Contacts of the strand formed by residues 260 - 264 (chain K) in PDB entry 5LS6
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 LEU 260 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252K MET* 4.1 7.4 - - + -
253K SER 3.3 5.8 - - - +
254K CYS* 3.8 16.6 - - + -
258K HIS 5.3 1.8 - - - +
259K SER* 1.3 74.5 - - - +
261K LYS* 1.3 65.9 + - - +
299K PHE* 5.0 0.6 - - - -
300K SER* 3.5 1.7 + - - -
301K THR* 3.1 32.9 + - + +
304K ILE* 3.8 14.6 - - + -
305K HIS* 3.7 17.0 - - + -
309K VAL* 4.2 4.0 - - + -
312K VAL* 3.7 19.5 - - + -
319K ILE* 4.5 0.2 - - + -
321K SER* 3.6 35.4 - - - +
331K TRP* 3.4 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233K GLU* 2.9 42.3 + - - +
234K GLY 3.9 15.3 + - - -
235K HIS* 3.9 21.3 - - + +
236K ARG* 6.2 0.7 - - - -
252K MET* 3.1 8.8 - - - +
253K SER 2.8 33.3 + - - -
257K ASP* 4.4 2.0 - - - -
259K SER* 3.6 21.0 - - - +
260K LEU* 1.3 80.9 - - - +
262K LEU* 1.3 59.7 + - - +
263K TRP* 3.6 26.3 - - + +
297K PRO* 4.1 4.8 - - + +
299K PHE 3.6 5.4 - - - +
300K SER* 3.2 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K LYS* 3.8 17.7 - - + -
251K ILE 3.4 10.8 - - - +
252K MET* 3.6 12.3 - - + -
261K LYS* 1.3 73.9 - - - +
263K TRP* 1.3 57.7 + - - +
264K ARG* 4.3 22.4 - - + +
297K PRO* 3.1 9.4 - - - +
298K ASP* 2.8 36.3 + - + +
299K PHE* 3.1 38.1 + - + +
314K TRP* 3.5 36.3 - - + -
333K PRO* 5.3 0.2 - - + -
340K ILE* 4.7 16.8 - - + -
343K ILE* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 263 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215K LEU* 4.3 4.3 - - + +
229K PHE* 3.4 70.2 - + + -
233K GLU 4.3 3.8 - - - -
234K GLY* 3.8 20.2 - - - -
235K HIS* 4.2 11.7 - + - -
250K LYS* 4.6 1.1 - - - -
251K ILE* 2.8 53.2 + - + +
253K SER* 3.0 22.5 + - - -
261K LYS* 3.6 33.8 + - + +
262K LEU* 1.3 77.2 - - - +
264K ARG* 1.3 64.7 + - - +
265K ILE* 3.6 3.1 + - - +
294K ILE* 4.0 19.5 - - + -
296K PHE 4.2 2.5 - - - -
297K PRO* 3.9 23.1 - - + -
298K ASP* 4.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229K PHE* 4.9 2.1 - - - -
249K GLU 3.9 4.7 - - - +
250K LYS* 4.2 17.9 - - + +
262K LEU* 4.3 16.2 - - + +
263K TRP* 1.3 75.2 - - - +
265K ILE* 1.3 64.8 + - - +
266K ASN* 3.7 21.9 - - - +
267K SER* 4.2 14.0 + - - -
270K MET* 4.1 9.4 - - - +
298K ASP* 3.3 44.3 + - + +
340K ILE 3.4 26.1 + - - -
341K ASP* 3.5 28.0 + - - +
343K ILE* 2.9 35.8 + - - +
----------------------------------------------------------
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