Contacts of the strand formed by residues 4081 - 4086 (chain C) in PDB entry 4O2W
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 VAL4081 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4042C ILE* 3.5 30.4 - - + +
4046C GLY* 3.2 26.5 + - - +
4048C VAL* 3.6 29.4 - - + -
4076C LEU* 4.1 28.7 - - + -
4079C PHE* 4.6 4.0 - - + +
4080C VAL* 1.3 72.6 - - - +
4082C THR* 1.3 60.6 + - - +
4083C GLN 3.6 20.2 - - - +
4084C LEU* 4.8 0.9 - - + -
4096C ALA* 4.2 11.2 - - + -
4097C LEU 3.5 7.0 - - - +
4098C THR* 4.3 8.5 - - + +
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Residues in contact with THR4082 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4031C GLN* 2.9 24.2 + - - -
4042C ILE* 4.3 2.0 - - - -
4080C VAL* 3.9 3.8 - - + +
4081C VAL* 1.3 76.7 - - - +
4083C GLN* 1.3 71.2 + - - +
4097C LEU* 2.9 23.7 + - - +
4098C THR 3.8 6.8 + - - -
4099C GLU* 3.8 36.6 - - + +
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Residues in contact with GLN4083 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4031C GLN* 4.4 6.1 - - - +
4042C ILE* 3.9 5.6 - - - -
4081C VAL* 3.6 4.6 - - - +
4082C THR* 1.3 90.3 + - - +
4084C LEU* 1.3 61.2 + - - +
4085C VAL* 5.8 2.8 - - + +
4096C ALA* 3.4 2.6 - - - -
4097C LEU* 2.8 42.1 + - + +
4137C VAL 2.9 28.6 + - - +
4138C GLN* 3.9 14.9 - - - +
4139C MET* 3.9 16.8 + - + +
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Residues in contact with LEU4084 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4031C GLN* 5.2 2.1 + - - +
4033C ILE* 3.5 29.9 - - + +
4040C PHE* 3.8 38.8 - - + -
4042C ILE* 3.8 19.0 - - + +
4048C VAL* 3.7 31.4 - - + -
4081C VAL* 4.8 0.4 - - + -
4083C GLN* 1.3 76.8 - - - +
4085C VAL* 1.3 83.4 + - - +
4086C THR* 4.5 0.2 - - - -
4094C SER* 4.8 1.8 - - - -
4095C MET 3.3 13.2 - - - +
4096C ALA* 4.4 7.2 - - + -
4106C TRP* 3.8 22.0 - - + -
4139C MET* 4.1 0.7 - - - -
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Residues in contact with VAL4085 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4033C ILE* 4.5 2.9 - - - -
4083C GLN* 5.8 3.1 - - + +
4084C LEU* 1.3 82.7 - - - +
4086C THR* 1.3 65.2 + - - +
4094C SER* 3.2 4.2 - - - -
4095C MET* 2.9 38.0 + - + +
4139C MET* 3.4 51.6 - - + +
4140C SER* 4.1 1.1 - - - +
4141C CYS* 3.9 28.5 - - - +
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Residues in contact with THR4086 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4033C ILE* 3.9 15.8 - - + +
4034C CYS 3.8 8.0 - - - +
4035C GLY* 3.4 29.2 - - - +
4036C GLN* 5.9 0.2 - - - +
4038C CYS* 4.5 5.0 - - - -
4040C PHE* 3.7 18.3 - - + -
4058C ARG* 5.5 1.6 - - - +
4084C LEU* 4.5 0.2 - - - -
4085C VAL* 1.3 78.4 - - - +
4087C SER* 1.3 65.5 + - - +
4088C CYS* 3.9 6.1 + - - -
4092C GLY* 6.0 0.2 - - - -
4093C HIS 3.2 8.2 + - - -
4094C SER* 2.6 22.7 + - - -
4141C CYS* 3.6 13.2 - - - +
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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