Contacts of the strand formed by residues 73 - 76 (chain J) in PDB entry 2CHT
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 73 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45J MET* 3.1 45.1 - - + +
47J LEU* 4.4 3.6 - - + -
59J ALA* 4.2 13.9 - - + +
62J VAL* 3.9 21.5 - - + -
71J VAL* 3.4 9.8 + - + +
72J PRO* 1.3 73.7 - - - +
74J THR* 1.3 64.2 + - - +
7K ARG* 3.0 30.5 + - - +
92K MET* 4.7 0.4 - - - -
210K TSA 3.4 25.2 - - + +
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Residues in contact with THR 74 (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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45J MET 3.2 2.4 + - - -
46J LEU* 3.3 30.9 - - + +
47J LEU* 3.0 22.7 + - - +
73J VAL* 1.3 80.1 - - - +
75J CYS* 1.3 67.2 + - - +
7K ARG* 3.5 21.6 + - - -
48K SER* 4.8 1.5 + - - +
76K MET* 4.3 13.7 - - + -
78K GLU* 3.8 6.1 + - - -
90K ARG* 4.0 6.2 - - + +
92K MET* 3.9 21.1 - - + -
210K TSA 3.4 17.1 + - - -
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Residues in contact with CYS 75 (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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47J LEU* 3.0 13.9 - - - +
57J PHE* 3.9 13.9 - - + -
58J PRO* 4.0 6.5 - - - -
59J ALA* 3.3 40.2 - - - -
74J THR* 1.3 79.9 + - - +
76J MET* 1.3 65.6 + - - +
48K SER* 4.7 1.9 + - - -
76K MET* 4.2 8.3 - - - +
78K GLU* 3.3 33.7 - - - +
79K MET* 3.9 14.6 - - - -
210K TSA 3.2 12.4 + - - -
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Residues in contact with MET 76 (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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46J LEU* 3.7 35.2 - - + -
47J LEU* 2.8 14.3 + - - +
48J SER* 3.3 23.5 - - - +
49J ALA 3.3 19.8 + - - -
74J THR 4.7 0.2 - - - +
75J CYS* 1.3 79.8 - - - +
77J GLN* 1.3 64.8 + - - +
90J ARG 5.3 0.9 - - - +
91J VAL 6.5 0.2 - - - -
92J MET* 5.6 0.4 - - + -
76K MET* 4.1 20.6 - - + +
77K GLN 3.6 11.2 - - - +
78K GLU* 4.5 1.1 - - - +
79K MET* 3.7 15.2 - - - +
46L LEU* 5.0 0.2 - - + -
74L THR* 3.9 24.0 - - + -
75L CYS 4.7 2.0 - - - +
76L MET* 3.5 35.2 - - + +
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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