + - - -
1244A CMK 3.7 35.8 + - - -
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Residues in contact with THR 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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76A GLY* 1.3 73.5 - - - +
78A ASP* 1.3 65.3 + - - +
80A LEU* 3.3 7.1 + - - +
81A VAL* 3.3 20.3 + - - +
94A ASN* 3.8 2.9 + - - +
176A TYR* 4.8 2.1 - - - -
178A TYR* 2.8 43.6 + - + +
183A LEU* 4.1 7.4 - - + +
186A TYR* 3.3 41.5 - - + -
201A GLU* 2.9 25.2 + - - +
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Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A HIS* 3.4 25.7 - - - +
74A GLU* 3.7 10.3 - - - +
75A SER* 2.8 39.3 + - - +
77A THR* 1.3 75.7 - - - +
79A ARG* 1.3 64.6 + - - +
81A VAL* 3.1 19.2 + - - +
82A GLU 3.6 0.5 + - - -
186A TYR* 3.3 3.9 - - - -
187A SER* 3.0 25.5 + - - +
204A ARG* 2.9 40.2 + - - -
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Residues in contact with ARG 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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8A PRO* 4.3 4.9 - - - -
9A ALA 4.9 1.2 - - - +
10A ARG* 4.0 18.0 - - - +
49A ALA* 3.4 34.8 + - + -
51A ASP* 4.0 15.7 - - - +
69A THR* 2.9 35.1 + - + +
70A ARG 2.9 23.0 + - - -
71A ASN 5.1 0.8 + - - -
73A HIS* 3.6 26.3 + - + +
75A SER 3.0 10.3 + - - +
76A GLY 3.0 11.7 + - - +
78A ASP* 1.3 77.6 - - - +
80A LEU* 1.3 61.4 + - + +
82A GLU* 3.2 14.7 + - - +
83A VAL* 3.5 11.0 + - - +
1244A CMK 2.7 44.2 + - - -
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Residues in contact with LEU 80 (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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6A VAL* 3.5 32.8 - - + -
8A PRO* 3.4 33.9 - - + -
49A ALA* 5.2 0.7 - - + -
76A GLY 2.9 10.7 + - - +
77A THR* 3.6 9.6 - - - +
78A ASP 3.2 0.4 - - - -
79A ARG* 1.3 76.2 - - + +
81A VAL* 1.3 59.9 + - - +
83A VAL* 3.1 8.4 + - - +
84A MET* 2.8 28.8 + - - +
92A TYR* 4.6 11.2 - - + -
93A ILE 4.5 2.2 - - - -
94A ASN* 3.5 35.2 - - + +
178A TYR* 3.8 16.8 - - + -
183A LEU* 4.5 10.2 - - + +
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Residues in contact with VAL 81 (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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73A HIS* 6.2 0.4 - - + -
77A THR 3.3 15.0 + - - +
78A ASP* 3.1 11.5 + - - +
80A LEU* 1.3 76.0 - - - +
82A GLU* 1.3 64.4 + - - +
84A MET* 3.0 28.4 + - + +
85A HIS* 3.1 27.5 + - + -
183A LEU* 3.2 36.3 - - + +
184A GLN* 5.4 2.0 - - - +
186A TYR* 4.0 15.5 - - + -
187A SER* 4.0 21.1 - - - +
188A GLN* 5.9 2.2 - - - +
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Residues in contact with GLU 82 (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 ILE* 5.6 1.3 - - + -
68A MET 3.8 5.7 - - - +
69A THR* 3.2 24.8 - - + +
70A ARG* 2.9 52.4 + - - +
73A HIS* 2.6 36.6 + - + +
78A ASP 3.6 1.8 + - - -
79A ARG 3.2 11.3 + - - +
81A VAL* 1.3 82.4 - - - +
83A VAL* 1.3 60.9 + - - +
85A HIS* 3.5 21.8 + - - +
86A LYS* 4.1 20.7 + - - +
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Residues in contact with VAL 83 (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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6A VAL* 4.0 29.6 - - + -
47A TRP* 5.3 2.5 - - + -
49A ALA* 3.9 15.9 - - + -
67A ILE* 3.9 36.3 - - + -
69A THR* 4.1 6.5 - - + -
79A ARG 3.6 13.0 - - - +
80A LEU* 3.1 9.8 + - - +
82A GLU* 1.3 74.4 - - - +
84A MET* 1.3 62.7 + - - +
86A LYS* 3.0 5.2 + - - +
87A VAL* 2.8 47.9 + - + +
92A TYR* 5.4 1.6 - - + -
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Residues in contact with MET 84 (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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80A LEU 2.8 13.2 + - - +
81A VAL* 3.2 26.7 - - + +
83A VAL* 1.3 76.9 - - - +
85A HIS* 1.3 87.5 + - + +
86A LYS 3.1 1.4 + - - -
87A VAL 3.2 15.8 + - - +
88A GLU* 4.7 0.2 - - - -
92A TYR* 3.3 43.7 + - + +
180A ARG* 3.5 23.2 + - + +
183A LEU* 3.9 11.2 - - + +
184A GLN* 3.7 44.6 - - - +
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Residues in contact with HIS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.1 31.1 + - + -
82A GLU* 3.8 11.7 + - - +
83A VAL 3.2 1.0 - - - -
84A MET* 1.3 102.5 - - + +
86A LYS* 1.3 63.4 + - + +
180A ARG* 5.2 6.8 + - - +
184A GLN* 5.4 6.1 + - - +
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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