Contacts of the strand formed by residues 4227 - 4232 (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 LYS4227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4163B TYR 3.8 3.7 - - - +
4164B GLY 3.5 2.8 - - - +
4211B PHE* 3.5 7.9 - - - +
4212B GLY* 2.7 35.8 + - - -
4219B LEU* 3.9 6.7 - - + -
4221B LEU* 3.8 24.0 - - + -
4223B ASN* 5.2 2.6 - - - +
4225B THR* 3.7 36.6 + - - +
4226B ALA* 1.3 77.2 + - - +
4228B SER* 1.3 59.5 + - - +
4229B SER 3.8 15.0 - - - +
4231B GLN* 3.7 31.0 + - + +
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Residues in contact with SER4228 (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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4163B TYR 5.4 0.4 - - - -
4164B GLY* 3.7 15.8 - - - +
4167B GLY* 3.2 13.5 - - - -
4168B LEU 3.2 1.2 + - - -
4169B GLY* 3.0 40.4 + - - -
4170B ASN* 3.8 22.0 - - - -
4171B THR* 5.1 4.0 - - - -
4226B ALA 4.4 0.2 + - - -
4227B LYS* 1.3 72.7 - - - +
4229B SER* 1.3 61.0 + - - +
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Residues in contact with SER4229 (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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4167B GLY 4.4 1.1 + - - -
4169B GLY* 3.9 14.6 + - - -
4182B ALA* 5.1 6.2 - - - +
4211B PHE* 3.7 10.6 - - - +
4227B LYS* 3.8 2.8 - - - +
4228B SER* 1.3 81.7 + - - +
4230B PRO* 1.3 77.6 - - - +
4231B GLN* 3.3 26.3 + - - +
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Residues in contact with PRO4230 (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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4167B GLY* 3.7 14.6 - - - +
4180B VAL* 4.1 17.9 - - + -
4182B ALA* 3.8 15.5 - - + -
4183B LEU* 4.1 15.5 - - + -
4209B TRP* 3.9 25.6 - - + -
4210B ALA 3.6 7.6 - - - +
4211B PHE* 3.6 25.3 - - + -
4229B SER* 1.3 89.8 - - - +
4231B GLN* 1.3 63.9 + - - +
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Residues in contact with GLN4231 (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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4209B TRP* 3.2 3.9 - - - -
4210B ALA* 2.9 31.3 + - - +
4221B LEU* 3.7 24.2 - - + +
4227B LYS* 3.7 39.3 + - + +
4229B SER* 3.3 30.2 + - - +
4230B PRO* 1.3 77.4 + - - +
4232B LYS* 1.3 65.8 + - - +
4233B ILE* 3.4 2.8 + - - +
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Residues in contact with LYS4232 (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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4207B MET* 6.4 0.2 - - + -
4208B VAL 3.5 9.0 - - - +
4209B TRP* 3.6 17.1 - - + +
4221B LEU* 3.3 13.2 - - - +
4231B GLN* 1.3 74.3 - - - +
4233B ILE* 1.3 59.9 + - - +
4234B ASP* 3.6 20.8 + - - +
4237B CYS* 4.4 11.4 - - - -
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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