Contacts of the helix formed by residues 7 - 18 (chain C) in PDB entry 1GZ0
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 GLY 7 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C TYR* 1.3 74.2 - - - +
8C ILE* 1.3 66.3 + - - -
9C HIS* 3.2 3.3 + - - -
10C ALA 3.2 3.2 + - - -
11C VAL* 3.1 24.7 + - - +
66C VAL 4.5 2.7 - - - -
67C HIS 3.4 13.1 + - - -
68C GLN* 3.4 12.6 - - - -
70C ILE* 3.1 17.4 + - - -
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Residues in contact with ILE 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLY* 1.3 71.3 - - - +
9C HIS* 1.3 70.4 - - + +
11C VAL* 3.7 1.9 - - - +
12C GLN* 2.7 51.4 + - + +
35C ARG* 3.8 43.1 - - + +
36C LEU* 3.1 35.0 - - + -
39C LEU* 3.6 20.4 - - + +
68C GLN* 2.9 21.5 + - + +
70C ILE* 4.1 2.7 - - + +
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Residues in contact with HIS 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLY 3.2 0.8 - - - -
8C ILE* 1.3 93.2 + - + +
10C ALA* 1.3 65.6 + - - +
12C GLN* 3.5 6.9 - - - +
13C ALA* 3.0 25.8 + - - +
68C GLN* 4.8 8.1 + - - -
114C ARG* 5.5 2.9 + - - -
143C CYS* 3.4 55.2 - - + +
144C GLY* 3.9 3.9 - - - +
198H GLU* 6.0 0.2 + - - -
222H VAL* 6.3 1.6 - - - -
223H SER* 4.4 17.7 + - - -
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.0 26.0 - - + -
6C TYR 3.6 22.9 + - - +
7C GLY 3.2 2.4 + - - +
9C HIS* 1.3 78.0 - - - +
11C VAL* 1.3 65.3 + - - +
13C ALA* 3.4 3.0 + - - +
14C LEU* 3.3 24.6 + - - +
144C GLY* 4.5 11.4 - - - +
147C GLU* 4.6 8.9 - - + +
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Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.1 20.9 - - + -
6C TYR 5.2 0.2 - - - -
7C GLY 3.1 20.9 + - - +
8C ILE 3.7 3.1 - - - +
10C ALA* 1.3 76.5 - - - +
12C GLN* 1.3 63.7 + - - +
14C LEU* 3.2 4.9 + - - +
15C LEU* 2.9 19.9 + - + +
22C PHE* 3.7 19.0 - - + -
25C VAL* 5.7 0.2 - - + -
39C LEU* 3.6 29.4 - - + -
43C LEU* 4.6 7.9 - - + -
70C ILE* 3.7 29.4 - - + +
71C ILE 5.4 0.2 - - - -
72C ALA* 4.8 7.4 - - + -
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 2.7 33.8 + - + +
9C HIS* 3.5 9.0 - - - +
10C ALA 3.3 0.2 - - - -
11C VAL* 1.3 73.0 - - - +
13C ALA* 1.3 58.5 + - - +
15C LEU* 3.0 12.0 + - - +
16C GLU* 2.6 61.7 + - - +
39C LEU* 4.1 21.1 - - - +
221H SER* 4.5 16.6 - - - +
223H SER* 6.4 1.3 - - - -
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Residues in contact with ALA 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C HIS 3.0 18.1 + - - +
10C ALA 3.7 4.3 - - - +
12C GLN* 1.3 75.6 - - - +
14C LEU* 1.3 52.5 + - - +
16C GLU* 3.2 1.7 + - - +
17C ARG* 2.6 40.8 + - - +
144C GLY* 3.6 26.2 - - - +
147C GLU* 4.2 8.3 - - + -
148C SER* 4.5 4.5 - - - +
221H SER* 3.7 25.5 - - - +
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 3.5 22.7 - - + -
10C ALA 3.3 10.9 + - - +
11C VAL 3.2 4.9 + - - +
13C ALA* 1.3 75.1 - - - +
15C LEU* 1.3 64.7 + - - +
17C ARG* 5.0 0.4 - - + -
18C ALA* 2.5 44.0 + - + +
21C ARG* 3.3 37.0 - - + +
22C PHE* 3.6 19.1 - - + -
74C VAL* 3.4 35.2 - - + -
147C GLU* 3.6 24.2 - - + +
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL 2.9 11.9 + - - +
12C GLN* 3.1 17.7 - - - +
14C LEU* 1.3 76.2 - - - +
16C GLU* 1.3 66.4 - - - +
19C PRO* 3.0 28.4 - - + +
22C PHE* 3.8 13.8 - - + -
39C LEU* 3.8 25.8 - - + +
42C ALA* 3.5 33.9 - - + +
43C LEU* 4.6 8.5 - - + +
46C GLN* 3.5 32.9 - - + +
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Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLN* 2.6 56.0 + - - +
15C LEU* 1.3 86.3 - - - +
17C ARG* 1.3 64.6 + - + +
19C PRO* 4.9 1.3 - - - +
220H GLY 4.9 4.0 - - - +
221H SER* 3.7 34.8 - - - +
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Residues in contact with ARG 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ALA 2.6 19.7 + - - +
14C LEU* 5.0 0.4 - - - -
16C GLU* 1.3 80.5 - - + +
18C ALA* 1.3 60.6 + - + +
19C PRO* 3.9 3.8 - - - +
20C GLU* 4.4 4.0 - - - +
117C ASP* 5.0 5.1 + - - -
120C GLY* 5.7 5.1 + - - -
121C VAL 4.8 11.3 + - - -
122C HIS* 5.8 6.3 - - - +
147C GLU 4.6 4.9 - - - +
148C SER* 3.1 49.4 + - - -
149C VAL* 5.9 2.0 - - - +
220H GLY* 6.2 4.2 - - - -
221H SER* 4.8 5.8 - - - +
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 2.5 28.4 + - + +
17C ARG* 1.3 79.6 - - + +
19C PRO* 1.3 65.7 - - - +
20C GLU* 3.0 31.9 + - - +
21C ARG* 3.1 32.9 + - - +
22C PHE 4.3 0.7 + - - -
147C GLU 5.7 2.0 - - - +
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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