Contacts of the helix formed by residues 258 - 277 (chain A) in PDB entry 4LEY
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 SER 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 2.8 24.9 + - - +
253A GLU* 3.6 23.2 - - - +
256A VAL 3.6 1.4 + - - -
257A LEU* 1.3 71.8 - - - +
259A ALA* 1.3 61.7 + - - +
260A THR* 3.4 3.5 + - - -
261A LYS* 3.4 26.0 + - - +
262A MET* 3.4 21.8 + - - +
360A GLY 3.2 15.8 + - - -
361A GLU* 4.1 8.2 + - - -
363A TRP* 4.3 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU 3.7 4.4 + - - -
258A SER* 1.3 71.9 - - - +
260A THR* 1.3 59.8 + - - +
262A MET* 3.5 2.0 + - - +
263A LEU* 2.9 32.7 + - - +
349A PRO* 3.9 29.7 - - + +
351A ASN* 5.8 1.3 - - - +
359A GLN 5.7 0.2 - - - +
360A GLY 2.9 12.4 + - - +
361A GLU* 4.1 0.8 - - - +
362A THR 4.2 9.9 - - - +
363A TRP* 3.6 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER* 4.0 3.8 - - - -
259A ALA* 1.3 75.0 - - - +
261A LYS* 1.3 63.4 + - + +
263A LEU* 3.5 5.8 + - - +
264A SER* 2.9 39.8 + - - +
351A ASN* 4.2 16.5 + - - -
353A LYS* 4.8 10.4 + - - +
360A GLY* 3.1 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A HIS 3.6 20.2 + - - +
251A PHE* 4.0 23.1 - - + +
252A LEU 3.1 23.2 + - - -
253A GLU* 3.9 20.7 - - + +
258A SER* 3.4 15.0 + - - +
260A THR* 1.3 75.7 - - + +
262A MET* 1.3 67.4 + - - +
264A SER* 3.0 7.2 + - - -
265A LYS* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 3.5 20.5 - - + -
218A LEU* 4.2 10.3 - - + -
248A LEU* 3.6 38.4 - - + -
251A PHE* 3.6 28.0 - - + -
257A LEU* 4.2 12.1 - - - -
258A SER 3.4 13.4 + - - +
259A ALA* 3.6 4.7 - - - +
261A LYS* 1.3 77.9 - - - +
263A LEU* 1.3 58.2 + - - +
265A LYS* 3.3 0.7 + - - +
266A PHE* 2.9 28.9 + - - +
310A LEU* 4.0 12.6 - - + -
312A LEU* 3.7 18.4 - - + -
363A TRP* 3.7 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA 2.9 20.0 + - - +
260A THR* 3.8 6.1 - - - +
262A MET* 1.3 76.9 - - - +
264A SER* 1.3 56.6 + - - +
266A PHE* 3.4 6.1 - - + +
267A ARG* 2.9 32.9 + - + +
287A GLU* 4.0 13.2 - - + +
291A SER 4.3 6.5 - - - +
292A PRO 3.9 22.4 - - - +
293A ALA 4.8 4.0 - - - +
294A VAL* 4.6 17.3 - - + -
310A LEU* 4.0 16.3 - - + +
349A PRO* 4.2 17.9 - - + -
351A ASN* 3.9 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A THR* 2.9 26.1 + - - +
261A LYS* 3.0 7.8 + - - -
263A LEU* 1.3 75.4 - - - +
265A LYS* 1.3 60.0 + - - +
267A ARG* 3.4 8.8 + - - +
268A LYS* 2.9 27.4 + - - +
287A GLU* 5.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 2.3 34.0 + - + +
189A PHE* 4.1 10.3 - - + -
251A PHE* 3.7 33.1 - - + -
261A LYS 2.9 9.3 + - - +
262A MET 3.7 2.0 - - - +
264A SER* 1.3 72.7 - - - +
266A PHE* 1.3 66.6 + - - +
268A LYS* 3.0 20.7 + - + +
269A ILE* 3.0 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A MET* 3.7 25.8 - - + -
189A PHE* 3.8 31.1 - + + -
192A VAL* 5.5 0.7 - - + -
216A PHE* 3.8 33.9 - + + -
262A MET 2.9 18.6 + - - +
263A LEU* 3.4 10.8 - - + +
265A LYS* 1.3 75.6 - - - +
267A ARG* 1.3 56.4 + - - +
269A ILE* 3.3 3.9 + - - +
270A ILE* 3.0 48.7 + - + +
294A VAL* 3.7 15.9 - - + -
308A ILE* 3.8 24.7 - - + -
310A LEU* 3.9 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 2.9 22.0 + - + +
264A SER* 3.5 8.7 - - - +
266A PHE* 1.3 77.4 - - - +
268A LYS* 1.3 58.2 + - - +
270A ILE* 3.5 3.7 + - - +
271A LYS* 2.9 55.7 + - + +
284A VAL* 4.0 10.5 - - - +
285A GLU 2.2 33.3 + - - -
286A LYS* 3.4 1.8 - - - +
287A GLU* 3.2 48.1 + - - +
293A ALA 4.0 7.1 + - - -
294A VAL* 4.0 40.9 - - + +
295A THR 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A SER 2.9 14.8 + - - +
265A LYS* 3.3 24.5 - - + +
267A ARG* 1.3 76.6 - - - +
269A ILE* 1.3 58.5 + - + +
271A LYS* 3.3 12.2 + - + +
272A GLU* 2.7 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG* 3.4 52.4 - - + +
182A MET* 3.9 17.7 - - + -
187A SER* 4.4 11.4 - - - -
188A GLU* 5.3 1.3 - - + +
189A PHE* 4.0 28.5 - - + -
265A LYS* 3.0 31.0 + - + +
266A PHE 3.7 5.8 - - - +
268A LYS* 1.3 73.2 - - + +
270A ILE* 1.3 65.3 + - - +
272A GLU* 3.4 8.8 + - - +
273A GLU* 2.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 4.1 17.9 - - + -
182A MET* 3.6 17.0 - - + -
216A PHE* 5.6 0.2 - - + -
266A PHE* 3.0 49.1 + - + +
267A ARG 3.8 4.0 - - - +
269A ILE* 1.3 76.7 - - - +
271A LYS* 1.3 57.3 + - - +
273A GLU* 3.8 1.0 - - - +
274A VAL* 2.9 35.4 + - + +
284A VAL* 4.8 2.0 - - + -
294A VAL* 3.7 25.8 - - + -
296A LEU* 3.8 26.2 - - + -
308A ILE* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 2.9 50.0 + - + +
268A LYS* 3.5 9.0 - - + +
270A ILE* 1.3 74.5 - - - +
272A GLU* 1.3 66.1 + - + +
274A VAL* 3.2 3.1 + - - +
275A LYS* 3.0 34.4 + - + +
284A VAL* 3.9 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG* 3.9 20.7 + - - +
268A LYS* 2.7 53.4 + - + +
269A ILE* 3.6 6.7 - - - +
271A LYS* 1.3 77.9 - - + +
273A GLU* 1.3 61.3 - - - +
275A LYS* 3.4 26.4 - - + +
276A GLU* 3.7 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 2.7 48.6 + - + +
178A LEU* 4.0 15.3 - - + -
181A ARG* 3.4 45.8 + - + +
185A ARG* 5.7 0.3 + - - -
269A ILE 2.9 17.8 + - - +
270A ILE 3.9 2.5 - - - +
272A GLU* 1.3 73.2 - - - +
274A VAL* 1.3 64.5 + - - +
276A GLU* 3.0 24.3 + - - +
277A ILE* 3.5 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 4.1 12.1 - - + -
270A ILE* 2.9 35.0 + - + +
271A LYS 3.2 4.7 + - - +
273A GLU* 1.3 75.6 - - - +
275A LYS* 1.3 64.2 + - + +
276A GLU 3.2 0.9 + - - -
277A ILE* 3.2 31.5 + - + +
282A VAL* 3.4 39.0 - - + +
283A SER* 4.4 1.8 - - - -
284A VAL* 4.1 20.0 - - + -
296A LEU* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS* 3.0 24.6 + - - +
272A GLU* 3.4 18.9 - - + +
273A GLU 3.2 0.2 - - - -
274A VAL* 1.3 78.7 - - + +
276A GLU* 1.3 67.1 + - - +
277A ILE 3.7 2.1 + - - +
278A LYS* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 3.5 26.7 + - - +
272A GLU 3.7 14.7 - - - +
273A GLU* 3.0 18.9 + - - +
275A LYS* 1.3 84.7 - - - +
277A ILE* 1.3 64.1 + - - +
278A LYS* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A VAL* 4.0 33.9 - - + +
177A ARG* 3.7 36.1 - - + +
178A LEU* 5.3 2.0 - - + -
273A GLU 3.7 8.5 - - - +
274A VAL* 3.2 23.8 + - + +
275A LYS 4.3 2.1 - - - +
276A GLU* 1.3 75.7 - - - +
278A LYS* 1.3 59.6 + - - +
279A ASP* 3.5 17.9 - - - +
280A ILE* 3.8 34.6 - - + +
282A VAL* 4.0 16.4 - - + +
----------------------------------------------------------
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