Contacts of the strand formed by residues 9 - 14 (chain J) in PDB entry 5GAH
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 VAL 9 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097A U 6.0 1.6 - - - +
1098A A 6.0 6.1 - - - +
8J TYR* 1.3 76.9 - - - +
10J LYS* 1.3 64.2 + - - +
11J LEU* 4.9 7.9 - - + -
27J ALA 5.0 4.5 - - - +
28J LEU* 4.0 22.7 - - + -
31J GLN* 3.2 35.9 - - + +
58J VAL* 3.8 4.4 - - - +
59J ILE* 2.9 55.1 + - + +
61J VAL* 4.9 2.7 - - + -
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Residues in contact with LYS 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058A U 5.1 7.9 + - - -
1059A G 5.4 3.0 + - - -
1061A U 2.8 46.3 + - + +
1070A A 3.9 24.9 - - + +
9J VAL* 1.3 76.3 - - - +
11J LEU* 1.3 76.9 + - - +
57J VAL 3.5 9.2 - - - +
58J VAL* 4.7 15.3 - - + -
59J ILE* 5.7 0.4 - - - -
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Residues in contact with LEU 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A U 3.9 18.2 - - - +
1070A A 4.9 7.9 - - - +
9J VAL* 4.9 10.8 - - + -
10J LYS* 1.3 95.0 - - - +
12J GLN* 1.3 61.1 + - - +
13J VAL* 4.1 15.7 - - + -
23J PRO 3.2 27.8 - - - +
24J VAL* 3.8 24.2 - - + +
27J ALA* 4.2 20.2 - - + -
28J LEU* 4.9 10.5 - - + -
38J PHE* 5.6 2.7 - - + -
56J PRO* 3.5 4.3 - - - +
57J VAL* 2.9 36.1 + - + +
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Residues in contact with GLN 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060A U 3.6 29.1 + - - -
1061A U 3.4 50.3 + - + +
1063A G 5.0 4.3 + - - -
11J LEU* 1.3 72.2 - - - +
13J VAL* 1.3 61.0 + - - +
14J ALA 4.3 0.7 + - - -
54J PRO* 4.3 18.1 - - + +
55J ILE 3.7 2.2 - - - -
56J PRO* 3.6 28.0 - - + +
75J PRO* 3.3 31.6 - - + +
78J VAL* 5.2 1.0 - - - +
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Residues in contact with VAL 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J LEU* 4.2 16.8 - - + -
12J GLN* 1.3 76.4 - - - +
14J ALA* 1.3 68.5 + - - +
17J MET* 3.2 29.2 - - + +
18J ALA* 4.6 8.3 - - + -
20J PRO* 6.3 0.4 - - + -
24J VAL* 5.5 7.2 - - + -
38J PHE* 4.2 13.9 - - + -
42J PHE* 3.4 15.7 - - + -
54J PRO* 4.0 0.7 - - - -
55J ILE* 2.9 33.3 + - - +
57J VAL* 3.7 24.5 - - + -
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Residues in contact with ALA 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J GLN 4.3 1.2 + - - -
13J VAL* 1.3 79.2 - - - +
15J ALA* 1.3 66.8 - - - +
16J GLY 3.7 0.7 - - - -
17J MET* 3.2 41.7 + - + +
42J PHE* 3.9 1.2 - - - -
52J GLY* 5.3 9.0 - - - +
53J LEU 3.6 10.8 - - - +
54J PRO* 3.9 10.6 - - + +
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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