Contacts of the strand formed by residues 204 - 207 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C PRO* 3.4 25.4 - - + -
144C ASN* 2.9 19.8 + - - -
157C LEU* 3.6 19.3 - - + +
159C ILE* 3.5 27.4 - - + -
176C LEU* 3.7 15.0 - - + -
178C TYR* 3.4 22.7 - + - -
179C SER* 3.4 22.2 - - - -
180C ASN* 2.7 30.1 + - - +
181C TRP* 3.6 35.1 - + + -
182C LYS* 2.9 28.4 + - - +
185C GLU* 3.8 1.2 - - - +
196C VAL* 4.1 9.6 - - + -
197C THR 3.4 6.5 - - - +
198C ILE* 4.3 5.8 - - + +
199C VAL* 5.3 0.9 - - - -
202C GLY 3.5 7.6 - - - -
203C LEU* 1.3 82.9 - - - +
205C ASN* 1.3 61.1 - - - +
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Residues in contact with ASN 205 (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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181C TRP* 4.2 3.4 - - - -
182C LYS* 5.2 7.6 - - + -
185C GLU* 2.8 27.1 - - + +
197C THR* 3.0 40.5 + - - +
199C VAL* 4.4 13.7 - - + +
204C TRP* 1.3 75.1 - - - +
206C ASP* 1.3 67.0 + - - +
207C ILE* 4.1 12.7 - - - +
701C NAG 3.1 26.3 + - - -
703C CA 2.5 23.6 - - - -
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Residues in contact with ASP 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C PHE* 4.0 12.5 - - + -
181C TRP* 3.9 8.0 - - + -
185C GLU* 2.9 9.6 + - - +
186C PRO* 3.5 18.2 - - + +
187C ASN* 3.1 10.4 + - - +
188C ASP* 2.7 30.3 + - - +
193C GLU* 2.8 16.0 - - + +
195C CYS 3.1 14.6 - - - +
196C VAL* 4.2 1.8 - - - +
205C ASN* 1.3 76.9 - - - +
207C ILE* 1.3 57.9 + - - +
701C NAG 3.2 2.8 + - - -
703C CA 2.2 53.4 - - - -
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Residues in contact with ILE 207 (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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156C PHE* 3.9 10.3 - - + -
193C GLU* 3.6 16.5 - - - +
194C ASP 3.4 3.1 + - - -
195C CYS 2.8 32.5 + - - +
197C THR* 3.5 35.2 - - + +
205C ASN* 4.1 7.2 - - - +
206C ASP* 1.3 74.6 - - - +
208C SER* 1.3 81.5 + - - +
209C CYS 3.3 0.2 + - - -
211C ALA* 4.4 6.1 - - + -
213C HIS* 4.0 18.2 - - + +
701C NAG 3.5 45.5 - - + +
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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