Contacts of the helix formed by residues 5 - 14 (chain N) in PDB entry 5GJQ
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 ALA 5 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N SER* 1.3 68.4 - - - +
6N ALA* 1.3 48.9 + - - -
7N GLY 3.2 1.3 - - - -
8N ILE* 2.6 22.4 + - + -
9N ILE* 2.4 46.8 + - + -
30N VAL* 6.3 1.6 - - + -
34N PHE* 3.8 17.6 - - + -
37N GLU* 2.4 28.8 + - + +
38N ILE* 3.7 25.6 - - + -
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Residues in contact with ALA 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N SER* 3.2 9.1 + - - +
5N ALA* 1.3 75.7 - - - +
7N GLY* 1.3 52.8 + - - +
9N ILE* 3.2 12.0 - - - +
10N SER* 2.7 31.2 + - - -
37N GLU* 3.4 5.9 + - - +
166T ARG 3.8 2.1 - - - +
169T ALA* 2.7 50.3 - - + +
170T GLN* 3.0 9.1 - - - +
172T LYS* 5.3 1.8 - - + -
173T CYS* 5.3 2.2 - - - -
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Residues in contact with GLY 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N SER 4.5 2.4 + - - -
5N ALA 3.2 0.6 - - - -
6N ALA* 1.3 72.9 - - - +
8N ILE* 1.3 50.9 + - - +
10N SER 2.7 1.4 + - - -
11N LEU* 2.3 43.2 + - - +
124T LEU* 5.9 5.6 - - - -
170T GLN* 2.4 42.9 + - - +
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Residues in contact with ILE 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N SER 5.7 0.4 - - - +
5N ALA* 2.6 24.1 + - + +
7N GLY* 1.3 68.1 - - - +
9N ILE* 1.3 64.5 + - - +
11N LEU* 3.8 19.4 - - + +
12N LEU* 3.0 23.6 + - - +
23N ALA* 5.0 1.4 - - - +
26N LYS* 5.2 6.5 - - + -
27N LEU* 3.4 40.4 - - + +
30N VAL* 5.0 10.3 - - + -
38N ILE* 5.5 3.1 - - + -
124T LEU* 5.7 6.7 - - + +
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Residues in contact with ILE 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5N ALA* 2.4 47.5 + - + +
6N ALA* 3.2 12.3 - - - +
8N ILE* 1.3 72.5 - - - +
10N SER* 1.3 60.1 + - - +
12N LEU* 3.2 19.6 - - - +
13N ASP* 4.3 3.1 + - - -
37N GLU* 4.5 15.7 - - + +
38N ILE* 4.7 6.9 - - + +
41N SER* 4.3 20.0 + - - +
166T ARG* 4.4 8.0 - - + +
169T ALA* 5.5 3.4 - - + -
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Residues in contact with SER 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N ALA 2.7 10.0 + - - -
7N GLY 2.7 3.6 + - - -
9N ILE* 1.3 68.7 - - - +
11N LEU* 1.3 60.6 + - - -
12N LEU 2.9 6.3 + - - -
13N ASP* 3.4 10.4 + - - +
14N GLU* 3.1 22.8 + - - +
166T ARG* 2.7 40.0 - - - +
170T GLN* 2.9 35.9 - - - -
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Residues in contact with LEU 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N GLY 2.3 35.3 + - - +
8N ILE* 3.8 19.1 - - + +
10N SER* 1.3 67.0 - - - +
12N LEU* 1.3 65.6 + - - +
14N GLU* 3.0 42.9 + - - +
19N LEU* 3.8 24.1 - - + +
20N LYS* 4.4 1.4 - - - +
22N PHE 5.6 0.7 - - - +
23N ALA* 3.8 30.0 - - + +
26N LYS* 6.2 2.5 - - + -
113T GLY 5.7 1.8 - - - +
116T LEU* 5.1 7.0 - - + +
117T GLY* 5.5 3.1 - - - -
120T LYS* 3.4 33.2 - - + -
170T GLN* 4.1 5.2 - - - +
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Residues in contact with LEU 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N ILE 3.0 13.0 + - - +
9N ILE* 3.2 16.4 - - - +
10N SER 2.9 1.4 + - - -
11N LEU* 1.3 79.7 - - - +
13N ASP* 1.3 63.9 + - - +
14N GLU 3.1 5.7 + - - +
20N LYS* 3.6 18.6 - - + +
23N ALA* 4.7 6.3 - - + +
24N LEU* 4.6 13.2 - - + -
27N LEU* 6.1 2.5 - - + -
41N SER* 3.5 33.4 - - - +
44N LYS* 3.6 30.1 - - + -
45N ILE* 4.2 9.4 - - + -
48N LEU* 3.3 33.3 - - + +
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Residues in contact with ASP 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N ILE 4.3 3.6 + - - -
10N SER 3.4 6.5 + - - +
12N LEU* 1.3 83.5 - - - +
14N GLU* 1.3 63.4 + - + +
15N ASP* 3.5 7.3 + - - -
20N LYS* 4.2 7.8 + - - +
44N LYS* 4.6 21.3 - - - -
48N LEU* 6.4 0.2 - - - -
162T PRO* 6.5 0.7 - - - -
163T SER* 6.6 0.2 - - - -
166T ARG* 5.7 7.4 - - + -
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Residues in contact with GLU 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N SER* 3.1 25.3 - - - +
11N LEU* 3.0 39.7 - - - +
12N LEU 3.0 1.4 - - - -
13N ASP* 1.3 78.3 - - + +
15N ASP* 1.3 68.6 - - - +
19N LEU* 4.6 4.3 - - + +
20N LYS* 3.1 23.2 - - - +
163T SER* 5.8 4.3 - - - -
166T ARG* 5.1 0.7 - - + +
167T TYR* 2.9 39.5 - - - +
170T GLN* 4.4 2.2 + - - +
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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