Contacts of the strand formed by residues 9 - 16 (chain A) in PDB entry 4FAO
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 GLN 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A SER 5.2 4.0 - - - +
7A HIS* 3.1 23.5 + - - +
8A CYS* 1.3 78.3 - - - +
10A LYS* 1.3 70.8 + - - +
11A THR* 4.3 6.4 + - - +
37A CYS* 3.6 3.8 - - - -
38A LYS* 2.9 35.4 + - + +
107A CYS* 3.7 10.7 - - - -
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLN* 1.3 82.9 - - - +
11A THR* 1.3 62.3 + - - +
35A TYR* 3.4 53.3 + - + -
36A GLU 3.6 3.1 - - - +
104A VAL* 3.8 21.4 + - + +
105A ALA* 3.2 27.7 + - - +
106A GLU* 5.1 1.1 - - - +
107A CYS* 3.7 12.9 - - + +
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Residues in contact with THR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLN* 4.3 6.4 + - - +
10A LYS* 1.3 77.0 + - - +
12A SER* 1.3 77.0 + - - +
35A TYR* 3.0 15.3 - - - -
36A GLU* 2.9 42.4 + - + -
38A LYS* 3.8 43.5 - - + +
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Residues in contact with SER 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 1.3 91.1 - - - +
13A LEU* 1.3 61.3 + - - +
14A ARG* 3.9 15.6 + - - +
33A GLU* 2.9 26.9 + - - -
35A TYR* 4.0 3.8 - - - -
36A GLU* 4.7 1.2 - - - +
38A LYS* 5.2 0.7 + - - -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR 3.5 0.2 + - - -
12A SER* 1.3 75.7 - - - +
14A ARG* 1.3 65.2 + - - +
15A VAL* 3.1 23.2 + - + -
33A GLU* 2.6 10.8 + - - -
34A ALA* 2.5 40.8 + - + +
35A TYR 3.7 22.7 - - - +
36A GLU* 4.0 15.7 - - + +
54B HIS* 4.8 0.7 - - - +
57B VAL* 5.8 0.2 - - + -
58B GLN* 4.7 25.8 - - + +
61B VAL* 4.4 10.3 - - + -
69B VAL* 3.7 29.2 - - + -
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Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 3.9 10.4 + - - +
13A LEU* 1.3 73.0 - - - +
15A VAL* 1.3 63.8 + - - +
16A ASN* 3.6 3.5 + - - +
31A GLU* 3.9 22.9 + - - +
32A TYR 3.5 2.5 - - - +
33A GLU* 3.2 28.2 + - - +
61B VAL* 5.9 1.2 - - - +
64E PHE* 3.4 57.2 - - - +
60I GLY* 6.3 0.6 - - - -
62I HIS* 6.0 3.8 - - - -
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.1 20.4 + - + +
14A ARG* 1.3 72.7 - - - +
16A ASN* 1.3 70.6 + - - +
17A PHE* 4.0 2.2 + - + +
19A ASP* 6.2 0.2 - - + -
20A ILE* 4.3 12.1 - - + -
31A GLU* 3.1 4.0 - - - +
32A TYR* 2.9 50.2 + - + -
34A ALA* 4.0 12.8 - - + -
57B VAL* 3.5 34.1 - - + -
61B VAL* 3.8 24.0 - - + -
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG 3.6 3.5 + - - +
15A VAL* 1.3 77.9 - - - +
17A PHE* 1.3 58.9 + - - +
18A GLU* 2.9 34.2 + - - +
19A ASP* 2.8 50.9 + - - +
20A ILE 3.6 2.3 + - - -
30A LYS* 3.3 11.6 - - - +
31A GLU* 3.6 25.9 + - + +
61B VAL* 5.8 0.2 - - - +
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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