Contacts of the helix formed by residues 253 - 264 (chain A) in PDB entry 2XMS
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 HIS 253 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 5.7 0.7 - - - -
156A ASN* 3.8 51.9 + - + +
158A ASP* 4.4 13.3 + - - +
186A HIS* 3.0 53.3 + + - -
223A TYR* 3.7 17.0 + + - -
247A VAL* 3.7 6.5 - - + -
251A ALA* 3.1 3.0 + - - +
252A PRO* 1.3 87.2 + - + +
254A GLU* 1.3 65.6 + - - +
255A ASP 3.4 2.0 - - - -
256A ALA* 3.3 10.8 + - + +
257A VAL* 3.0 22.0 + - - +
279A GLY 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 3.7 17.2 - - + +
248A GLY 3.9 12.8 - - - +
249A ASP* 3.9 4.5 - - - +
250A GLN* 2.9 33.4 + - - +
251A ALA 3.1 14.2 + - - +
252A PRO 3.3 1.2 - - - -
253A HIS* 1.3 78.2 - - - +
255A ASP* 1.3 71.6 + - - +
257A VAL* 3.2 2.1 + - - +
258A VAL* 3.0 38.0 + - + +
273A LYS* 2.7 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PRO 4.9 1.2 + - - -
253A HIS 3.4 0.4 - - - -
254A GLU* 1.3 86.3 - - - +
256A ALA* 1.3 57.7 + - - +
258A VAL* 3.5 7.4 + - - +
259A GLU* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE 3.8 11.1 - - - +
158A ASP* 3.5 37.2 - - + +
159A PRO* 4.3 5.1 - - + +
160A ASN* 5.4 1.8 - - - +
253A HIS* 3.3 13.0 + - - +
255A ASP* 1.3 79.4 - - - +
257A VAL* 1.3 57.8 + - - +
259A GLU* 3.4 10.6 + - - +
260A CYS* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ASN* 3.7 4.7 - - - +
157A ILE* 3.4 33.4 - - + +
245A LEU* 3.9 23.3 - - + +
246A VAL 4.2 4.9 - - - +
247A VAL* 3.7 26.9 - - + -
253A HIS 3.0 17.6 + - - +
254A GLU 3.9 1.6 - - - +
256A ALA* 1.3 77.3 - - - +
258A VAL* 1.3 50.9 + - - +
260A CYS* 3.3 6.3 + - - +
261A ASN* 2.8 32.6 + - - +
271A PHE* 3.5 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLU* 3.0 35.2 + - + +
255A ASP* 3.7 8.1 - - - +
257A VAL* 1.3 75.3 - - - +
259A GLU* 1.3 63.1 + - - +
261A ASN* 3.3 7.3 + - - +
262A SER* 3.3 18.0 + - - -
271A PHE* 3.7 30.1 - - + -
273A LYS* 4.4 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PRO* 5.3 4.5 - - - +
160A ASN* 3.3 30.0 + - - +
255A ASP 3.0 17.8 + - - +
256A ALA* 3.6 8.4 - - - +
258A VAL* 1.3 74.8 - - - +
260A CYS* 1.3 64.7 + - - +
262A SER* 2.6 29.0 + - - +
263A LYS* 3.4 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 5.9 0.4 - - - -
157A ILE* 4.0 23.8 - - + -
159A PRO* 4.2 14.1 - - + +
231A PHE* 3.7 32.3 - - - -
245A LEU* 4.1 12.1 - - + -
256A ALA 2.9 19.3 + - - +
257A VAL* 3.3 10.1 + - - +
259A GLU* 1.3 76.4 - - - +
261A ASN* 1.3 62.9 + - - +
263A LYS* 3.0 18.7 + - - +
264A LEU* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 2.9 18.0 + - - +
245A LEU* 3.5 14.0 - - + +
257A VAL 2.8 15.4 + - - +
258A VAL 3.4 11.4 + - - +
259A GLU 3.3 0.2 - - - -
260A CYS* 1.3 73.8 - - - +
262A SER* 1.3 57.8 + - - +
263A LYS 3.4 0.5 + - - -
264A LEU* 3.7 7.4 + - - +
269A THR* 3.5 23.9 - - - +
270A SER 4.8 0.2 - - - -
271A PHE* 3.7 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 3.1 31.0 + - - +
258A VAL 3.3 8.6 + - - -
259A GLU* 2.6 28.6 + - - +
261A ASN* 1.3 77.2 - - - +
263A LYS* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PRO* 6.2 3.1 - - + +
160A ASN* 5.2 6.1 - - - +
229A LEU 5.7 1.6 + - - -
230A ASN* 5.3 4.6 + - - -
231A PHE* 3.3 47.0 + - + +
232A GLU* 3.8 6.4 - - - +
233A ARG* 3.1 32.9 + - - +
238A THR* 4.8 2.6 + - - -
259A GLU* 3.4 39.4 + - - +
260A CYS* 3.0 10.2 + - - +
262A SER* 1.3 81.2 - - - +
264A LEU* 1.3 62.7 + - - +
265A ASP 4.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 5.5 0.4 - - + -
231A PHE* 4.0 29.8 - - + -
233A ARG* 2.8 34.4 + - - -
238A THR* 4.8 2.7 - - - +
239A LEU* 4.1 32.8 - - + +
243A VAL* 4.0 28.9 - - + -
245A LEU* 4.0 23.8 - - + -
260A CYS* 3.2 16.0 + - - +
261A ASN 3.7 2.7 + - - +
262A SER 3.5 0.4 - - - -
263A LYS* 1.3 80.7 - - - +
265A ASP* 1.3 59.4 + - - +
266A PRO* 3.1 1.4 - - - +
269A THR* 3.4 20.2 - - + +
----------------------------------------------------------
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