Contacts of the helix formed by residues 261 - 277 (chain A) in PDB entry 5XVO
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 LEU 261 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.9 25.4 - - + -
186A ILE* 4.0 17.7 - - + -
187A PHE* 5.8 2.0 - - + -
221A PHE* 3.9 32.5 - - + -
224A LEU* 4.0 13.0 - - + -
247A LEU* 3.4 44.8 + - + +
248A PHE* 5.3 3.5 + - + +
250A ASN 4.2 5.3 + - - -
252A TYR* 4.2 10.0 - - + -
259A MET 3.9 0.8 + - - -
260A PHE* 1.3 73.6 - - - +
262A THR* 1.3 58.2 + - + +
264A ILE* 3.2 13.7 + - + +
265A ALA* 2.9 29.5 + - + +
286A PHE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 6.5 0.2 - - - -
2A GLY 5.2 2.6 + - - -
38A ASP* 3.1 30.8 + - - +
39A VAL* 5.5 0.2 - - + -
186A ILE* 4.5 14.8 - - + -
189A ARG* 3.5 21.8 - - - +
190A GLU* 3.9 3.8 - - - +
248A PHE* 4.4 18.6 - - + +
260A PHE* 4.6 6.2 - - - +
261A LEU* 1.3 76.3 - - - +
263A ASN* 1.3 67.1 + - - +
265A ALA* 3.4 8.1 + - - +
266A THR* 2.9 29.8 + - - -
102E ARG* 5.6 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.7 18.1 - - - +
259A MET* 3.9 18.9 - - + +
260A PHE* 3.3 16.2 + - - +
262A THR* 1.3 84.2 + - - +
264A ILE* 1.3 65.3 + - - +
266A THR* 3.4 7.6 + - - -
267A ASP* 3.2 21.3 + - - +
17R A 3.1 47.4 + - - +
18R T 3.5 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 3.9 26.2 - - + -
252A TYR* 3.9 22.9 - - + +
254A TYR* 3.6 50.2 - - + -
259A MET* 3.7 33.2 - - + +
260A PHE 3.0 17.3 + - - +
261A LEU* 3.5 12.8 - - + +
263A ASN* 1.3 74.2 - - - +
265A ALA* 1.3 56.5 + - - +
267A ASP* 3.0 3.8 + - - +
268A TYR* 2.7 32.9 + - + +
286A PHE* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.5 29.8 - - + -
187A PHE* 3.7 29.2 - - + -
190A GLU* 4.0 4.9 - - + -
261A LEU* 2.9 18.9 + - + +
262A THR 3.6 2.9 - - - +
264A ILE* 1.3 77.6 - - - +
266A THR* 1.3 59.6 + - - +
268A TYR* 3.9 2.6 - - - +
269A THR* 2.7 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.8 15.5 - - + +
190A GLU* 3.0 32.0 + - - +
193A GLN* 5.0 2.2 - - - +
262A THR 2.9 17.5 + - - -
263A ASN* 3.5 10.1 - - - -
264A ILE 3.1 0.2 - - - -
265A ALA* 1.3 77.2 - - - +
267A ASP* 1.3 65.1 + - - +
269A THR* 3.8 1.4 - - - -
270A LYS* 3.0 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 2.7 36.3 + - + -
255A LYS* 3.5 10.7 + - - +
259A MET* 5.2 6.1 - - + -
263A ASN 3.2 8.9 + - - +
264A ILE 3.0 6.5 + - - +
266A THR* 1.3 79.0 - - - +
268A TYR* 1.3 64.1 + - - +
270A LYS* 3.3 4.8 + - - -
271A HIS* 3.0 55.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE* 3.9 15.8 - - + +
111A GLN* 3.3 21.3 + - - -
187A PHE* 4.1 9.2 - + - -
217A LEU* 3.7 24.2 - - + -
220A PRO* 3.3 17.7 - - + +
221A PHE* 3.9 21.3 - + + -
254A TYR* 3.6 19.9 + + + +
264A ILE 2.7 22.6 + - - +
265A ALA* 3.9 5.8 - - - +
267A ASP* 1.3 74.9 + - - +
269A THR* 1.3 65.2 + - - +
271A HIS 3.3 0.2 + - - -
272A VAL* 3.0 44.9 + - + +
283A VAL* 4.7 0.2 - - - +
284A PRO* 3.3 38.2 + - + +
286A PHE* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE* 3.4 23.2 - - - -
190A GLU* 3.7 16.3 - - + +
191A LEU* 3.8 22.7 - - + +
194A THR* 4.0 15.3 - - - +
217A LEU* 3.7 25.4 - - + +
265A ALA 2.7 21.2 + - - -
266A THR 3.8 2.9 - - - -
268A TYR* 1.3 77.2 - - - +
270A LYS* 1.3 64.5 + - - +
272A VAL* 3.3 2.4 + - - +
273A VAL* 3.0 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 4.0 7.1 - - - +
190A GLU* 5.1 0.8 + - - -
193A GLN* 2.5 30.1 + - - +
194A THR* 3.7 28.7 + - + +
266A THR* 3.0 37.2 + - + +
267A ASP* 3.3 6.3 + - - +
269A THR* 1.3 77.2 - - - +
271A HIS* 1.3 61.7 + - + +
273A VAL* 3.4 7.3 + - - +
274A LYS* 3.0 33.4 + - + +
33Q C 3.5 31.6 - - - +
34Q T 3.0 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LYS* 4.1 15.4 + - - -
267A ASP* 3.0 52.9 + - - +
270A LYS* 1.3 78.6 - - + +
272A VAL* 1.3 66.5 + - - +
274A LYS* 3.0 15.9 + - + +
275A VAL* 2.9 26.2 + - - +
280A GLU* 2.7 33.3 + - - +
284A PRO* 3.8 22.4 - - + -
32Q A 5.8 5.1 + - - -
33Q C 5.3 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 3.9 15.7 - - + +
108A ILE* 4.3 7.4 - - + -
217A LEU* 3.8 26.5 - - + -
268A TYR* 3.0 45.1 + - + +
269A THR* 3.6 8.7 - - - +
271A HIS* 1.3 74.9 - - - +
273A VAL* 1.3 59.6 + - + +
275A VAL* 3.2 6.5 + - - +
276A LEU* 2.9 43.5 + - + +
283A VAL* 5.1 4.5 - - + -
284A PRO* 3.9 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 3.6 31.9 - - - +
96A TRP* 4.5 6.3 - - + -
191A LEU* 4.2 17.5 - - + -
194A THR* 4.1 19.3 - - + -
196A CYS* 3.9 18.8 - - - -
269A THR* 3.0 19.1 + - + +
270A LYS 3.5 8.5 - - - +
272A VAL* 1.3 80.9 - - + +
274A LYS* 1.3 58.2 + - + +
276A LEU* 3.2 9.5 + - + +
277A ASN* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS* 3.0 19.3 + - + +
271A HIS* 3.0 21.2 + - + +
273A VAL* 1.3 74.9 - - + +
275A VAL* 1.3 61.6 + - - +
277A ASN* 3.2 9.1 + - - +
278A GLN 3.1 4.5 + - - -
279A GLU* 2.9 55.9 + - + +
280A GLU* 3.6 32.1 - - + +
33Q C 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 3.1 39.9 + - - +
104A VAL* 3.6 21.8 - - + -
271A HIS 2.9 17.3 + - - +
272A VAL* 3.6 8.5 - - - +
274A LYS* 1.3 73.9 - - - +
276A LEU* 1.3 65.1 + - - +
278A GLN 3.0 8.8 + - - -
280A GLU* 3.4 26.7 - - + +
282A GLY 3.5 33.2 - - - +
283A VAL* 4.1 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.3 61.4 - - + +
100A ARG* 3.7 16.9 - - + +
101A LYS* 4.0 19.3 - - + +
104A VAL* 3.9 24.0 - - + -
202A LEU* 3.9 26.7 - - + -
213A LEU* 5.4 2.5 - - + -
217A LEU* 5.6 0.7 - - + -
272A VAL* 2.9 35.1 + - + +
273A VAL* 3.2 6.5 + - + +
275A VAL* 1.3 76.6 - - - +
277A ASN* 1.3 59.3 + - - +
278A GLN* 3.2 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 3.1 34.1 + - - +
92A ARG* 3.6 24.2 + - - +
96A TRP* 2.8 30.3 + - - +
273A VAL* 2.8 26.2 + - - +
274A LYS* 3.5 6.4 - - - +
275A VAL 3.2 0.4 - - - -
276A LEU* 1.3 74.3 - - - +
278A GLN* 1.3 68.5 + - - +
279A GLU* 3.3 31.2 + - + +
----------------------------------------------------------
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