Contacts of the helix formed by residues 245 - 259 (chain A) in PDB entry 2XAF
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 ASP 245 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TYR 3.6 6.5 + - - +
244A SER* 1.3 81.0 + - - +
246A THR* 1.3 60.1 + - - +
247A VAL* 2.9 30.1 + - - +
248A LEU* 3.5 29.2 + - + +
249A VAL* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.6 13.3 - - - -
235A LEU* 3.8 33.0 - - + -
243A ASN 4.3 3.1 - - - +
244A SER 3.3 11.7 + - - +
245A ASP* 1.3 71.6 + - - +
247A VAL* 1.3 63.4 + - - +
248A LEU 3.2 1.8 - - - -
249A VAL* 3.8 5.6 - - - -
250A HIS* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 2.9 26.2 - - - +
246A THR* 1.3 76.9 + - - +
248A LEU* 1.3 64.4 + - + +
250A HIS* 4.0 4.8 - - + +
251A ARG* 2.9 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 5.1 0.4 - - - +
199A ILE* 3.7 34.5 - - + -
206A THR* 5.5 3.1 - - - +
209A VAL* 5.3 6.5 - - + -
210A PHE* 4.5 13.5 - - + +
213A ILE* 4.0 26.5 - - + -
245A ASP* 3.5 31.4 + - + +
246A THR 3.2 0.6 - - - -
247A VAL* 1.3 74.7 - - + +
249A VAL* 1.3 69.5 + - - +
250A HIS 2.9 1.1 - - - -
251A ARG* 2.7 35.2 + - + +
252A VAL* 2.8 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 4.0 19.7 - - + +
217A THR* 5.6 0.2 - - - +
231A PHE* 3.4 18.8 - - + -
234A THR* 4.3 18.4 - - + -
235A LEU* 4.1 16.6 - - + -
238A LEU* 3.8 31.9 - - + -
242A TYR 4.4 7.6 - - - +
243A ASN* 4.6 0.4 - - - -
245A ASP 3.1 19.3 + - - +
246A THR* 3.4 7.2 + - - +
248A LEU* 1.3 75.1 - - + +
250A HIS* 1.3 57.0 + - - +
252A VAL* 4.0 1.1 - - - +
253A HIS* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.2 50.4 - + + +
246A THR 2.9 14.8 + - - +
247A VAL* 4.0 5.4 - - + +
248A LEU 2.7 3.4 + - - -
249A VAL* 1.3 70.8 - - - +
251A ARG* 1.3 67.2 + - - +
252A VAL 3.0 2.6 + - - -
253A HIS* 3.3 4.1 + - - -
254A SER* 2.9 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A CYS 3.5 13.1 + - - -
196A PHE* 3.2 37.2 - - + -
198A ASP* 2.5 44.2 + - - -
199A ILE* 4.6 0.4 - - - -
247A VAL* 2.9 26.2 + - + +
248A LEU* 2.7 25.1 + - + +
250A HIS* 1.3 73.6 - - - +
252A VAL* 1.3 55.5 + - - +
254A SER* 3.7 2.1 - - - -
255A TYR* 3.2 26.2 + - - +
834A TYR* 3.2 39.0 + - - +
835A THR 4.5 4.4 + - - -
836A LEU 4.2 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 3.9 15.3 - - + -
210A PHE* 3.6 34.3 - - + -
213A ILE* 4.4 12.1 - - + -
214A ARG* 4.0 31.6 - - + +
217A THR* 4.7 2.0 - - - +
248A LEU* 2.8 25.0 + - + +
249A VAL* 4.0 4.9 - - - +
251A ARG* 1.3 74.3 - - - +
253A HIS* 1.3 68.6 + - - +
254A SER 2.9 2.3 + - - -
255A TYR* 3.2 3.4 + - + +
256A LEU* 3.0 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A THR* 4.6 8.1 - - + -
228A GLN* 6.3 0.7 - - - -
229A LEU* 2.6 28.9 + - + -
230A THR* 3.4 6.8 - - - -
231A PHE* 3.6 30.2 + - + +
234A THR* 3.7 24.0 - - + +
249A VAL 3.0 19.3 + - - +
250A HIS* 4.0 4.8 + - - +
252A VAL* 1.3 79.2 - - - +
254A SER* 1.3 62.9 + - - +
256A LEU* 3.6 9.3 + - - +
257A GLU* 3.0 51.9 + - + +
262A ILE* 3.7 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A HIS* 2.9 37.9 + - - -
251A ARG 3.7 4.9 - - - -
252A VAL 2.9 0.8 - - - -
253A HIS* 1.3 79.1 + - - +
255A TYR* 1.3 67.7 - - - +
257A GLU* 2.8 17.2 + - - +
258A ARG* 2.8 16.8 + - - +
834A TYR* 3.8 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 5.0 3.3 - - - +
189A THR* 4.1 0.9 + - - -
191A GLN* 3.2 34.2 + - + +
192A GLU* 3.0 42.8 + - + +
195A CYS* 3.8 9.0 - - - -
196A PHE* 3.7 26.5 - + + -
210A PHE* 5.9 2.0 - + - -
214A ARG* 5.5 0.9 - - + -
251A ARG 3.2 15.5 + - - +
252A VAL* 3.6 4.7 - - + +
254A SER* 1.3 77.2 - - - +
256A LEU* 1.3 103.4 + - + +
258A ARG* 3.3 2.2 + - - +
259A HIS* 3.1 56.0 + + + +
261A LEU* 4.5 12.7 - - + +
834A TYR* 4.1 16.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLU* 5.4 0.2 - - - +
214A ARG* 4.1 24.0 - - + +
217A THR* 3.8 34.5 - - + -
218A LEU* 4.5 7.6 - - + -
252A VAL* 3.0 29.6 + - + +
253A HIS* 3.6 2.7 - - - +
255A TYR* 1.3 106.7 - - + +
257A GLU* 1.3 62.7 + - - +
259A HIS* 3.3 4.2 + - - -
261A LEU* 3.2 47.5 + - + +
262A ILE* 3.6 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLN* 3.9 15.2 + - - -
253A HIS* 3.0 34.7 + - - +
254A SER* 2.8 10.9 + - - +
256A LEU* 1.3 76.3 - - - +
258A ARG* 1.3 65.7 + - - +
260A GLY* 3.2 11.6 + - - -
262A ILE* 3.5 15.0 - - + +
263A ASN* 3.4 31.7 + - + +
296A GLN* 3.9 4.2 + - - -
299A SER* 5.3 5.1 + - - +
300A PHE* 3.8 18.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER 2.8 14.8 + - - +
255A TYR 3.5 5.2 - - - +
257A GLU* 1.3 79.6 - - - +
259A HIS* 1.3 67.6 + - + +
260A GLY 3.2 2.9 + - - -
296A GLN* 4.7 1.2 + - - +
300A PHE* 3.3 31.7 - - - +
819A LEU 5.1 0.5 - - - +
823A GLY* 3.5 28.1 + - - -
826A ALA* 3.5 23.7 + - - +
827A ASP* 2.9 44.0 + - - +
830A LEU* 4.7 11.7 - - - +
831A GLY 3.7 15.0 + - - -
834A TYR* 3.2 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLN* 3.6 28.6 + - - +
195A CYS* 4.5 6.7 - - - -
255A TYR* 3.1 52.1 + + + +
256A LEU 3.7 1.3 - - - +
257A GLU 3.2 0.2 - - - -
258A ARG* 1.3 84.2 - - + +
260A GLY* 1.3 60.7 + - - +
261A LEU* 3.2 19.9 + - + +
819A LEU* 4.5 14.8 - - - +
820A ARG* 5.5 5.5 - - - +
823A GLY* 4.1 16.2 - - - -
824A ARG* 5.9 0.4 - - - -
827A ASP* 3.6 17.6 + - - -
834A TYR* 3.6 17.6 + + - -
----------------------------------------------------------
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