Contacts of the strand formed by residues 9 - 14 (chain J) in PDB entry 5A0Q
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 9 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8J GLY* 1.4 73.2 - - - -
10J VAL* 1.3 64.4 + - - +
11J MET 4.0 1.3 - - - +
23J ALA* 3.7 15.0 - - - +
24J ASP* 2.9 23.8 + - + +
40J LYS* 4.3 1.4 - - - +
53J ALA* 4.1 1.4 - - - +
138J SER 3.9 3.8 - - - -
139J GLY* 4.2 2.0 - - - -
140J THR 4.6 1.3 - - - +
141J CYS* 4.7 6.1 - - + -
145J MET* 4.1 17.3 - - + -
170J MET* 5.2 2.2 - - - -
174J VAL* 4.0 27.6 - - + -
180J SER* 3.8 8.2 + - - +
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Residues in contact with VAL 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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9J ALA* 1.3 72.4 - - - +
11J MET* 1.3 68.2 + - - +
21J ILE* 5.0 2.7 - - + -
22J ALA 3.9 5.6 - - - +
23J ALA* 4.8 2.9 - - + -
40J LYS* 5.7 0.7 - - + -
41J ILE* 6.4 0.4 - - + -
51J GLY* 3.4 26.9 - - - +
52J LEU 4.0 4.0 - - - +
53J ALA* 2.9 46.7 - - + +
105J GLU 4.3 4.3 - - - +
107J VAL* 3.7 22.2 - - + +
136J VAL 4.0 1.0 - - - +
137J VAL* 3.5 4.5 - - - -
138J SER 2.8 38.3 + - - +
145J MET* 4.1 2.2 - - - +
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Residues in contact with MET 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ALA* 4.0 1.2 - - - +
10J VAL* 1.3 75.8 - - - +
12J ALA* 1.4 68.2 + - - +
13J MET* 5.1 5.4 - - + -
21J ILE* 3.3 8.7 - - - +
22J ALA* 3.0 44.8 + - + +
23J ALA* 4.8 0.4 - - - +
135J PHE* 5.3 0.9 - - + -
137J VAL* 3.6 14.1 - - + -
145J MET* 3.5 31.0 - - - +
149J CYS* 3.7 25.6 - - + -
166J ILE* 4.1 16.4 - - + -
169J ALA* 4.0 17.3 - - + -
170J MET* 3.7 31.6 - - + -
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Residues in contact with ALA 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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11J MET* 1.4 80.7 - - - +
13J MET* 1.4 62.1 + - - +
20J ALA 3.8 7.9 - - - +
21J ILE* 4.0 12.6 - - + +
107J VAL* 3.6 23.1 - - + -
109J ALA* 4.6 8.5 - - + -
120J ILE* 4.9 5.4 - - + -
135J PHE* 3.2 7.7 - - - +
136J VAL* 3.1 39.3 + - + +
166J ILE* 4.7 0.7 - - - -
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Residues in contact with MET 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 MET* 5.1 5.2 - - + -
12J ALA* 1.4 75.5 - - - +
14J LYS* 1.3 60.9 + - - +
15J GLY 4.2 0.4 + - - -
19J VAL* 3.7 1.2 - - - +
20J ALA* 2.8 45.3 + - + +
120J ILE* 4.4 4.6 - - - +
134J ASP 3.6 6.1 - - - -
135J PHE* 3.8 10.8 - - + +
149J CYS* 5.7 5.6 - - - -
153J TRP* 3.9 24.7 - - + +
157J MET* 3.8 12.8 - - + -
162J LEU* 3.3 51.4 - - + +
165J THR* 4.0 18.2 - - - -
166J ILE* 3.9 23.1 - - + +
169J ALA* 6.2 0.7 - - - -
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Residues in contact with LYS 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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13J MET* 1.3 72.5 - - - +
15J GLY* 1.3 61.1 + - - +
16J LYS 5.9 0.2 - - - -
18J CYS 4.5 4.0 - - - +
19J VAL* 4.4 2.0 - - + -
118J PRO* 3.5 46.7 - - + +
119J PHE* 5.4 0.4 - - - +
120J ILE* 3.8 33.9 - - + +
134J ASP* 2.8 28.2 + - - +
153J TRP* 3.2 31.5 + - - -
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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