Contacts of the helix formed by residues 7 - 15 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D VAL* 1.3 69.6 - - - +
8D PRO* 1.3 62.6 - - + -
9D GLN* 3.0 32.7 + - + +
10D GLN* 2.3 56.2 + - + +
11D ALA* 3.0 6.1 + - - +
130D ILE* 3.6 26.5 - - + +
148D TRP* 3.1 42.6 - + + -
161D GLN 3.2 7.3 + - - -
162D ALA* 3.1 45.1 - - + -
165D PHE* 3.8 12.6 + - - +
177D TRP* 5.2 3.7 + - - -
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Residues in contact with PRO 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL 3.2 8.9 - - - +
7D HIS* 1.3 90.3 - - + +
9D GLN* 1.3 59.4 + - - +
11D ALA* 3.8 3.2 + - + +
12D PHE* 3.4 22.9 + - - +
103D PHE* 4.3 33.2 - - + -
114D GLN* 6.1 2.5 - - - +
122D TYR* 4.5 11.6 - - - +
148D TRP* 4.4 5.4 - - + -
157D ILE* 6.1 6.7 - - + -
162D ALA* 3.7 25.4 - - + +
163D LYS* 6.1 1.6 - - + -
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Residues in contact with GLN 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D HIS* 2.7 20.9 + - + +
8D PRO* 1.3 75.7 - - - +
10D GLN* 1.3 64.6 + - - +
12D PHE* 4.0 1.7 - - - +
13D CYS* 3.2 22.2 + - - +
121D ARG 5.1 0.2 - - - +
122D TYR* 3.2 51.1 + - + +
125D GLY* 3.4 26.9 + - - +
130D ILE* 4.0 8.6 - - - +
165D PHE 3.9 1.2 - - - +
166D ALA* 2.8 36.3 - - - +
167D CYS* 3.3 24.9 - - - +
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Residues in contact with GLN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PRO 4.5 0.9 - - - +
6D VAL* 3.4 19.8 - - + +
7D HIS* 2.3 58.5 + - + +
9D GLN* 1.3 71.6 - - - +
11D ALA* 1.3 57.6 + - - +
13D CYS* 3.6 5.0 + - - +
14D ASN* 2.9 38.2 + - - +
129D LYS* 5.6 0.8 - - - +
130D ILE* 3.1 44.5 + - + +
131D THR 5.1 1.3 + - - +
132D ARG* 6.3 0.2 - - - +
148D TRP* 5.4 2.9 - - - -
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Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 4.6 20.4 - - + +
7D HIS 3.0 10.1 + - - +
8D PRO* 4.4 3.6 - - + +
10D GLN* 1.3 73.8 - - - +
12D PHE* 1.3 56.5 + - - +
13D CYS 2.9 4.7 - - - -
14D ASN* 2.6 30.4 + - - +
15D ALA* 2.9 13.9 + - - +
101D CYS 5.1 3.1 - - - +
102D ASP* 5.7 0.9 - - - -
103D PHE* 4.5 21.3 - - + +
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Residues in contact with PHE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PRO 3.4 18.0 + - - +
9D GLN* 4.0 6.7 - - - +
11D ALA* 1.3 77.4 - - - +
13D CYS* 1.3 62.8 + - - +
15D ALA* 3.8 11.7 - - - +
18D VAL* 3.7 37.0 - - + +
53D PHE* 4.6 5.6 - - + -
54D LYS* 3.5 22.9 - - + -
87D ALA* 5.2 1.8 - - - -
103D PHE* 4.2 17.1 - + + +
118D LEU* 3.3 59.0 - - + -
122D TYR* 3.5 29.2 - + + -
123D GLN* 4.4 11.2 - - + -
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Residues in contact with CYS 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN* 3.2 16.9 + - - +
10D GLN* 3.7 6.7 - - - +
11D ALA 2.9 0.8 - - - -
12D PHE* 1.3 77.6 - - - +
14D ASN* 1.3 58.1 + - - +
15D ALA 3.1 4.9 - - - -
54D LYS* 2.7 26.2 + - - +
122D TYR 3.8 11.2 - - - -
123D GLN* 3.7 4.0 - - - -
125D GLY 3.5 8.5 - - - +
126D CYS* 2.0 65.2 - - + +
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Residues in contact with ASN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 5.9 1.6 - - - +
10D GLN* 2.9 31.0 + - - +
11D ALA* 2.6 17.4 + - - +
13D CYS* 1.3 74.0 - - - +
15D ALA* 1.3 59.3 + - - -
16D ASP* 3.7 4.3 + - - +
54D LYS* 4.6 0.2 - - - -
88D GLY 5.7 0.2 - - - -
89D LYS* 5.6 7.6 - - - +
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ALA 2.9 10.8 + - - +
12D PHE 3.8 10.5 - - - +
13D CYS 3.1 1.6 - - - -
14D ASN* 1.3 78.2 - - - +
16D ASP* 1.3 59.2 + - - +
17D VAL 2.9 24.5 - - - +
18D VAL* 3.9 6.7 - - + -
54D LYS* 2.7 35.2 + - - -
87D ALA* 4.0 5.4 - - + -
88D GLY* 3.8 17.3 - - - +
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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