Contacts of the helix formed by residues 265 - 279 (chain H) in PDB entry 1PV2
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 ALA 265 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H LEU* 4.7 1.6 - - - -
249H GLY* 3.4 18.1 - - - +
250H ARG 3.8 0.2 - - - +
251H VAL* 3.7 14.8 - - + -
260H GLY* 3.9 3.6 - - - -
261H ASP* 3.4 32.1 - - - +
262H SER 3.0 9.4 + - - +
264H PHE* 1.3 77.3 - - - +
266H ALA* 1.3 59.5 + - - +
267H ASN 3.4 0.7 - - - -
268H ALA* 4.0 4.3 - - - -
269H LEU* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ILE* 3.7 27.8 - - + +
77H GLU* 4.2 8.1 - - - -
80H LEU* 3.7 16.4 - - + -
81H PRO* 3.8 13.5 - - + +
184H LEU* 4.2 11.2 - - + -
262H SER 3.8 1.8 + - - -
263H PRO 3.3 17.6 + - - +
264H PHE 3.2 1.6 - - - -
265H ALA* 1.3 77.7 - - - +
267H ASN* 1.3 64.3 + - - +
269H LEU* 3.9 0.3 - - - +
270H GLY* 3.1 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 267 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ASP* 4.2 18.5 - - + +
36H LEU* 3.3 22.8 - - - +
37H ASP* 3.1 33.0 + - - +
80H LEU* 3.7 12.5 - - + +
84H HIS* 2.8 34.6 + - - -
264H PHE 4.4 4.8 + - - +
265H ALA 3.4 0.4 - - - -
266H ALA* 1.3 79.1 - - - +
268H ALA* 1.3 57.9 + - - +
270H GLY* 3.2 2.9 + - - -
271H LYS* 2.9 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H GLY 4.7 8.3 - - - +
251H VAL* 3.7 25.6 - - + +
264H PHE 5.0 2.1 + - - +
265H ALA* 3.6 5.6 + - - +
266H ALA 3.4 0.4 - - - -
267H ASN* 1.3 79.3 - - - +
269H LEU* 1.3 52.0 + - - +
271H LYS* 3.1 16.3 + - - +
272H LEU* 2.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H PRO* 4.5 10.7 - - + +
150H PHE* 4.8 0.4 - - + -
182H ILE* 3.9 17.9 - - + -
183H SER 3.2 21.8 - - - +
184H LEU* 3.8 25.1 - - + -
251H VAL* 3.4 12.0 - - + +
258H LEU* 3.7 39.7 - - + +
259H THR 3.8 11.7 - - - +
260H GLY* 4.4 1.1 - - - +
265H ALA 2.9 18.9 + - - +
266H ALA 3.9 2.0 - - - +
268H ALA* 1.3 74.8 - - - +
270H GLY* 1.3 60.1 + - - +
272H LEU* 4.2 4.9 - - + -
273H ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 270 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H PRO* 3.6 28.9 - - - +
84H HIS* 3.4 22.8 - - - +
85H LEU 4.8 0.3 + - - -
266H ALA 3.1 11.4 + - - -
267H ASN 3.6 3.6 - - - -
269H LEU* 1.3 77.0 - - - +
271H LYS* 1.3 63.3 + - - +
273H ALA* 3.8 3.9 - - - +
274H ALA* 3.2 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ASP* 3.5 25.4 + - - +
38H GLY* 4.4 14.6 - - - +
41H TYR* 3.4 10.5 + - - +
84H HIS* 3.6 15.5 - - + -
267H ASN* 2.9 26.7 + - - +
268H ALA* 3.1 16.7 + - - +
270H GLY* 1.3 74.6 - - - +
272H LEU* 1.3 64.8 + - - +
275H GLN* 3.1 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H VAL* 4.3 20.6 - - + -
252H HIS* 4.0 24.5 - - - +
253H LYS* 4.2 17.0 - - + +
258H LEU* 4.3 14.1 - - + -
268H ALA 2.7 19.7 + - - +
269H LEU* 3.8 7.9 - - + +
271H LYS* 1.3 72.8 - - - +
273H ALA* 1.3 62.5 + - - +
275H GLN* 3.3 10.3 + - + +
276H GLU* 3.0 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H PRO* 6.0 1.1 - - + -
85H LEU* 4.0 24.5 - - + -
182H ILE* 4.2 13.9 - - + -
258H LEU* 3.5 20.8 - - + +
269H LEU 2.9 17.8 + - - +
270H GLY* 3.8 5.2 - - - +
271H LYS 3.3 0.2 - - - -
272H LEU* 1.3 75.5 - - - +
274H ALA* 1.3 65.6 + - - +
276H GLU* 2.9 4.0 + - - -
277H MET* 2.8 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H TYR* 3.4 42.2 - - + +
84H HIS 4.3 4.5 - - - +
85H LEU* 3.7 14.2 - - + +
88H ALA* 4.0 14.4 - - + -
270H GLY 3.2 9.5 + - - +
273H ALA* 1.3 78.4 - - - +
275H GLN* 1.3 62.5 + - - +
277H MET* 3.9 1.5 - - - +
278H LEU* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 275 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H TYR* 3.5 27.8 + - + -
271H LYS* 3.1 41.0 + - - +
272H LEU* 3.6 11.0 + - + +
273H ALA 3.1 0.2 - - - -
274H ALA* 1.3 78.0 - - - +
276H GLU* 1.3 64.3 + - + +
278H LEU* 3.3 8.9 + - + +
279H ALA* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H PHE* 3.4 30.2 - - + -
253H LYS* 2.6 43.0 + - - +
255H ARG 4.9 2.3 - - - +
258H LEU* 4.3 9.9 - - + -
272H LEU* 3.0 39.6 + - + +
273H ALA 2.9 2.8 + - - +
275H GLN* 1.3 77.2 - - + +
277H MET* 1.3 60.8 + - - +
279H ALA* 3.5 15.2 + - - +
280H ALA* 3.6 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 277 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H ILE* 4.2 11.4 - - + -
85H LEU* 3.6 18.6 - - + -
90H PHE* 3.5 46.7 - - + -
147H ALA* 3.9 11.7 - - + +
148H ALA* 4.1 7.0 - - - -
180H PHE* 3.7 46.9 - - + -
182H ILE* 4.6 5.6 - - - -
273H ALA* 2.8 28.8 + - + +
274H ALA 4.0 1.3 - - - +
276H GLU* 1.3 76.0 - - - +
278H LEU* 1.3 63.8 + - - +
280H ALA 3.6 2.2 + - - -
281H TYR* 3.2 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H TYR* 4.4 20.2 - - + -
43H LYS 3.7 25.1 - - - +
45H TYR* 3.7 26.2 - - + +
88H ALA* 3.9 24.7 - - + +
90H PHE* 4.5 2.2 - - + -
274H ALA 3.0 26.3 + - - +
275H GLN* 3.7 7.9 - - + +
277H MET* 1.3 74.7 - - - +
279H ALA* 1.3 57.6 + - - +
280H ALA 3.1 8.8 + - - -
281H TYR* 3.5 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H GLN 3.3 13.2 + - - +
276H GLU* 3.5 10.5 + - - +
277H MET 3.3 0.4 - - - -
278H LEU* 1.3 77.0 - - - +
280H ALA* 1.3 57.7 + - - +
281H TYR 3.7 1.6 - - - -
----------------------------------------------------------
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