Contacts of the strand formed by residues 3999 - 4004 (chain B) 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 VAL3999 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3997B CYS* 3.7 15.5 + - - -
3998B ASP* 1.3 77.2 - - - +
4000B TYR* 1.3 66.7 + - - +
4001B LEU* 3.9 25.4 - - + -
4022B ALA* 3.5 5.2 - - - +
4023B ALA* 2.9 31.8 + - + +
4026B PHE* 3.4 53.2 - - + +
4027B SER* 5.5 0.8 + - - -
4029B ALA* 4.4 0.2 - - + -
4032B VAL* 4.2 17.0 - - + -
4356B ALA* 5.2 0.7 - - + -
4357B ALA 3.6 6.5 - - - +
4358B TRP* 3.7 8.5 - - + -
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Residues in contact with TYR4000 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3998B ASP* 3.9 35.6 + - + +
3999B VAL* 1.3 74.3 - - - +
4001B LEU* 1.3 64.4 + - - +
4002B TRP* 3.5 4.1 - - + -
4020B PRO* 4.0 23.3 - - + -
4021B ALA 3.2 7.0 - - - +
4022B ALA* 3.9 30.5 - - + -
4339B GLY 5.6 0.7 - - - -
4340B LEU* 4.0 19.7 - - + -
4343B LYS* 3.5 52.7 + - + +
4345B VAL* 5.3 2.0 - - + -
4356B ALA* 3.3 3.8 - - - +
4357B ALA 2.9 43.8 + - - +
4358B TRP* 5.2 0.4 - - - -
4359B THR* 4.9 2.0 - - + -
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Residues in contact with LEU4001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3999B VAL* 3.9 11.7 - - + -
4000B TYR* 1.3 76.1 - - - +
4002B TRP* 1.3 65.3 + - - +
4009B GLN 4.6 0.9 - - - +
4010B LEU* 3.5 52.5 - - + +
4013B ALA* 4.4 4.7 - - + +
4017B VAL* 3.7 5.6 - - - +
4021B ALA* 2.8 31.0 + - - +
4023B ALA* 3.7 22.9 - - + -
4026B PHE* 3.9 23.8 - - + -
4032B VAL* 4.5 2.2 - - + -
4034B CYS* 5.2 1.1 - - - -
4039B THR* 5.0 4.9 - - + -
4354B HIS* 5.8 0.2 - - + -
4355B SER 3.4 5.8 - - - +
4356B ALA* 3.6 27.6 - - + -
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Residues in contact with TRP4002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4000B TYR* 3.5 19.1 - - + -
4001B LEU* 1.3 83.7 - - - +
4003B GLY* 1.3 60.6 + - - +
4010B LEU* 3.9 6.5 - - - +
4017B VAL* 3.6 22.9 - - + +
4019B VAL 3.9 9.0 - - - +
4020B PRO* 3.5 26.0 - - + -
4304B LEU* 4.4 16.4 - - + +
4312B VAL* 5.4 3.1 - - + -
4321B GLY 3.4 7.2 - - - -
4322B GLN 2.9 24.1 + - - -
4323B LEU 3.5 4.2 - - - -
4324B GLY* 3.2 33.8 - - - +
4337B VAL* 5.2 2.0 - - + -
4340B LEU* 3.7 22.9 - - + -
4348B ILE* 5.8 0.4 - - + -
4354B HIS* 3.1 7.6 - - - +
4355B SER* 2.9 47.9 + - - +
4356B ALA 3.9 6.1 - - - -
4357B ALA* 3.6 21.8 - - + -
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Residues in contact with GLY4003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4002B TRP* 1.3 75.6 - - - +
4004B ALA* 1.3 64.6 + - - -
4010B LEU* 3.6 5.1 - - - +
4016B ASN* 3.7 1.6 - - - -
4017B VAL 2.8 35.4 + - - -
4320B GLU 3.4 19.1 - - - -
4321B GLY 3.8 10.7 + - - -
4322B GLN* 3.9 2.0 - - - -
4353B CYS 3.6 8.1 - - - -
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Residues in contact with ALA4004 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4003B GLY* 1.3 73.4 - - - -
4005B GLY* 1.3 58.4 + - - +
4006B ARG* 4.2 1.6 - - - +
4009B GLN* 3.1 22.9 + - - +
4010B LEU* 3.6 3.8 - - - +
4015B ARG 4.3 1.3 - - - -
4016B ASN* 4.9 3.4 - - - -
4320B GLU* 3.6 26.2 + - + +
4353B CYS* 2.8 36.2 + - - +
4354B HIS* 3.5 9.4 - - - +
4403B UNX 3.8 16.8 - - - +
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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