Contacts of the helix formed by residues 5 - 16 (chain G) in PDB entry 6O81
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 GLU 5 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4G LYS* 1.3 73.0 - - - +
6G LEU* 1.3 60.3 + - - +
8G GLU* 3.8 7.7 - - - +
9G TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LYS* 3.3 3.0 - - + +
5G GLU* 1.3 76.6 - - - +
7G ILE* 1.3 60.3 + - - +
9G TYR* 3.4 1.9 + - - -
10G PHE* 2.9 26.0 + - - +
29G THR* 3.3 23.7 - - + +
33G PHE* 5.0 18.8 - - + -
52G ALA* 5.6 9.2 - - + -
55G THR* 5.7 9.2 - - - -
56G LEU* 5.2 7.4 - - + -
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Residues in contact with ILE 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LYS* 3.8 18.2 + - + +
5G GLU 3.4 0.2 - - - -
6G LEU* 1.3 78.5 - - - +
8G GLU* 1.3 58.3 + - - +
10G PHE* 3.7 8.9 - - + +
11G LYS* 2.9 29.8 + - - +
55G THR* 5.6 6.0 - - - +
56G LEU* 5.2 4.7 - - + -
59G VAL* 5.2 14.6 - - + -
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Residues in contact with GLU 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LYS 3.6 11.3 + - - +
5G GLU* 3.5 11.6 + - - +
6G LEU 3.3 0.4 - - - -
7G ILE* 1.3 79.7 - - - +
9G TYR* 1.3 56.9 + - - +
11G LYS* 3.4 5.7 + - - +
12G SER* 2.9 29.7 + - - -
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Residues in contact with TYR 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G GLU 2.9 18.9 + - - +
6G LEU* 3.8 4.0 - - - +
8G GLU* 1.3 73.6 - - - +
10G PHE* 1.3 60.1 + - - +
12G SER* 3.3 8.4 + - - -
13G GLN* 2.9 64.2 + - + +
28G ARG* 3.8 15.1 + - - +
29G THR* 3.7 29.8 - - + -
32G GLU* 3.4 46.5 + - + +
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Residues in contact with PHE 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LEU 2.9 18.1 + - - +
7G ILE* 3.7 7.2 - - - +
9G TYR* 1.3 77.0 - - - +
11G LYS* 1.3 61.3 + - + +
13G GLN* 3.3 2.2 + - - -
14G MET* 2.9 36.2 + - + +
22G SER* 3.3 35.9 - - - -
25G ALA* 3.7 13.5 - - + -
26G ALA* 3.4 15.3 - - + -
29G THR* 3.6 21.6 + - - +
56G LEU* 3.7 22.4 - - + -
59G VAL* 5.8 6.7 - - + -
60G ASP* 4.2 20.0 - - + -
65G VAL* 4.2 13.2 - - + -
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Residues in contact with LYS 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE 2.9 18.2 + - - +
8G GLU* 3.8 6.3 - - - +
10G PHE* 1.3 81.7 - - + +
12G SER* 1.3 57.0 + - - +
14G MET* 4.5 6.1 - - + +
15G LYS* 2.9 50.7 + - + +
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Residues in contact with SER 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G GLU 2.9 17.6 + - - -
9G TYR* 3.7 11.9 - - - -
10G PHE 3.3 0.2 - - - -
11G LYS* 1.3 76.8 - - - +
13G GLN* 1.3 63.3 + - - +
15G LYS* 5.0 1.6 - - - -
16G GLU* 3.3 25.3 + - - +
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Residues in contact with GLN 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G TYR* 2.9 60.4 + - + +
10G PHE* 3.3 5.4 + - - +
12G SER* 1.3 82.1 + - - +
14G MET* 1.3 58.6 + - - +
16G GLU* 4.2 6.8 + - - +
17G ASP 4.5 3.3 + - - -
20G MET* 3.4 27.2 - - - +
25G ALA* 4.0 18.4 - - + +
28G ARG* 3.2 36.4 + - + +
29G THR* 4.9 1.1 - - - +
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Residues in contact with MET 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G PHE* 2.9 29.0 + - + +
11G LYS* 4.2 7.6 - - + +
13G GLN* 1.3 79.2 - - - +
15G LYS* 1.3 59.6 + - - +
16G GLU 3.4 0.2 - - - -
17G ASP 3.2 20.8 - - - +
18G PRO* 4.9 1.6 - - - +
20G MET* 5.2 5.4 - - - +
21G ALA 5.3 5.2 - - - +
22G SER* 5.5 3.8 - - - -
25G ALA* 4.4 12.6 - - + -
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Residues in contact with LYS 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G LYS* 2.9 35.5 + - + +
12G SER* 4.9 2.0 - - - +
14G MET* 1.3 75.4 - - - +
16G GLU* 1.3 61.5 - - - +
17G ASP* 3.3 3.3 + - - -
18G PRO* 4.9 2.8 - - - +
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Residues in contact with GLU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G SER 3.3 19.8 + - - +
13G GLN* 4.6 4.5 - - - +
14G MET 3.4 0.8 - - - -
15G LYS* 1.3 79.3 - - - +
17G ASP* 1.3 58.5 - - + +
18G PRO* 4.1 4.5 - - - +
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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