Contacts of the strand formed by residues 238 - 241 (chain A) in PDB entry 1KEV
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 ARG 238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA* 2.9 35.0 + - + +
163A ASP* 3.2 20.6 + - - +
164A ILE* 4.6 8.5 - - + +
165A GLN* 3.8 18.8 + - - +
168A SER* 4.7 10.6 + - - -
169A SER 3.1 9.1 + - - +
170A VAL* 3.5 21.0 - - + -
171A VAL 3.1 21.1 + - - -
236A VAL* 3.6 5.0 - - - +
237A ASP* 1.3 106.6 + - + +
239A VAL* 1.3 71.0 + - - +
240A ILE* 5.8 0.2 - - + -
256A VAL* 4.6 0.4 - - - -
259A GLY 4.8 3.0 + - - -
260A GLY* 4.1 11.1 - - - -
261A ILE* 3.5 33.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA* 5.6 0.2 - - - +
171A VAL* 3.3 12.1 - - + +
173A ILE* 4.0 20.9 - - + -
236A VAL* 3.9 17.3 - - + -
238A ARG* 1.3 80.9 - - - +
240A ILE* 1.3 68.2 + - - +
241A MET* 4.7 2.2 - - + -
252A ALA* 3.7 28.5 - - + +
255A MET* 4.2 14.4 - - + -
256A VAL* 4.1 18.4 - - + -
261A ILE 3.2 6.5 + - - +
262A ILE* 3.4 8.6 - - + +
263A SER* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLY* 3.9 30.5 - - - +
159A ALA* 4.1 9.6 - - + +
162A ALA* 4.5 8.1 - - + -
164A ILE* 5.1 0.7 - - + -
170A VAL* 4.4 15.7 - - + -
171A VAL 2.9 12.0 + - - +
172A VAL* 3.5 19.0 - - + +
173A ILE* 2.9 26.7 + - - +
182A GLY* 4.3 19.5 - - - +
186A ALA* 4.9 4.0 - - + -
238A ARG* 5.8 0.2 - - + -
239A VAL* 1.3 77.2 - - - +
241A MET* 1.3 65.7 + - - +
242A ALA* 3.5 5.9 + - + +
263A SER* 3.3 12.3 - - - +
265A ILE* 4.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 4.2 16.8 - - + -
239A VAL* 4.1 1.1 + - + -
240A ILE* 1.3 71.9 - - - +
242A ALA* 1.3 59.2 + - - +
243A GLY 3.8 2.7 - - - +
246A SER 5.5 0.2 - - - +
248A THR* 3.7 23.1 - - - +
249A LEU* 4.0 36.8 - - + +
252A ALA* 4.4 9.2 - - + -
262A ILE* 3.8 28.3 - - + -
263A SER 2.8 11.6 + - - +
264A ASN* 3.5 27.4 - - + +
265A ILE* 3.0 26.5 + - - +
266A ASN* 3.2 9.1 + - + +
268A HIS* 4.0 14.8 - - + +
274A LEU* 5.0 2.5 - - + -
281B TRP* 6.2 1.3 - - + -
----------------------------------------------------------
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