Contacts of the strand formed by residues 4136 - 4141 (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 VAL4136 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4097C LEU* 3.4 35.5 - - + +
4101C GLY* 3.2 17.0 + - - +
4103C VAL* 3.5 23.3 - - + -
4131C LEU* 4.1 19.5 - - + -
4134C GLU* 4.6 6.3 - - + +
4135C GLU* 1.3 75.9 - - - +
4137C VAL* 1.3 66.2 + - - +
4138C GLN 3.7 16.6 - - - +
4139C MET* 3.9 6.1 - - + -
4148C VAL* 3.8 18.4 - - + -
4149C VAL 3.6 11.4 - - - +
4150C THR* 4.2 7.6 - - + +
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Residues in contact with VAL4137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4083C GLN* 2.9 25.3 + - - -
4097C LEU* 3.9 9.6 - - - -
4135C GLU* 4.5 8.7 - - - +
4136C VAL* 1.3 77.8 - - - +
4138C GLN* 1.3 66.4 + - + +
4149C VAL* 2.8 23.1 + - + +
4150C THR 3.5 16.8 - - - +
4151C SER* 4.0 24.9 - - - +
4189C GLY* 5.2 3.6 - - - +
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Residues in contact with GLN4138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4083C GLN* 3.9 10.3 - - - +
4136C VAL* 3.7 2.4 - - - +
4137C VAL* 1.3 81.5 - - + +
4139C MET* 1.3 86.4 + - - +
4140C SER* 4.8 0.4 - - - -
4148C VAL* 3.4 2.8 - - - -
4149C VAL* 2.9 36.1 + - + +
4189C GLY 4.3 11.9 - - - +
4190C GLN* 3.4 30.1 - - + +
4191C VAL* 2.8 49.5 + - - +
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Residues in contact with MET4139 (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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4083C GLN* 3.8 35.5 + - + +
4085C VAL* 3.4 33.5 - - + +
4095C MET* 3.6 41.1 - - + +
4096C ALA 4.1 1.6 - - - -
4097C LEU* 3.9 25.8 - - + +
4103C VAL* 4.1 10.5 - - - -
4136C VAL* 3.9 15.3 - - + -
4138C GLN* 1.3 101.5 + - - +
4140C SER* 1.3 61.8 + - - +
4147C ALA 3.4 8.3 - - - +
4148C VAL* 3.9 6.5 - - + +
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Residues in contact with SER4140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4085C VAL* 4.1 4.3 - - - -
4095C MET* 3.4 9.3 - - - +
4139C MET* 1.3 77.9 - - - +
4141C CYS* 1.3 61.3 + - - +
4146C SER* 3.4 1.4 - - - -
4147C ALA 2.8 35.8 + - - +
4191C VAL* 3.6 23.8 - - - -
4192C ALA* 3.6 2.6 - - - -
4193C CYS* 3.0 38.2 + - - +
4402C UNX 4.1 7.6 + - - -
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Residues in contact with CYS4141 (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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4085C VAL* 3.8 29.1 - - - +
4086C THR* 3.6 24.0 - - - +
4087C SER* 3.6 10.2 - - - +
4088C CYS 5.0 0.7 + - - -
4093C HIS* 3.7 38.4 - - + -
4094C SER* 3.9 6.7 - - - -
4095C MET* 4.0 11.7 - - - -
4140C SER* 1.3 74.4 + - - +
4142C GLY* 1.3 61.7 + - - +
4145C HIS 3.9 3.4 - - - -
4193C CYS* 3.9 10.1 - - - +
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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
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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