Contacts of the strand formed by residues 76 - 79 (chain J) in PDB entry 3STJ
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 TYR 76 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69J ILE* 3.5 3.5 - - - -
70J ILE* 2.7 52.3 + - + +
71J ASN* 2.9 29.8 + - + +
74J LYS* 3.6 37.2 + - + +
75J GLY* 1.3 76.1 - - - +
77J VAL* 1.4 55.9 + - - +
105J ILE* 4.6 8.7 - - + -
115J LEU* 4.3 13.2 - - + -
116J LEU 3.5 9.0 - - - -
117J GLN* 3.6 29.3 + - + -
232J ILE* 3.8 40.0 + - + +
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Residues in contact with VAL 77 (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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27J VAL* 4.0 11.0 - - + -
29J VAL* 4.7 0.9 - - + -
67J GLY* 4.0 9.0 - - - -
68J VAL 3.3 15.0 - - - +
69J ILE* 3.9 16.2 - - + -
75J GLY 4.0 2.2 - - - +
76J TYR* 1.4 75.7 - - - +
78J LEU* 1.3 73.2 + - - +
79J THR* 3.9 1.1 + - - -
92J ILE* 4.5 9.0 - - + -
115J LEU* 3.5 5.5 - - - +
116J LEU* 2.8 61.4 + - + +
118J ILE* 3.6 33.7 - - + -
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Residues in contact with LEU 78 (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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67J GLY* 3.2 5.5 - - - -
68J VAL* 2.8 37.7 + - + +
70J ILE* 3.6 34.9 - - + +
76J TYR 4.2 0.8 + - - -
77J VAL* 1.3 71.5 - - - +
79J THR* 1.3 61.8 + - - +
113J ILE* 3.8 26.5 - - + -
114J ALA 3.6 15.7 - - - +
115J LEU* 4.4 11.8 - - + +
188J GLY 3.6 3.8 - - - +
198J LEU* 4.7 7.4 - - + -
201J ILE* 4.2 20.0 - - + -
224J ALA* 3.9 32.8 - - + +
225J ARG 4.8 0.2 - - - +
228J ALA* 4.6 3.6 - - + -
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Residues in contact with THR 79 (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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29J VAL* 4.4 2.4 - - - +
66J SER 3.0 21.2 + - - -
67J GLY* 4.4 2.7 - - - -
78J LEU* 1.3 76.1 - - - +
80J ASN* 1.4 72.1 + - - +
83J VAL* 3.8 13.0 - - - +
84J ILE* 3.9 7.4 - - + -
112J ASP 4.1 0.2 - - - +
113J ILE* 3.7 10.9 - - - +
114J ALA* 3.0 41.0 + - + +
116J LEU* 3.8 34.1 - - + -
188J GLY* 4.0 11.0 - - - -
201J ILE* 4.6 3.7 - - - +
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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