Contacts of the strand formed by residues 257 - 264 (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 VAL 257 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 4.2 7.6 - - + -
250A TYR 3.5 9.6 - - - +
251A THR* 4.3 6.1 - - + +
255A GLY 3.8 9.4 - - - +
256A ARG* 1.3 75.9 - - - +
258A LEU* 1.3 63.0 + - - +
281A TYR* 3.1 5.2 - - - +
282A SER* 2.8 40.8 + - - +
285A ASN* 4.9 5.8 - - - -
286A GLY 4.9 0.4 - - - +
289A TRP* 3.5 25.0 - - + -
657A THR* 4.0 22.7 - - + -
659A LEU* 3.7 24.2 - - + -
660A PRO* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.3 5.4 - - - +
250A TYR* 2.7 41.6 + - + +
252A LEU* 4.2 18.8 - - + -
256A ARG 4.0 0.8 + - - -
257A VAL* 1.3 75.7 - - - +
259A SER* 1.3 67.1 + - - +
279A THR* 4.0 14.8 - - - +
280A SER 3.4 20.2 - - - +
281A TYR* 4.1 8.7 - - + -
289A TRP* 4.6 0.2 - - - -
330A ILE* 3.9 24.2 - - + +
339A THR* 3.6 31.2 - - + -
467A ARG 4.7 0.9 - - - +
468A GLY* 4.4 16.4 - - - -
471A TRP* 3.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 4.6 2.0 - - - -
233A PHE* 3.3 23.9 - - - -
248A THR* 2.8 19.8 + - - -
249A LEU* 3.7 13.7 - - - -
257A VAL 4.2 0.2 + - - -
258A LEU* 1.3 76.4 - - - +
260A SER* 1.3 60.9 + - - +
279A THR* 3.0 8.0 - - - -
280A SER 2.8 38.9 + - - -
289A TRP* 4.1 9.4 - - - -
330A ILE* 4.2 2.9 - - - -
667A LEU* 3.3 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 4.5 0.2 - - - -
247A PRO* 3.6 0.2 - - - +
248A THR* 2.3 57.6 + - - +
259A SER* 1.3 78.4 + - - +
261A ILE* 1.3 66.5 + - - +
277A ILE* 4.3 1.8 - - - -
278A ALA 3.2 6.7 - - - -
279A THR* 3.6 18.6 - - - -
328A SER* 3.0 20.4 + - - -
330A ILE* 3.3 16.4 - - - +
341A LEU* 3.8 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.5 48.7 - - + -
244A PHE* 3.8 26.5 - - + -
245A ARG 3.1 24.0 - - - +
246A ILE 3.6 8.7 - - - +
247A PRO* 4.1 11.0 - - + -
260A SER* 1.3 75.7 - - - +
262A ASP* 1.3 65.3 + - - +
263A ALA 3.4 0.2 + - - -
277A ILE* 3.4 8.4 - - - +
278A ALA* 2.9 35.9 + - + +
328A SER* 4.0 2.6 + - - -
667A LEU* 4.8 0.7 - - + -
685A VAL* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 3.3 10.4 - - - +
245A ARG 2.9 32.5 + - - +
246A ILE* 3.6 16.4 + - - +
261A ILE* 1.3 70.8 - - - +
263A ALA* 1.3 60.1 + - - +
264A ARG* 2.8 44.5 + - + +
275A ILE* 3.8 8.8 - - + +
276A ASN 3.7 5.2 - - - -
277A ILE* 3.6 8.9 - - - +
326A ILE* 3.1 14.2 - - - +
327A ASP* 3.1 22.0 + - - -
328A SER 4.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A THR* 4.1 16.4 - - + -
241A ALA* 3.8 17.3 - - + -
243A TYR 3.8 0.2 - - - -
244A PHE* 3.9 18.2 - - + -
261A ILE 3.4 2.4 + - - -
262A ASP* 1.3 70.2 - - - +
264A ARG* 1.3 58.4 + - - +
265A TYR* 3.2 15.6 - - + +
275A ILE* 3.2 2.4 - - - -
276A ASN* 2.6 42.1 + - + +
278A ALA* 4.4 8.3 - - + -
294A PHE* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ALA* 3.8 2.1 - - - +
243A TYR* 2.9 44.2 + - + +
244A PHE 5.2 0.2 - - - -
245A ARG* 3.7 25.3 - - - +
246A ILE* 3.3 19.6 - - - +
262A ASP* 2.8 43.4 + - + +
263A ALA* 1.3 72.1 - - - +
265A TYR* 1.3 63.9 + - - +
266A GLY 3.7 0.7 - - - +
267A GLY 3.5 12.8 - - - +
268A THR* 2.9 26.2 + - - +
269A HIS 3.3 16.5 + - - +
270A ASP* 2.9 25.0 + - - -
273A SER* 5.6 0.4 - - - +
274A LYS 3.9 3.1 - - - -
275A ILE* 3.8 13.9 - - + +
326A ILE* 3.3 22.2 - - - +
327A ASP* 4.3 1.0 + - - -
701A CXS 5.3 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