Contacts of the strand formed by residues 94 - 98 (chain J) in PDB entry 1JJ2
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 94 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18J ILE* 4.5 4.9 - - - +
19J THR* 3.2 11.4 - - - +
21J ALA* 4.0 6.5 - - + -
73J VAL* 3.6 4.4 - - - +
74J VAL* 2.7 31.4 + - + -
75J ARG* 2.8 61.7 + - + +
92J ASP* 4.0 2.5 - - - +
93J ASN* 1.3 76.5 - - - +
95J ALA* 1.3 57.0 + - - +
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Residues in contact with ALA 95 (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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18J ILE* 3.5 24.2 - - + +
19J THR 2.9 5.7 + - - -
20J CYS* 3.3 8.7 - - - -
21J ALA 2.9 21.7 + - - -
29J LEU* 4.0 13.2 - - + +
53J ILE* 4.6 3.6 - - + -
71J ALA* 4.2 8.7 - - + -
72J VAL 3.1 20.0 - - - +
73J VAL* 4.1 2.7 - - - -
74J VAL 4.1 0.9 - - - +
94J ALA* 1.3 75.5 - - - +
96J VAL* 1.3 65.0 + - - +
97J ILE 4.3 0.2 - - - -
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Residues in contact with VAL 96 (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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21J ALA* 3.5 25.6 - - + +
22J ASP* 3.7 11.7 - - + +
71J ALA* 3.3 3.1 - - - -
72J VAL* 2.9 30.3 + - + +
74J VAL* 3.7 23.1 - - + -
95J ALA* 1.3 77.7 - - - +
97J ILE* 1.3 73.2 - - - +
98J VAL* 3.4 3.3 + - + +
104J PRO* 4.2 11.4 - - + -
106J GLY 6.0 0.2 - - - +
109J LEU* 3.4 35.2 - - + -
113J ILE* 4.8 1.3 - - + -
124J VAL* 4.9 10.3 - - + -
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Residues in contact with ILE 97 (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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20J CYS* 3.7 13.0 - - - -
22J ASP* 3.1 12.2 + - - +
24J THR* 3.4 22.7 - - - +
26J ALA* 3.8 13.5 - - + -
29J LEU* 4.3 14.1 - - + -
64J MET* 3.7 18.6 - - + -
69J LEU* 3.9 23.6 - - + -
70J GLU 3.5 14.4 - - - +
71J ALA* 3.9 2.2 - - + -
95J ALA 4.3 0.2 + - - -
96J VAL* 1.3 73.3 - - - +
98J VAL* 1.3 67.3 + - - +
104J PRO* 3.5 6.9 - - - +
105J ARG* 2.9 45.8 + - + -
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Residues in contact with VAL 98 (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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52J LYS* 4.5 16.8 - - + -
69J LEU* 5.3 0.5 - - - +
70J GLU* 2.9 41.1 + - + +
71J ALA* 4.4 4.7 - - - +
72J VAL* 4.7 9.4 - - + -
96J VAL* 3.4 6.4 + - + +
97J ILE* 1.3 80.8 - - - +
99J ASP* 1.3 70.7 + - - +
102J GLU* 3.1 41.3 - - + +
103J ASP 3.6 9.6 - - - +
104J PRO* 4.0 2.2 - - + -
105J ARG* 4.3 3.1 - - - +
124J VAL* 4.1 13.7 - - + -
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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