Contacts of the strand formed by residues 204 - 207 (chain B) in PDB entry 1KWV
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 TRP 204 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO* 4.1 8.7 - - + -
144B ASN* 2.8 22.1 + - - -
157B LEU* 3.6 22.3 - - + +
159B ILE* 3.7 28.0 - - + -
176B LEU* 4.0 8.7 - - + -
178B TYR* 3.5 42.6 - + - -
179B SER* 3.6 16.2 - - - -
180B ASN* 2.8 33.4 + - - +
181B TRP* 3.6 28.2 - + + -
182B LYS* 2.9 30.4 + - - +
185B GLU* 4.0 0.9 - - - +
196B VAL* 4.0 18.4 - - + -
197B THR 3.4 5.4 - - - +
198B ILE* 4.3 4.5 - - + -
199B VAL* 4.8 1.1 - - - -
202B GLY 3.4 7.9 - - - -
203B LEU* 1.3 81.7 - - - +
205B ASN* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B TRP* 4.0 5.4 - - - -
182B LYS* 5.3 4.7 - - + -
185B GLU* 2.7 26.3 - - + +
197B THR* 2.9 43.8 + - - +
199B VAL* 4.5 13.7 - - + +
204B TRP* 1.3 78.5 - - - +
206B ASP* 1.3 67.4 + - - +
207B ILE* 3.6 10.5 + - - +
601B NAG 3.2 22.3 + - - -
603B CA 2.6 23.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 5.4 0.5 - - - +
168B PHE* 4.2 8.3 - - + -
181B TRP* 3.6 10.8 - - + -
185B GLU* 2.7 10.4 + - - +
186B PRO* 3.3 18.7 - - + +
187B ASN 3.1 9.2 + - - -
188B ASP* 2.6 32.1 + - - +
193B GLU* 2.6 21.4 - - - +
195B CYS 3.0 14.4 - - - +
205B ASN* 1.3 77.8 - - - +
207B ILE* 1.3 56.4 + - - +
601B NAG 3.2 1.7 + - - -
603B CA 2.3 50.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PHE* 3.8 11.2 - - + -
193B GLU* 3.5 25.6 - - - +
194B ASP 3.5 2.3 + - - -
195B CYS* 2.8 32.1 + - - +
197B THR* 3.5 31.0 - - + +
205B ASN* 4.2 10.3 - - - +
206B ASP* 1.3 74.5 - - - +
208B SER* 1.3 83.0 + - - +
211B ALA* 4.1 7.9 - - + -
213B HIS* 4.0 18.6 - - + +
601B NAG 3.7 26.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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