Contacts of the strand formed by residues 238 - 245 (chain A) in PDB entry 1K63
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 LYS 238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.1 19.1 - - + +
130A TYR* 4.5 4.7 - - + -
231A LEU* 3.5 36.8 + - + -
234A SER* 2.7 32.2 + - - -
236A ILE* 2.7 26.2 + - + +
237A PRO* 1.3 75.9 - - - +
239A LEU* 1.3 61.0 + - - +
240A PHE 4.1 0.4 - - - -
260A TRP* 3.9 18.2 - - + -
261A PRO* 2.8 19.3 + - - +
262A ASN 2.9 7.4 + - - +
263A GLN* 3.4 27.7 - - + +
264A THR* 2.9 24.9 + - - -
289A PHE* 3.7 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE 2.8 8.9 + - - -
129A ALA* 3.3 3.7 - - + -
130A TYR* 3.0 30.4 + - - +
238A LYS* 1.3 73.6 - - - +
240A PHE* 1.3 64.7 + - - +
241A ILE* 3.6 23.7 + - + +
264A THR* 3.4 31.6 - - + +
265A GLU* 4.6 1.6 - - - +
266A ILE* 4.8 5.2 - - + -
285A ALA* 3.6 35.0 - - + +
286A ILE* 3.8 18.6 - - + +
289A PHE* 3.8 28.9 - - + -
292A ARG* 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 3.4 38.1 - + - +
131A MET* 5.3 1.8 - - - -
132A GLU 5.5 0.2 - - - -
239A LEU* 1.3 72.5 - - - +
241A ILE* 1.3 67.0 + - - +
242A ASN* 3.3 40.0 + - + -
249A THR* 3.7 31.6 - - + -
254A ARG* 4.0 17.3 - - + -
257A CYS* 4.5 6.1 - - + -
258A ARG* 4.2 7.4 - - + -
263A GLN* 3.6 21.2 - - - +
264A THR 2.8 11.6 + - - +
265A GLU* 3.3 33.0 - - + +
266A ILE 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 4.6 3.6 - - + -
130A TYR 2.9 13.9 + - - +
131A MET* 3.3 46.4 - - + +
132A GLU 4.5 1.7 + - - -
239A LEU* 3.9 20.2 - - + -
240A PHE* 1.3 76.3 - - - +
242A ASN* 1.3 61.0 + - - +
243A ALA* 4.1 0.5 + - - +
266A ILE* 3.6 15.0 - - + -
268A VAL* 4.2 15.5 - - + -
274A ILE* 4.1 14.2 - - + +
282A ILE* 3.8 34.8 - - + +
285A ALA* 5.3 0.2 - - + -
286A ILE* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.3 24.9 + - + -
241A ILE* 1.3 77.9 - - - +
243A ALA* 1.3 62.2 + - - +
244A GLU* 4.2 5.3 + - - +
249A THR 4.0 2.9 - - - +
254A ARG* 2.8 43.8 + - - +
258A ARG* 3.4 19.0 - - - +
265A GLU* 4.3 4.5 - - + -
266A ILE 2.8 15.6 + - - +
267A THR* 3.0 29.2 + - - +
268A VAL* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 4.6 8.2 + - + +
241A ILE 5.1 0.2 - - - +
242A ASN* 1.3 80.4 + - - +
244A GLU* 1.3 63.2 + - - +
246A GLY* 3.5 23.8 + - - -
249A THR 5.1 1.4 + - - +
254A ARG* 3.0 24.1 + - - -
267A THR* 4.2 0.7 - - - -
268A VAL 3.2 8.1 - - - +
270A GLY 3.8 2.7 - - - +
271A ALA 4.3 0.4 - - - +
274A ILE* 3.7 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 4.8 0.5 - - - +
242A ASN* 4.2 4.0 + - - -
243A ALA* 1.3 75.0 - - - +
245A PRO* 1.3 73.7 - - + +
254A ARG* 3.5 25.9 + - - -
258A ARG* 5.7 0.3 + - - -
267A THR* 3.5 24.2 - - + -
268A VAL 3.0 8.1 + - - +
269A ALA* 3.3 10.1 - - - +
270A GLY 2.9 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 4.6 16.4 - - + -
243A ALA 3.6 2.6 - - - +
244A GLU* 1.3 94.9 - - - +
246A GLY* 1.3 70.3 + - - +
250A THR* 3.6 12.8 - - - +
254A ARG* 4.6 2.8 + - - -
270A GLY 3.1 13.9 - - - +
271A ALA* 4.5 8.3 - - + +
----------------------------------------------------------
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