Contacts of the helix formed by residues 253 - 268 (chain A) in PDB entry 3F4V
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 SER 253 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A SER* 3.1 10.8 + - - -
252A ASN* 1.3 79.8 - - - +
254A THR* 1.3 65.5 + - - +
255A GLU* 3.7 9.7 + - - +
256A ASP* 3.0 33.8 + - - -
257A GLN* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN 3.6 1.8 + - - -
253A SER* 1.3 71.2 - - - +
255A GLU* 1.3 58.2 + - - +
257A GLN* 3.9 4.9 - - - +
258A ALA* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A SER* 3.1 11.2 + - - +
254A THR* 1.3 81.1 - - - +
256A ASP* 1.3 66.7 + - - +
258A ALA* 3.4 6.3 + - - +
259A ALA* 3.0 27.7 + - - +
262A ARG* 5.0 1.2 + - - -
321A LYS* 4.8 6.6 + - - -
322A GLY* 3.2 20.1 - - - +
323A GLN* 3.6 31.5 + - - +
324A GLN* 4.0 6.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
249A ALA* 3.4 10.4 - - - +
250A LEU* 3.8 13.7 - - - +
251A SER* 2.6 45.9 + - - +
253A SER* 3.0 18.8 + - - +
255A GLU* 1.3 78.3 - - - +
257A GLN* 1.3 66.0 + - - +
259A ALA* 3.3 2.4 + - - +
260A ALA* 3.0 19.4 + - - +
320A MET 4.0 1.7 - - - +
321A LYS* 3.6 18.9 + - - +
322A GLY* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA* 3.4 19.6 + - - +
251A SER 4.0 4.0 + - - +
252A ASN* 2.8 37.8 + - - +
253A SER 2.9 18.7 + - - +
254A THR* 3.9 4.7 - - - +
256A ASP* 1.3 75.2 - - - +
258A ALA* 1.3 63.2 + - - +
260A ALA* 3.4 2.6 + - - +
261A GLN* 3.1 23.6 + - - +
264A ARG* 4.7 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 2.9 21.5 + - + +
255A GLU* 3.7 7.2 - - - +
257A GLN* 1.3 76.9 - - - +
259A ALA* 1.3 58.8 + - - +
261A GLN* 3.3 7.0 + - - +
262A ARG* 2.8 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU 3.0 8.4 + - - +
256A ASP 3.6 5.4 - - - +
257A GLN 3.3 0.2 - - - -
258A ALA* 1.3 76.6 - - - +
260A ALA* 1.3 62.7 + - - +
262A ARG* 3.1 18.8 + - - +
263A ALA* 2.9 21.1 + - - +
320A MET* 4.3 5.4 - - + -
321A LYS 3.6 11.4 - - - +
322A GLY* 3.5 32.3 - - - +
339A VAL* 3.4 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TYR* 3.9 4.5 - - - +
248A GLU 3.9 4.5 - - - -
249A ALA* 3.5 31.6 - - + +
256A ASP 3.0 14.0 + - - +
257A GLN* 3.9 3.8 - - - +
258A ALA 3.4 0.2 - - - -
259A ALA* 1.3 76.5 - - - +
261A GLN* 1.3 59.1 + - - +
263A ALA* 3.4 2.8 + - - +
264A ARG* 3.0 49.6 + - - +
320A MET* 3.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLN 3.1 17.2 + - - +
258A ALA* 3.7 6.5 - - - +
260A ALA* 1.3 76.2 - - - +
262A ARG* 1.3 64.4 + - - +
264A ARG* 2.9 31.1 + - - +
265A ASP* 2.9 46.8 + - - +
372A TYR* 2.8 36.9 + - - -
376A LYS* 3.7 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU 5.0 0.6 + - - -
258A ALA* 2.8 37.8 + - - +
259A ALA* 3.5 26.4 - - - +
261A GLN* 1.3 71.6 - - - +
263A ALA* 1.3 57.9 + - - +
265A ASP* 3.2 6.3 + - - +
266A PHE* 2.9 40.0 + - + -
283A ILE* 3.8 34.3 - - + +
287A LEU* 4.0 5.8 - - - -
322A GLY* 4.6 0.4 - - - -
323A GLN* 4.2 16.2 + - - +
325A LEU* 3.6 37.3 - - - +
337A TRP* 2.9 27.6 + - - +
338A GLN 2.8 22.4 + - - -
339A VAL* 4.0 0.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
247A TYR* 3.6 28.4 - - + -
259A ALA 2.9 12.7 + - - +
260A ALA 3.5 8.3 - - - +
262A ARG* 1.3 73.4 - - - +
264A ARG* 1.3 65.6 + - - +
266A PHE 3.8 0.5 - - - -
267A HIS* 3.0 27.5 + - - +
320A MET* 4.1 10.1 - - + -
337A TRP* 3.7 28.5 - - + -
339A VAL* 4.4 2.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
244A PHE* 4.5 8.3 - - + -
246A TRP* 3.3 32.6 - - + -
247A TYR* 2.8 39.4 + - + -
248A GLU* 4.4 4.4 + - - +
249A ALA 4.5 1.4 - - - +
257A GLN* 4.7 9.1 + - - -
260A ALA* 3.0 31.0 + - - +
261A GLN* 2.9 45.2 + - - +
263A ALA* 1.3 75.0 - - - +
265A ASP* 1.3 60.3 + - - +
267A HIS* 4.5 1.6 - - - -
268A ILE* 2.9 32.1 + - - +
269A GLY 3.2 4.9 + - - -
372A TYR* 3.5 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLN* 2.9 41.0 + - - +
262A ARG* 3.6 4.4 - - - +
264A ARG* 1.3 78.2 - - - +
266A PHE* 1.3 57.4 + - - +
269A GLY* 3.2 5.4 + - - +
270A TRP 2.8 28.6 + - - -
273A ASP* 4.2 9.9 - - - +
281A PRO* 3.6 16.6 - - + +
283A ILE* 3.6 31.8 + - + +
284A MET* 3.7 1.5 - - - +
372A TYR* 3.8 5.9 + - - -
376A LYS* 3.8 11.3 + - - -
377A TYR* 4.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 3.7 8.5 - - - -
262A ARG* 2.9 31.9 + - - +
265A ASP* 1.3 72.1 - - - +
267A HIS* 1.3 55.3 + - - +
270A TRP* 3.5 15.3 - - - +
283A ILE* 4.2 13.5 - - + -
284A MET* 3.7 38.4 - - + -
287A LEU* 4.1 18.6 - - + -
288A VAL* 3.7 29.6 - - + -
333A TYR* 2.7 30.6 + + - -
336A ASP* 3.7 21.1 - - + -
337A TRP* 3.4 51.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 3.3 54.2 + - - +
243A ASP* 2.9 39.1 + - - +
244A PHE* 3.9 10.3 - + + -
245A ASN* 3.5 29.5 + - + -
247A TYR* 2.6 36.3 + + + +
263A ALA 3.0 18.2 + - - +
264A ARG* 3.8 2.7 - - - +
266A PHE* 1.3 80.7 - - - +
268A ILE* 1.3 62.2 + - + +
270A TRP* 4.3 0.8 - - - +
271A TYR* 4.1 11.4 - - - -
333A TYR* 4.1 1.6 - - - -
337A TRP* 4.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.7 39.0 - - + -
243A ASP 3.8 11.2 - - - +
244A PHE* 3.7 45.3 - - + -
264A ARG 2.9 14.9 + - - +
267A HIS* 1.3 73.5 - - + +
269A GLY* 1.3 66.6 + - - +
270A TRP 3.2 2.0 - - - -
271A TYR* 3.1 6.1 + - + +
272A LEU* 2.9 45.2 + - + +
312A ILE* 3.9 13.7 - - + -
372A TYR* 4.1 15.5 - - + -
377A TYR* 5.1 0.7 - - - +
----------------------------------------------------------
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