Contacts of the strand formed by residues 238 - 244 (chain B) in PDB entry 6S1M
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 VAL 238 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 4.7 5.2 - - + -
26B ARG* 3.3 25.0 + - - +
195B PHE* 3.7 14.4 - - + +
197B LEU* 4.5 15.9 - - + +
222B VAL* 4.7 20.2 - - + -
234B SER 4.2 10.1 - - - +
235B ALA* 3.7 18.6 - - + +
236B ALA 3.4 0.8 - - - -
237B HIS* 1.3 73.1 - - - +
239B SER* 1.3 61.8 + - - +
240B ARG 3.4 21.8 - - - +
241B VAL* 4.9 0.9 - - + -
290B VAL* 4.7 2.5 - - + +
439B LEU* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 5.1 3.5 - - - +
27B VAL* 4.2 20.9 - - - -
28B PRO 4.7 1.3 + - - -
29B VAL* 3.5 32.4 - - - +
194B ARG* 4.5 15.6 + - - -
195B PHE 3.0 14.7 + - - -
196B VAL* 5.2 1.8 - - - -
237B HIS 3.2 4.1 + - - -
238B VAL* 1.3 74.1 - - - +
240B ARG* 1.3 72.8 + - - +
290B VAL* 5.6 1.3 - - - -
291B PRO* 3.8 13.2 - - - +
336B ILE* 5.4 2.2 - - - +
442B LEU* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.7 25.1 - - - +
32B TYR* 3.3 46.1 - - - +
195B PHE 4.0 3.2 + - - -
196B VAL* 4.2 13.5 - - + -
197B LEU 3.7 11.8 + - - -
238B VAL* 3.4 15.0 - - - +
239B SER* 1.3 91.5 - - - +
241B VAL* 1.3 72.6 + - - +
242B ILE* 5.5 4.2 - - + +
290B VAL* 5.3 1.1 - - - -
291B PRO* 3.9 27.4 + - - +
292B VAL 5.2 0.8 + - - -
293B ASP* 2.4 36.8 + - - +
326B GLN* 4.6 2.0 + - - -
336B ILE* 4.0 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 6.0 0.2 - - - -
197B LEU* 3.9 22.7 - - + +
199B VAL* 5.3 2.2 - - + -
222B VAL* 4.3 18.6 - - + -
238B VAL* 4.9 0.4 - - + -
240B ARG* 1.3 80.4 - - - +
242B ILE* 1.3 71.4 + - - +
243B LEU* 4.6 11.7 - - + -
286B LEU* 5.0 10.3 - - + -
290B VAL* 3.8 26.0 - - + -
291B PRO 3.2 11.6 + - - +
292B VAL* 3.5 19.1 - - + -
293B ASP* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 5.0 10.5 - - + -
197B LEU 3.2 9.5 + - - +
198B LEU* 3.8 29.7 - - + +
199B VAL* 3.3 25.5 + - - +
240B ARG* 5.5 3.1 - - + -
241B VAL* 1.3 77.0 - - - +
243B LEU* 1.3 71.5 + - - +
244B ALA* 4.6 7.0 - - + -
293B ASP* 3.8 20.9 - - + +
295B MET* 4.8 9.2 - - - -
332B TYR* 4.3 15.5 - - + -
336B ILE* 4.1 24.9 - - + -
341B PHE* 5.1 9.6 - - + -
403B PHE* 4.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.7 31.0 - - + +
200B SER* 5.8 1.1 - - - -
202B LEU* 4.3 24.0 - - + -
218B LEU* 6.4 0.2 - - + -
241B VAL* 4.2 11.0 - - + -
242B ILE* 1.3 73.9 - - - +
244B ALA* 1.3 59.8 + - - +
245B GLY 3.8 1.1 - - - -
247B LEU* 4.3 20.0 - - + -
279B LEU* 5.8 1.3 - - + -
282B ILE* 6.2 0.9 - - + -
283B LEU* 4.0 27.4 - - + -
286B LEU* 4.9 12.1 - - + -
292B VAL* 4.2 10.5 - - + -
293B ASP 3.0 14.1 + - - +
294B VAL* 4.4 6.5 - - + -
295B MET* 3.3 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 5.4 2.2 - - + -
199B VAL 3.1 10.6 + - - +
200B SER* 3.0 29.7 + - - +
242B ILE* 4.6 6.7 - - + -
243B LEU* 1.3 72.3 - - - +
245B GLY* 1.3 65.9 + - - +
247B LEU* 5.3 0.8 - - - +
295B MET* 4.3 14.8 - - + -
344B THR 4.8 6.1 - - - +
345B SER* 4.0 9.6 + - - +
403B PHE* 4.4 23.8 - - + -
404B CYS 5.3 1.8 - - - +
405B GLY* 5.0 0.7 - - - -
406B ASN* 3.9 3.5 + - - +
428B VAL* 6.0 0.4 - - + -
----------------------------------------------------------
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