Contacts of the strand formed by residues 79 - 83 (chain G) in PDB entry 2ZJP
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 PHE 79 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G GLN* 3.7 22.9 - - + -
40G ASN 2.9 12.6 + - - +
41G TRP* 3.2 58.1 - + + +
42G VAL* 3.6 18.6 + - - +
78G ASP* 1.3 76.5 - - - +
80G VAL* 1.3 61.2 - - - +
81G VAL* 4.2 1.1 - - - -
146G THR* 4.9 1.6 - - + -
147G ARG* 3.3 65.5 - - + +
149G LYS* 5.1 1.8 - - - -
8X A 3.6 44.0 - - - -
9X U 6.1 0.2 - - - -
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Residues in contact with VAL 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G VAL* 4.4 5.4 - - + +
44G VAL* 3.8 28.0 - - + +
58G ILE* 4.1 21.5 - - + +
61G ARG* 4.3 21.5 - - + +
62G ILE* 3.2 35.2 - - + -
78G ASP 3.5 7.0 - - - +
79G PHE* 1.3 79.2 - - - +
81G VAL* 1.3 61.3 + - - +
147G ARG 3.0 12.2 + - - +
148G LEU* 3.5 4.9 - - - +
149G LYS 2.8 30.8 + - - +
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Residues in contact with VAL 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G TRP* 3.6 34.1 - - + +
42G VAL 3.7 11.7 + - - +
43G VAL* 4.3 10.1 - - + -
44G VAL* 2.9 29.3 + - - +
79G PHE* 5.8 0.2 - - + -
80G VAL* 1.3 78.5 - - - +
82G VAL* 1.3 69.0 + - - +
83G ILE* 4.3 0.7 - - + +
149G LYS* 2.9 23.6 - - + +
151G TYR* 4.0 19.5 - - + +
161G GLN* 3.8 34.1 - - + +
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Residues in contact with VAL 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G VAL* 4.1 7.4 - - + +
46G ALA* 4.2 15.9 - - + -
54G LEU* 4.6 2.7 - - + -
58G ILE* 3.8 27.4 - - + -
80G VAL 4.2 0.7 - - - +
81G VAL* 1.3 79.6 - - - +
83G ILE* 1.3 68.9 + - - +
85G ALA* 4.7 2.7 - - + -
127G ILE* 4.9 5.4 - - + -
148G LEU* 3.7 15.5 - - + -
149G LYS 2.6 20.3 + - - +
150G VAL* 3.1 29.7 - - + +
151G TYR* 2.8 29.3 + - - +
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Residues in contact with ILE 83 (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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43G VAL* 4.3 7.2 - - + -
44G VAL 3.4 18.0 + - - +
45G ASP* 3.5 23.8 - - - +
46G ALA* 3.7 11.1 + - - +
81G VAL* 5.1 0.9 - - + -
82G VAL* 1.3 75.2 - - - +
84G ASN* 1.3 71.1 + - - +
85G ALA* 2.7 21.3 + - - +
151G TYR* 3.4 6.3 - - + -
153G GLY 3.6 5.8 - - - +
154G GLU* 4.1 13.5 - - + +
157G PRO* 4.1 21.1 - - + -
158G HIS* 4.2 20.9 - - + +
161G GLN* 4.2 7.6 - - - +
167G LYS* 3.8 23.1 - - - +
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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
------------------------------------------------------------
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