Contacts of the strand formed by residues 330 - 338 (chain B) in PDB entry 4R8U
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 330 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B MET* 4.8 0.9 - - - +
252B GLU 4.6 0.3 - - - +
253B ASP* 3.2 3.3 - - - -
254B ILE* 2.8 50.8 + - + +
291B LEU* 4.3 15.0 - - + -
292B LYS 3.5 7.4 - - - +
293B PHE* 3.8 22.4 - - + -
321B TRP* 3.5 25.6 - - + -
325B ARG* 4.0 10.8 - - - -
329B GLY* 1.3 76.8 - - - -
331B ARG* 1.3 62.4 + - - +
332B LEU 3.4 27.4 - - - +
333B VAL* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.6 31.2 - - - +
249B THR* 3.2 23.7 + - - +
250B MET* 2.7 36.0 + - - -
253B ASP* 3.3 23.1 - - - +
292B LYS* 2.9 26.2 + - + +
293B PHE 3.7 16.6 - - - +
294B ASP* 4.8 5.3 + - - +
296B PHE* 3.1 33.9 - - - -
329B GLY 4.2 1.4 + - - -
330B VAL* 1.3 72.4 - - - +
332B LEU* 1.3 57.5 + - + +
19C T 2.9 43.0 + - - +
20C A 3.0 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU* 3.9 20.4 - - + +
248B ARG 3.2 11.4 - - - +
249B THR* 3.6 8.5 - - - +
250B MET* 4.6 0.7 - - - -
290B LYS* 3.8 33.7 - - + +
291B LEU* 3.6 2.9 - - - -
292B LYS* 3.1 53.8 + - + -
330B VAL* 3.4 8.9 - - - +
331B ARG* 1.3 84.7 - - + +
333B VAL* 1.3 77.4 + - - +
334B GLY 3.9 0.9 - - - +
20C A 5.6 1.3 - - + -
21C G 3.5 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU* 3.3 2.8 - - - -
248B ARG 3.0 30.1 + - - -
250B MET* 4.0 7.1 - - + +
254B ILE* 4.4 9.2 - - + -
260B CYS* 4.3 16.6 - - - -
263B ILE* 3.8 24.7 - - + -
264B ILE* 3.9 30.5 - - + -
267B LEU* 3.4 12.8 - - + +
289B VAL* 6.2 1.8 - - + -
290B LYS 3.6 5.8 - - - +
291B LEU* 4.3 7.4 - - + -
330B VAL* 4.3 11.4 - - + -
332B LEU* 1.3 80.7 - - - +
334B GLY* 1.3 64.3 + - - +
335B LEU* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL 3.6 7.0 - - - -
247B GLU* 3.7 11.0 - - - -
267B LEU* 4.6 0.7 - - - -
289B VAL* 3.2 7.4 - - - +
290B LYS* 2.7 51.2 + - - +
332B LEU* 3.9 0.8 - - - +
333B VAL* 1.3 77.1 - - - +
335B LEU* 1.3 68.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLY* 3.2 3.6 - - - -
246B VAL* 2.8 37.0 + - + +
247B GLU* 5.7 0.5 - - - +
264B ILE* 4.2 28.7 - - + +
267B LEU* 4.0 17.7 - - + +
268B TYR* 3.9 33.9 - - + +
271B LEU* 3.8 18.8 - - + -
288B GLY 3.5 2.5 - - - +
289B VAL* 3.9 20.6 - - + -
313B LEU* 4.0 25.4 - - + -
334B GLY* 1.3 82.7 - - - +
336B HIS* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B SER* 3.4 22.2 + - - -
244B VAL 3.7 9.9 - - - -
245B GLY* 4.4 8.7 - - - -
271B LEU* 4.6 1.2 - - - +
287B GLN* 3.3 3.3 - - - +
288B GLY* 2.7 46.3 + - - +
289B VAL* 5.6 2.7 - - - -
290B LYS* 6.1 2.9 - - + -
302B GLU* 3.8 22.8 + - + +
313B LEU* 4.9 0.3 - - - +
335B LEU* 1.3 75.6 - - - +
337B VAL* 1.3 83.1 + - - +
338B THR* 3.6 16.2 - - - -
23C G 5.9 0.2 - - - -
24C T 5.6 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B SER* 3.1 8.3 - - - -
244B VAL* 2.9 47.6 + - + +
271B LEU* 4.0 11.0 - - + -
275B LEU* 4.3 12.8 - - + -
284B ILE* 3.9 17.7 - - + -
286B ARG 3.3 9.4 - - - +
287B GLN* 3.9 4.9 - - + -
308B LEU* 3.9 28.5 - - + -
336B HIS* 1.3 83.3 - - - +
338B THR* 1.3 61.5 + - - +
339B LEU* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LYS* 3.6 14.1 - - + +
243B SER* 4.3 2.1 - - - -
284B ILE* 3.5 4.9 - - - +
285B ALA* 2.9 25.2 + - + -
286B ARG* 2.9 40.9 + - + +
302B GLU* 3.8 4.7 + - - -
336B HIS* 3.6 17.3 - - - -
337B VAL* 1.3 72.6 - - - +
339B LEU* 1.3 72.7 + - - +
----------------------------------------------------------
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