Contacts of the strand formed by residues 4208 - 4212 (chain D) 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 VAL4208 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4199D LEU* 4.9 3.8 - - + -
4200D ALA 3.2 11.7 - - - +
4201D VAL* 4.1 13.0 - - + -
4207D MET* 1.3 81.8 - - - +
4209D TRP* 1.3 70.2 + - - +
4232D LYS* 3.6 4.9 - - - +
4233D ILE* 2.9 45.7 + - + +
4236D LEU* 4.0 25.8 - - + +
4237D CYS* 3.7 7.6 - - - -
4241D ILE* 3.7 30.3 - - + -
4244D VAL* 4.3 14.6 - - + -
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Residues in contact with TRP4209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4183D LEU* 3.5 21.8 - - + +
4186D TYR* 3.8 45.1 - + + -
4188D ILE* 3.5 24.9 - - + -
4199D LEU* 3.2 5.7 - - - +
4200D ALA* 2.7 48.5 + - + +
4202D SER* 3.8 23.6 - - - -
4207D MET* 3.6 15.9 - - + -
4208D VAL* 1.3 79.3 - - - +
4210D ALA* 1.3 61.3 + - - +
4211D PHE* 4.8 2.2 - - + -
4230D PRO* 3.9 23.1 - - + -
4231D GLN 3.2 7.4 - - - +
4232D LYS* 3.5 53.6 - - + +
4233D ILE* 4.4 0.9 - - - -
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Residues in contact with ALA4210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4198D THR 3.4 4.7 - - - -
4199D LEU* 3.6 17.5 - - + -
4209D TRP* 1.3 74.6 - - - +
4211D PHE* 1.3 65.7 + - - +
4219D LEU* 3.4 39.3 - - + +
4221D LEU* 5.0 2.8 - - + +
4227D LYS* 4.9 0.5 - - - +
4229D SER 4.0 0.7 - - - +
4231D GLN* 2.9 36.0 + - - +
4233D ILE* 3.8 5.6 - - + -
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Residues in contact with PHE4211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4155D LEU* 4.4 18.6 - - + -
4157D THR* 4.8 3.1 - - + -
4164D GLY 3.8 2.2 - - - +
4165D ARG 3.3 25.4 - - - -
4166D LEU 3.7 5.6 - - - -
4167D GLY* 3.4 27.4 - - - -
4180D VAL* 5.1 0.9 - - + -
4183D LEU* 4.9 0.2 - - + -
4197D HIS* 3.4 4.0 - - - +
4198D THR* 2.8 59.5 + - + +
4200D ALA* 4.6 16.8 - - + -
4209D TRP* 4.9 2.0 - - + -
4210D ALA* 1.3 82.1 - - - +
4212D GLY* 1.3 60.8 + - - +
4219D LEU* 3.7 8.9 - - - +
4227D LYS* 3.7 12.8 - - - +
4229D SER 3.9 13.5 - - - +
4230D PRO* 3.6 28.9 - - + -
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Residues in contact with GLY4212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4163D TYR 3.1 16.6 - - - -
4164D GLY 3.7 0.6 + - - -
4165D ARG* 3.7 13.2 - - - -
4196D ASN 3.7 8.5 - - - -
4211D PHE* 1.3 75.7 - - - +
4213D ASP* 1.3 69.9 + - - -
4219D LEU* 3.5 3.1 - - - +
4226D ALA* 3.2 0.9 - - - -
4227D LYS 2.8 33.7 + - - -
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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