Contacts of the strand formed by residues 262 - 270 (chain A) in PDB entry 1WKM
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 ILE 262 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A TYR* 3.7 29.4 - - + -
207A MET 3.2 11.4 - - - +
208A TYR* 4.0 14.4 - - - +
209A VAL* 3.6 6.7 - - - -
223A LEU* 4.2 12.1 - - + -
226A ILE* 4.2 22.9 - - + -
235A PHE* 4.8 0.4 - - + -
253A LEU* 3.9 31.6 - - + +
256A LEU* 3.8 9.0 - - + -
257A GLU* 3.6 36.5 - - + +
260A GLY* 3.4 2.3 - - - -
261A ALA* 1.3 87.9 + - + +
263A TYR* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A TYR* 3.0 12.9 - - - +
207A MET* 2.7 59.3 + - + +
209A VAL* 3.5 30.8 - - + +
210A ARG* 5.9 0.9 + - - -
257A GLU* 5.0 0.2 - - - -
262A ILE* 1.3 75.6 - - - +
264A GLY* 1.3 61.5 + - - +
265A TYR* 3.7 22.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 3.9 3.4 - - - -
206A TYR* 3.6 16.6 - - - -
257A GLU* 3.4 26.5 + - - +
262A ILE 4.1 1.0 + - - -
263A TYR* 1.3 75.2 - - - +
265A TYR* 1.3 62.6 + - - -
266A PRO* 2.9 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS* 4.0 38.1 - + + +
161A HIS* 5.3 11.4 + + - -
203A THR* 3.7 3.5 - - - +
204A LEU 4.3 3.1 + - - -
205A ILE* 2.7 55.6 + - + +
206A TYR* 4.1 3.1 - - - -
207A MET* 3.2 49.6 - - + +
234A PRO* 4.6 8.7 - - + +
263A TYR* 3.7 21.2 - + + -
264A GLY* 1.3 75.8 - - - -
266A PRO* 1.3 68.0 - - + +
267A VAL 3.6 0.9 + - - -
1298A MET* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS* 3.9 6.1 + - - +
199A GLU* 3.3 42.0 - - + +
200A VAL 3.8 14.1 - - - +
201A PRO* 5.3 0.2 - - + -
202A PRO 3.8 7.2 - - - +
203A THR* 4.0 15.7 - - - +
257A GLU* 5.8 0.4 - - - +
264A GLY 2.9 16.2 - - - +
265A TYR* 1.3 90.4 - - - +
267A VAL* 1.3 66.2 - - - +
268A LEU* 3.5 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.6 34.5 - - + -
61A ALA 4.3 1.6 - - - +
62A HIS 3.8 16.4 - - - +
63A TYR* 3.8 22.2 - - + -
199A GLU* 3.7 1.6 - - - -
200A VAL* 2.9 52.1 + - + +
201A PRO 5.0 0.7 - - - +
202A PRO* 3.3 32.2 + - + +
204A LEU* 4.4 6.7 - - + +
265A TYR 3.6 0.8 + - - -
266A PRO* 1.3 71.8 - - - +
268A LEU* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.5 6.6 - - - +
60A ALA* 2.8 28.6 + - + -
61A ALA* 3.0 22.5 + - + +
62A HIS* 3.8 27.4 - - + +
149A ASN 5.7 0.4 - - - +
150A LEU* 4.2 18.8 - - + -
197A VAL* 3.5 29.2 - - + -
198A ILE 3.4 8.3 - - - +
199A GLU* 3.7 28.0 - - + +
266A PRO 3.6 16.8 - - - +
267A VAL* 1.3 74.7 - - - +
269A LYS* 1.3 56.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.5 34.1 - - + +
59A ILE* 4.3 11.0 - - + +
197A VAL* 3.6 4.0 - - - -
198A ILE* 2.7 47.7 + - - +
200A VAL* 4.1 32.8 - - + +
267A VAL 4.0 0.4 + - - -
268A LEU* 1.3 74.6 - - - +
270A GLU* 1.3 71.2 + - - +
271A ILE* 3.4 1.0 + - - +
273A ASN* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU 2.9 14.7 + - - +
60A ALA 4.8 0.2 - - - +
147A ILE* 5.1 2.7 - - + -
191A THR* 3.4 22.9 - - + +
193A GLY* 3.5 5.2 - - - -
194A ALA* 3.0 9.8 + - - -
195A GLY 2.8 29.5 + - - -
196A GLN 3.1 18.1 + - - +
197A VAL* 4.0 4.9 - - - +
269A LYS* 1.3 84.7 + - - +
271A ILE* 1.3 67.6 + - - +
272A ARG* 2.5 39.3 + - - +
273A ASN* 3.0 21.0 + - - +
274A GLY 3.3 23.3 + - - +
276A VAL* 3.8 9.9 - - + -
----------------------------------------------------------
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