Contacts of the strand formed by residues 163 - 169 (chain A) in PDB entry 3V3K
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 GLY 163 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A CYS* 1.3 84.0 - - - +
164A HIS* 1.3 65.6 + - - -
198A PHE* 3.3 10.2 - - - -
199A MET* 2.9 29.7 + - - -
227A LEU* 3.7 17.3 - - - -
229A CYS 3.6 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLY* 1.3 76.5 - - - -
165A CYS* 1.3 61.0 + - - +
166A LEU 4.2 0.7 - - - -
198A PHE* 3.8 3.1 - - - -
199A MET* 3.4 39.0 + - + +
201A GLU* 5.6 4.4 + - - -
218A LEU* 3.4 27.5 - - + +
221A GLN* 4.2 24.4 + - + +
222A ASP 5.5 1.0 + - - -
224A HIS* 3.7 17.4 - + + -
227A LEU* 3.3 28.5 - - + +
229A CYS 4.4 2.2 + - - -
230A CYS* 3.9 4.3 - - - +
231A VAL 3.4 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS* 1.3 77.9 - - - +
166A LEU* 1.3 64.3 + - - +
167A ILE* 3.7 14.4 + - - -
193A PHE* 3.7 37.2 - - - -
198A PHE* 3.9 22.7 - - + -
199A MET 3.1 7.7 + - - -
200A VAL* 3.5 11.1 - - - +
201A GLU* 3.0 25.5 + - - +
231A VAL* 3.5 21.5 - - + -
233A VAL* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS 4.2 0.6 - - - -
165A CYS* 1.3 74.0 - - - +
167A ILE* 1.3 62.2 - - - +
168A ILE* 4.1 15.5 - - + -
201A GLU* 3.6 20.4 - - + +
203A LYS* 4.0 34.1 - - + +
214A ALA* 3.8 29.4 - - + +
215A LEU* 3.8 26.5 - - + -
218A LEU* 3.7 26.4 - - + +
231A VAL 3.3 6.5 + - - +
232A VAL* 3.5 7.0 - - + -
233A VAL 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A CYS* 4.0 16.8 - - - +
166A LEU* 1.3 78.8 - - - +
168A ILE* 1.3 68.8 + - - +
169A ASN* 3.6 2.3 + - + -
186A CYS* 4.2 23.1 - - - +
189A LEU* 4.1 15.7 - - + +
190A ARG* 4.0 20.6 - - - +
193A PHE* 4.7 0.4 - - + -
200A VAL* 4.0 21.5 - - + -
201A GLU 3.0 11.5 + - - +
202A VAL* 3.5 9.3 - - + +
203A LYS 2.9 26.4 + - - +
233A VAL* 3.4 26.5 - - + +
235A LEU* 4.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 4.3 17.5 - - + -
167A ILE* 1.3 73.6 - - - +
169A ASN* 1.3 61.2 - - - +
170A ASN* 3.4 22.9 - - - +
203A LYS* 3.5 5.2 - - + +
206A LEU* 3.6 30.1 - - + -
211A MET* 3.8 48.9 - - + +
214A ALA* 4.8 0.2 - - + -
215A LEU* 4.4 15.5 - - + -
232A VAL* 5.8 0.2 - - + -
233A VAL 3.1 10.6 + - - +
234A ILE* 3.5 15.2 - - + -
235A LEU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.6 3.6 + - + +
168A ILE* 1.3 73.6 - - - +
170A ASN* 1.3 60.4 + - - +
171A VAL* 3.4 14.3 + - - +
182A SER* 2.9 29.0 + - - +
183A ASN* 3.2 28.9 - - - +
186A CYS* 3.5 36.3 - - - +
202A VAL* 4.7 3.8 - - + +
203A LYS 3.2 11.3 + - - +
204A GLY* 3.6 5.2 - - - -
205A ASP* 3.2 18.3 + - - +
235A LEU* 3.4 12.9 - - + +
----------------------------------------------------------
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