Contacts of the helix formed by residues 252 - 262 (chain A) in PDB entry 2PGW
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 THR 252 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MSE 3.6 42.8 - - + -
100A ARG* 3.9 19.3 - - + +
103A ASN* 4.0 6.7 - - - +
251A PHE* 1.3 74.4 - - - +
253A LEU* 1.3 64.1 + - - +
254A TYR* 3.2 10.3 + - - +
255A ASP* 2.9 35.4 + - - +
256A VAL* 3.0 26.2 + - - +
275A ILE* 3.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MSE 5.2 1.5 - - - -
252A THR* 1.3 73.8 - - - +
254A TYR* 1.3 68.1 + - + +
256A VAL* 3.4 6.7 + - + +
257A TYR* 3.1 26.0 + - - +
275A ILE* 3.3 14.1 - - + +
280A PRO 5.0 0.9 - - - +
283A LYS* 3.7 46.4 - - + +
284A ALA* 3.8 8.1 - - + +
287A VAL* 3.8 13.2 - - + +
286B ALA 4.0 9.6 - - - +
289B GLU* 4.2 21.8 - - + +
290B ALA* 3.7 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MSE 4.0 24.2 - - + -
252A THR* 3.1 5.6 - - - +
253A LEU* 1.3 86.3 - - + +
255A ASP* 1.3 60.4 + - - +
257A TYR* 3.3 6.4 + - - +
258A GLU* 2.9 36.0 + - + +
289B GLU* 3.4 42.7 + - + +
290B ALA* 3.4 19.7 - - - -
292B GLY 4.8 0.2 - - - -
226G VAL* 4.8 8.5 - - + +
228G TRP* 3.3 67.3 - + + +
229G SER* 4.4 9.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
100A ARG* 3.1 35.3 + - - -
230A ILE* 4.0 3.3 - - + +
249A ALA 3.6 15.3 - - - +
250A ALA* 3.9 0.9 - - - -
251A PHE 3.1 9.7 + - - +
252A THR* 2.9 39.0 + - - +
254A TYR* 1.3 77.3 - - - +
256A VAL* 1.3 58.2 + - - +
258A GLU* 3.2 7.2 + - - +
259A ILE* 2.9 35.8 + - - +
2100A GOL 3.8 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ALA* 4.5 9.9 - - + -
252A THR 3.0 14.0 + - - +
253A LEU* 3.5 8.3 - - - +
255A ASP* 1.3 76.9 - - - +
257A TYR* 1.3 63.6 + - - +
259A ILE* 3.2 5.6 + - - +
260A CYS* 2.9 26.0 + - - -
268A ILE* 3.9 25.3 - - + +
270A ILE* 3.8 25.4 - - + -
284A ALA* 3.8 33.7 - - + +
287A VAL* 4.0 14.6 - - + -
288A ALA* 4.5 1.3 - - + +
295A ILE* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU 3.1 15.1 + - - +
254A TYR 3.3 7.4 + - - +
256A VAL* 1.3 76.2 - - - +
258A GLU* 1.3 70.9 + - - +
260A CYS* 3.3 2.4 + - - +
261A ARG* 2.8 52.1 + - + +
287A VAL* 3.9 21.5 - - + +
257B TYR* 3.8 25.6 - + - -
260B CYS* 3.3 36.9 + - + +
261B ARG* 3.3 6.9 + - - -
263B ARG* 4.7 7.1 + - - -
287B VAL* 4.7 4.7 - - + -
290B ALA* 3.6 31.2 - - + +
291B ALA* 3.7 22.3 - - + +
229G SER* 6.0 0.4 - - - -
231G PRO* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 3.7 17.9 - - + -
254A TYR* 2.9 23.3 + - + +
255A ASP* 3.5 6.3 - - - +
257A TYR* 1.3 82.9 - - - +
259A ILE* 1.3 65.4 + - - +
261A ARG* 2.9 36.4 + - - -
262A GLN* 2.9 54.6 + - - +
230G ILE* 6.1 1.1 - - - -
231G PRO* 3.4 21.1 - - - +
258G GLU* 4.9 1.6 - - - +
262G GLN* 4.5 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 3.7 15.9 - - + -
233A MSE 3.9 12.1 - - + -
246A ALA* 3.7 15.9 - - + -
249A ALA 4.0 6.1 - - - +
250A ALA* 3.5 37.0 - - + +
255A ASP 2.9 19.8 + - - +
256A VAL 3.6 4.3 - - - +
258A GLU* 1.3 76.6 - - - +
260A CYS* 1.3 58.1 + - - +
263A ARG* 3.0 6.9 + - - -
264A ALA* 2.9 44.6 + - + -
265A ALA* 3.9 23.3 + - + +
268A ILE* 4.0 16.8 - - + -
293A LEU* 5.3 1.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
256A VAL* 2.9 23.8 + - - +
257A TYR* 3.6 5.6 - - - +
259A ILE* 1.3 78.2 - - - +
261A ARG* 1.3 59.9 + - - +
263A ARG* 3.0 32.6 + - - -
268A ILE* 3.9 19.7 - - - -
287A VAL* 4.1 9.4 - - + -
288A ALA* 3.9 17.5 - - - -
291A ALA* 3.5 21.5 - - + -
293A LEU* 4.0 12.3 - - - -
257B TYR* 3.3 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 2.8 40.7 + - + +
258A GLU* 2.9 45.5 + - - +
260A CYS* 1.3 73.9 - - - +
262A GLN* 1.3 72.3 + - + +
263A ARG* 3.3 7.2 + - - +
257B TYR* 3.2 12.7 + - - +
261B ARG* 4.7 26.7 + - + +
231G PRO* 3.7 13.3 - - - +
261G ARG* 4.7 3.4 - - - +
262G GLN* 3.5 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 3.5 23.9 + - - +
231A PRO* 3.9 16.8 - - - +
234A ALA* 4.4 9.6 - - + +
238A GLU* 4.9 4.2 - - - +
258A GLU* 2.9 41.6 + - - +
259A ILE 4.3 1.6 - - - +
261A ARG* 1.3 92.0 + - + +
263A ARG* 1.3 71.9 + - - +
264A ALA* 3.1 7.9 + - + +
258G GLU* 4.4 2.6 - - - +
261G ARG* 3.8 26.5 + - - +
----------------------------------------------------------
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