Contacts of the strand formed by residues 251 - 256 (chain A) in PDB entry 6BW4
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 251 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 3.8 9.3 - - + -
227A THR* 6.1 0.4 - - - -
246A VAL* 3.3 7.4 - - - +
247A ALA 3.3 23.3 + - - +
249A ASP* 3.1 34.4 + - - +
250A GLN* 1.3 80.7 - - - +
252A LEU* 1.3 60.2 + - - +
253A MET* 4.0 16.4 - - + -
268A SER* 3.3 22.2 - - - +
269A VAL 3.1 9.9 - - - +
270A ASP* 2.6 28.2 + - - +
271A ALA* 4.6 2.0 - - - -
276A VAL* 4.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER 3.4 14.6 - - - +
246A VAL* 3.7 17.3 - - + -
251A LYS* 1.3 71.8 - - - +
253A MET* 1.3 66.9 + - - +
254A ILE* 4.2 11.7 - - + -
268A SER* 3.5 1.7 - - - -
269A VAL* 2.8 53.5 + - + +
271A ALA* 4.1 11.6 - - + +
279A LEU* 4.0 17.3 - - + -
289A LEU* 4.0 17.5 - - + -
291A THR* 4.2 3.4 - - + -
301A TRP* 4.0 38.8 - - + +
306A LEU* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY* 3.6 23.6 - - - +
226A HIS* 3.5 37.2 - - + +
244A GLY* 3.2 5.4 - - - -
245A SER* 2.8 38.5 + - - +
249A ASP* 4.2 1.3 - - - +
251A LYS* 4.0 16.2 - - + -
252A LEU* 1.3 77.9 - - - +
254A ILE* 1.3 63.7 + - - +
255A TRP* 3.5 35.4 - - - +
265A PRO* 3.8 18.8 - - + -
267A HIS 3.4 6.3 - - - +
268A SER* 3.9 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.5 27.6 - - + -
243A PHE 3.4 2.0 - - - +
244A GLY* 4.2 11.9 - - - -
252A LEU* 4.2 17.9 - - + +
253A MET* 1.3 80.8 - - - +
255A TRP* 1.3 59.3 + - - +
265A PRO* 3.4 1.7 - - - +
266A SER* 2.8 34.7 + - - -
267A HIS* 2.9 31.8 + - + -
281A PHE* 4.5 9.6 - - + -
289A LEU* 4.7 2.2 - - + -
303A LEU* 3.8 29.4 - - + -
306A LEU* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.9 10.9 - - + +
223A PHE* 3.7 25.6 - + + -
225A GLY* 3.6 31.6 - - - -
226A HIS 4.8 0.7 - - - -
241A SER 3.6 0.4 - - - +
242A LEU* 3.4 9.5 - - - +
243A PHE* 2.7 73.5 + + + +
245A SER* 2.8 25.7 + - - -
253A MET* 3.5 34.0 - - - +
254A ILE* 1.3 74.3 - - - +
256A ASP* 1.3 63.5 + - - +
257A THR 4.2 0.4 - - - -
261A ASN 5.0 2.0 - - - -
262A THR* 3.6 20.0 - - - -
264A LYS 3.7 7.6 - - - -
265A PRO* 3.6 34.3 - - + -
266A SER* 4.3 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 5.3 4.0 - - - -
241A SER* 3.3 11.4 - - - -
242A LEU* 5.3 8.1 - - + +
243A PHE* 5.3 0.4 - - - -
255A TRP* 1.3 78.0 - - - +
257A THR* 1.3 61.9 + - - +
258A ARG* 2.7 64.2 + - - +
259A SER* 3.1 26.2 + - - +
266A SER* 3.6 18.4 + - - +
----------------------------------------------------------
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