Contacts of the helix formed by residues 285 - 296 (chain B) in PDB entry 1PXV
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 PHE 285 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 3.5 17.9 - + - -
283B ALA* 4.1 8.7 - - + -
284B THR* 1.3 78.0 - - - +
286B PRO* 1.3 77.1 - - + +
287B ASN* 3.3 3.1 - - + +
288B GLN* 2.8 39.5 + - + +
289B MET* 3.2 15.4 + - - +
74D GLU* 5.8 0.9 - - - -
93D SER* 4.4 4.5 - - - -
95D GLN* 3.5 22.0 - - + -
96D GLY* 3.4 35.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 1.3 91.0 - - + +
287B ASN* 1.3 67.4 + - - +
289B MET* 3.1 25.5 + - - +
290B ILE* 3.3 16.5 + - + +
325B LEU* 5.4 2.2 - - + -
390B MET* 3.9 17.5 - - + +
95D GLN 5.9 0.7 - - - +
96D GLY* 5.9 0.4 - - - -
97D ILE* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 3.3 2.5 - - + +
286B PRO* 1.3 84.0 - - - +
288B GLN* 1.3 58.5 + - - +
290B ILE* 3.3 16.0 + - - +
291B GLU* 2.9 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B MET* 5.1 0.4 - - - +
270B LEU* 3.8 43.2 + - + +
271B TYR* 3.4 31.0 + - - -
283B ALA 3.9 0.2 - - - +
284B THR* 3.4 12.4 - - + +
285B PHE* 2.8 44.4 + - + +
287B ASN* 1.3 78.5 - - - +
289B MET* 1.3 58.2 + - - +
291B GLU* 4.5 9.4 - - - +
292B TYR* 2.8 33.3 + - - +
464B GAI 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ALA* 3.9 21.5 - - + -
248B MET* 4.0 10.1 - - + +
284B THR* 3.8 17.9 - - + +
285B PHE 3.5 8.1 - - - +
286B PRO* 3.1 17.2 + - - +
288B GLN* 1.3 78.3 - - - +
290B ILE* 1.3 59.9 + - - +
293B GLY 3.2 15.8 + - - -
323B MET* 3.7 18.6 - - + -
325B LEU* 3.7 30.1 - - + -
390B MET* 3.9 13.7 - - + -
393B TYR* 2.9 30.5 + - - +
97D ILE* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO* 3.3 15.1 + - + +
287B ASN* 3.8 18.6 - - - +
288B GLN 3.3 0.2 - - - -
289B MET* 1.3 75.5 - - - +
291B GLU* 1.3 62.9 + - + +
293B GLY* 3.3 2.4 + - - -
294B LYS* 2.9 57.8 + - + +
300B ILE* 3.6 33.6 - - + +
301B HIS* 5.2 0.2 - - - -
302B TYR* 4.8 9.4 - - + +
390B MET* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASN* 2.9 40.5 + - + +
288B GLN* 4.2 6.7 - - - +
290B ILE* 1.3 75.0 - - + +
292B TYR* 1.3 60.5 + - - +
294B LYS* 3.3 12.4 + - + +
295B SER* 2.9 28.2 + - - -
464B GAI 3.9 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B MET* 4.0 23.8 - - + -
252B LEU* 3.7 21.5 - - + -
261B TYR* 3.3 27.9 - - - -
266B ILE* 3.4 41.3 - - + +
269B THR* 4.4 23.3 - - + -
270B LEU* 4.5 8.3 - - + -
288B GLN 2.8 24.0 + - - +
289B MET 4.1 2.9 - - - +
291B GLU* 1.3 69.8 - - - +
293B GLY* 1.3 67.5 - - - +
295B SER* 2.7 31.4 + - - -
296B GLN* 3.2 22.5 + - + +
464B GAI 3.7 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 5.5 0.7 - - - -
289B MET 3.2 10.0 + - - -
290B ILE 3.7 2.7 - - - -
292B TYR* 1.3 80.0 - - - +
294B LYS* 1.3 63.1 + - - +
296B GLN* 2.9 15.9 + - - +
297B GLY 3.3 0.2 + - - -
298B ARG* 2.9 28.0 + - - +
300B ILE* 3.9 16.6 - - - -
393B TYR* 4.1 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE* 2.9 44.5 + - + +
291B GLU* 3.5 12.3 - - + +
293B GLY* 1.3 76.1 - - - +
295B SER* 1.3 61.5 + - - +
297B GLY* 3.0 14.6 + - - -
298B ARG 3.3 14.6 - - - +
299B ASP* 3.8 23.1 + - - +
300B ILE 4.6 4.4 + - - +
301B HIS* 6.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B THR* 5.7 0.9 - - - +
291B GLU 2.9 12.4 + - - -
292B TYR* 2.7 28.3 + - - -
294B LYS* 1.3 75.0 - - - +
296B GLN* 1.3 78.1 + - - +
297B GLY 3.3 1.8 + - - -
464B GAI 4.2 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 4.4 12.8 - - + -
256B LYS* 2.8 32.0 + - - +
261B TYR* 2.6 39.6 + - + +
292B TYR* 3.4 40.2 + - + +
293B GLY 2.9 9.4 + - - +
295B SER* 1.3 104.3 + - - +
297B GLY* 1.3 60.6 + - - +
298B ARG* 3.3 3.6 + - - +
----------------------------------------------------------
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