Contacts of the helix formed by residues 7 - 15 (chain C) in PDB entry 1GXD
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 HIS 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 VAL* 1.3 73.6 - - - +
8C PRO* 1.3 58.0 - - + +
9C GLN* 2.4 52.5 + - + -
10C GLN* 2.7 23.2 + - + +
11C ALA 3.5 2.6 + - - -
122C TYR* 4.2 4.2 + - - -
130C ILE* 3.6 36.7 - - + +
148C TRP* 3.8 20.7 + - + -
161C GLN* 2.6 33.0 + - + -
162C ALA* 3.1 24.3 - - - +
165C PHE* 2.7 26.7 + - + -
166C ALA* 4.3 1.0 + - - -
177C TRP* 6.0 1.7 - + - -
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Residues in contact with PRO 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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6C VAL 3.7 7.1 - - - +
7C HIS* 1.3 90.8 - - - +
9C GLN* 1.3 58.9 + - - +
11C ALA* 3.7 20.6 - - + +
12C PHE* 4.0 2.1 + - - +
103C PHE* 3.9 34.1 - - + -
114C GLN* 4.5 9.9 - - - +
122C TYR* 3.0 36.5 - - + +
148C TRP* 5.2 0.2 - - + -
157C ILE* 5.3 6.3 - - + -
158C ASN* 5.7 2.9 - - - +
162C ALA* 3.8 24.9 - - + +
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Residues in contact with GLN 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 HIS* 2.4 36.5 + - + -
8C PRO* 1.3 67.0 - - - +
10C GLN* 1.3 68.9 + - - +
11C ALA 3.0 1.3 - - - -
12C PHE* 2.9 16.5 + - - +
13C CYS* 3.1 20.7 + - - -
122C TYR* 3.4 40.8 + - + +
125C GLY* 2.7 35.8 + - - -
126C CYS* 3.9 0.8 - - - +
128C CYS 4.6 2.0 + - - -
130C ILE* 3.8 15.2 - - + +
166C ALA* 3.7 4.2 - - - +
167C CYS* 2.9 36.8 + - - +
168C ILE* 6.0 0.2 - - - +
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Residues in contact with GLN 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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6C VAL* 4.4 19.3 - - + +
7C HIS 2.7 18.2 + - - +
9C GLN* 1.3 77.8 - - - +
11C ALA* 1.3 51.2 + - - +
13C CYS* 2.7 16.8 + - - +
14C ASN* 2.5 70.0 + - - +
126C CYS 5.1 2.4 + - - -
128C CYS 4.0 18.8 + - - -
129C LYS* 5.1 3.2 - - - +
130C ILE* 4.7 22.4 - - + +
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Residues in contact with ALA 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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6C VAL* 5.4 6.7 - - + +
7C HIS 3.5 2.8 + - - +
8C PRO* 3.7 13.5 - - + +
10C GLN* 1.3 76.5 - - - +
12C PHE* 1.3 57.8 + - - +
13C CYS 2.8 0.9 + - - -
14C ASN* 5.2 1.8 - - - -
15C ALA* 2.8 40.3 + - + +
18C VAL* 5.3 0.9 - - - -
87C ALA* 5.8 1.3 - - + -
102C ASP* 5.6 0.7 - - - +
103C PHE* 3.6 46.0 - - + -
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Residues in contact with PHE 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 PRO 4.4 0.7 - - - +
9C GLN 2.9 11.5 + - - +
11C ALA* 1.3 74.7 - - - +
13C CYS* 1.3 58.1 + - - +
15C ALA 4.6 0.2 - - - -
18C VAL* 3.7 20.4 - - + -
53C PHE* 3.2 39.3 - - + -
54C LYS* 3.5 34.4 - - + +
118C LEU* 2.9 44.4 - - + -
119C ASN 5.4 0.7 - - - -
122C TYR* 4.1 32.5 - + + -
123C GLN* 3.6 34.6 - - + +
126C CYS* 4.4 1.9 - - - -
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Residues in contact with CYS 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 GLN* 3.1 26.6 + - - +
10C GLN* 2.7 18.0 + - - +
11C ALA 2.8 0.2 + - - -
12C PHE* 1.3 80.9 - - - +
14C ASN* 1.3 66.5 + - - +
15C ALA 3.3 1.3 - - - -
54C LYS* 3.1 20.5 + - - +
122C TYR 4.2 4.3 - - - -
126C CYS* 2.0 57.7 - - + +
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Residues in contact with ASN 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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6C VAL* 6.2 1.2 - - - +
10C GLN* 2.5 57.4 + - - +
11C ALA* 4.5 1.3 - - - +
13C CYS* 1.3 75.6 - - - +
15C ALA* 1.3 59.4 + - - +
16C ASP* 3.8 6.6 + - - +
54C LYS* 4.7 0.2 - - - -
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Residues in contact with ALA 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 ALA* 2.8 21.9 + - - +
13C CYS 4.4 0.2 - - - -
14C ASN* 1.3 78.0 - - - +
16C ASP* 1.3 60.0 + - - +
18C VAL* 4.1 4.7 - - + -
54C LYS* 2.6 36.1 + - - +
87C ALA* 3.4 41.5 - - + +
88C GLY 6.1 0.2 - - - -
102C ASP* 5.3 2.5 - - - +
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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