Contacts of the strand formed by residues 275 - 282 (chain A) in PDB entry 4FOV
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 275 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP* 3.8 13.5 - - + +
263A ALA 3.2 13.0 - - - +
264A ARG* 3.8 37.9 - - + +
265A TYR* 4.2 0.7 - - - -
269A HIS 3.9 7.6 - - - +
271A SER* 3.7 35.7 - - - +
273A SER* 4.1 8.3 - - - -
274A LYS* 1.3 82.5 - - - +
276A ASN* 1.3 78.4 + - - +
277A ILE* 5.0 0.2 - - + -
298A PHE* 5.3 0.5 - - - -
323A ALA 4.6 0.9 - - - +
324A SER* 3.5 11.6 - - - +
325A PHE* 3.0 42.8 + - - +
326A ILE* 3.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP* 3.6 1.7 - - - -
263A ALA* 2.6 38.4 + - + +
265A TYR* 3.2 28.8 + - + -
274A LYS* 3.8 7.3 + - - +
275A ILE* 1.3 82.3 - - - +
277A ILE* 1.3 61.3 + - - +
278A ALA 4.0 0.2 - - - -
294A PHE* 3.5 26.1 - - + -
296A MET 3.4 9.0 - - - +
297A LYS* 3.3 24.4 - - - +
298A PHE* 3.3 9.2 + - - +
303A GLU* 3.3 22.8 + - - +
325A PHE* 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER* 4.3 0.7 - - - -
261A ILE 3.4 9.0 - - - +
262A ASP* 3.6 23.8 - - - +
276A ASN* 1.3 75.3 - - - +
278A ALA* 1.3 66.5 + - - +
294A PHE* 3.5 6.4 - - - +
295A ALA* 2.8 30.4 + - + -
296A MET* 2.9 26.4 + - + +
325A PHE* 3.6 25.8 - - + +
326A ILE* 4.0 10.5 - - - +
328A SER* 3.8 27.1 - - - +
341A LEU* 4.1 17.0 - - + -
343A ALA* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 4.0 13.2 - - + -
239A THR* 3.7 29.4 - - + -
260A SER* 3.2 4.9 - - - -
261A ILE* 2.9 38.9 + - + +
263A ALA* 4.4 5.2 - - + -
276A ASN 3.9 1.0 + - - -
277A ILE* 1.3 73.2 - - - +
279A THR* 1.3 66.1 + - - +
292A PRO* 4.5 0.7 - - + -
293A ILE 3.3 11.9 - - - +
294A PHE* 4.2 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.8 3.8 - - - -
258A LEU* 4.0 10.5 - - + -
259A SER 3.0 14.1 - - - +
260A SER* 3.6 14.6 - - - -
277A ILE* 4.8 0.2 - - + -
278A ALA* 1.3 79.9 - - - +
280A SER* 1.3 60.8 + - - +
281A TYR* 5.8 0.7 - - - -
291A GLU 4.6 0.2 - - - +
292A PRO* 3.1 6.2 - - - +
293A ILE* 2.8 44.2 + - - +
295A ALA* 4.0 4.5 - - + -
341A LEU* 3.7 18.8 - - + -
468A GLY 4.2 4.0 + - - -
471A TRP* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 3.7 20.9 - - - +
233A PHE* 3.8 8.7 - - - -
258A LEU* 3.4 2.9 - - - +
259A SER* 2.8 31.9 + - - +
279A THR* 1.3 75.4 - - - +
281A TYR* 1.3 67.7 + - - +
289A TRP* 3.5 14.3 - - - +
290A SER* 2.7 39.8 + - - -
292A PRO* 4.5 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 3.4 42.1 + - + -
257A VAL 3.1 12.8 - - - +
258A LEU* 4.1 8.1 - - + -
279A THR 5.8 0.2 - - - -
280A SER* 1.3 81.2 + - - +
282A SER* 1.3 60.1 + - - +
283A ASP* 4.2 9.2 - - - -
289A TRP* 3.3 8.7 - - - -
290A SER* 3.0 49.0 + - - -
291A GLU 6.0 0.2 - - - -
293A ILE* 5.7 2.5 - - + -
467A ARG 4.1 7.4 - - - -
468A GLY 3.5 29.8 - - - -
469A GLU* 3.5 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLY 4.2 1.0 - - - +
256A ARG* 3.4 4.5 - - - +
257A VAL* 2.8 34.6 + - - +
281A TYR* 1.3 75.1 - - - +
283A ASP* 1.3 61.0 + - - +
284A ASP* 2.9 7.4 + - - -
285A ASN 5.0 0.2 + - - -
286A GLY* 2.8 28.1 + - - -
288A THR 2.8 23.9 + - - -
289A TRP* 3.5 25.8 - - - -
----------------------------------------------------------
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