Contacts of the helix formed by residues 250 - 273 (chain A) in PDB entry 2Y0N
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 ASN 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 3.6 7.7 - - - -
247A ALA* 3.1 23.6 + - - +
249A LYS* 1.3 74.0 - - - +
251A VAL* 1.3 70.1 + - - +
252A ASP* 3.6 15.5 + - - +
253A LEU* 3.2 25.5 + - + +
254A CYS 3.1 17.8 + - - -
553H VAL 4.2 2.6 + - - -
554H THR* 3.5 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 5.0 6.1 - - + +
217A PHE* 3.7 17.5 - - + -
218A ALA* 3.9 31.0 - - + +
221A ALA* 5.6 2.5 - - + -
249A LYS 3.1 8.5 + - - +
250A ASN* 1.3 74.6 + - - +
252A ASP* 1.3 67.1 + - - +
254A CYS* 3.3 3.3 - - + +
255A LYS* 3.1 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASN* 3.2 15.5 + - - +
251A VAL* 1.3 84.0 - - - +
253A LEU* 1.3 64.2 + - - +
255A LYS* 3.3 28.8 + - - +
256A GLU* 3.3 18.5 + - - +
554H THR 4.9 6.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
247A ALA* 3.5 35.2 - - + -
250A ASN* 3.2 20.7 + - + +
252A ASP* 1.3 76.3 - - - +
254A CYS* 1.3 65.1 + - - +
256A GLU* 3.4 7.9 + - - +
257A MET* 3.3 17.5 + - - +
479A ALA* 4.5 6.7 - - + -
483A HIS* 3.7 15.1 + - + +
553H VAL* 4.0 12.3 - - + +
554H THR* 3.5 28.0 + - - +
555H SER* 3.7 7.2 - - - +
556H PHE* 3.6 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TYR* 3.5 36.3 - - - -
214A VAL* 4.5 9.2 - - - -
217A PHE* 3.5 42.6 - - + -
250A ASN 3.1 5.3 + - - -
251A VAL* 3.3 11.4 - - - +
253A LEU* 1.3 75.4 - - - +
255A LYS* 1.3 64.2 + - - +
257A MET* 2.9 15.0 + - - +
258A VAL* 3.0 20.2 + - - +
483A HIS* 3.8 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 4.1 27.6 - - + -
251A VAL* 3.1 26.8 + - - +
252A ASP* 3.3 22.4 + - - +
254A CYS* 1.3 76.8 - - - +
256A GLU* 1.3 61.8 + - - +
258A VAL* 3.3 9.7 + - - +
259A ASP* 3.1 24.8 + - - +
441C PHE* 3.7 18.2 - - + +
442C ASP* 3.5 34.9 + - - +
443C GLN* 3.8 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASP* 3.3 13.0 + - - +
253A LEU* 3.6 11.5 - - - +
254A CYS 3.2 0.6 - - - -
255A LYS* 1.3 74.3 - - + +
257A MET* 1.3 67.6 + - - +
259A ASP* 3.3 5.8 + - - +
260A GLY* 2.8 21.7 + - - -
443C GLN* 5.3 5.6 - - - +
577E PHE* 4.4 4.5 + - - -
554H THR 4.1 2.1 - - - +
555H SER* 2.7 29.5 + - - -
556H PHE* 3.0 36.2 + - + -
557H PHE* 3.5 32.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TYR* 4.3 16.6 - - + -
253A LEU 3.3 8.4 + - - +
254A CYS* 2.9 9.3 + - - +
256A GLU* 1.3 79.6 - - - +
258A VAL* 1.3 83.0 + - + +
260A GLY 3.1 1.9 + - - -
261A LEU* 2.8 50.0 + - + +
480A LEU* 4.3 8.5 - - + -
483A HIS* 3.5 37.9 - - + +
484A PHE* 3.5 35.4 - - + -
487A PHE* 4.5 9.0 - - + -
577E PHE* 3.2 16.9 - - + -
556H PHE* 4.3 3.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 3.2 52.6 - - + +
213A TYR* 4.3 5.8 - - + -
214A VAL* 3.7 22.9 - - + -
254A CYS* 3.0 21.0 + - - +
255A LYS* 3.7 5.6 - - - +
257A MET* 1.3 93.9 - - + +
259A ASP* 1.3 63.9 + - - +
261A LEU* 3.2 8.2 + - - +
262A ARG* 3.1 17.7 + - - +
441C PHE* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LYS 3.1 17.3 + - - +
256A GLU* 3.7 5.2 - - - +
258A VAL* 1.3 75.1 - - - +
260A GLY* 1.3 65.3 + - - +
262A ARG* 2.3 44.8 + - - +
263A ILE* 3.1 35.9 + - - +
441C PHE* 4.6 11.8 - - + -
443C GLN* 3.8 27.2 - - - +
557H PHE* 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLU 2.8 13.4 + - - -
257A MET 3.5 4.0 - - - -
259A ASP* 1.3 75.9 - - - +
261A LEU* 1.3 48.4 + - - +
263A ILE* 3.3 4.3 + - - +
264A THR* 2.6 40.4 + - - -
576E ALA* 3.9 6.4 - - - +
577E PHE* 3.4 33.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 6.1 0.2 - - - -
210A LEU* 4.4 18.8 - - + -
257A MET* 2.8 52.3 + - + +
258A VAL* 3.2 10.5 + - - +
260A GLY* 1.3 74.3 - - - +
262A ARG* 1.3 58.0 + - - +
264A THR* 3.8 2.4 - - - -
265A PHE* 2.8 31.6 + - - +
456A LEU* 4.3 7.5 - - + +
459A LEU* 3.9 24.2 - - + +
460A PHE* 3.6 35.0 - - + -
463A LEU* 4.8 5.4 - - + -
484A PHE* 4.4 6.7 - - + -
487A PHE* 4.7 4.0 - - + -
577E PHE* 3.5 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 5.1 2.5 - - + -
207A ILE* 3.8 23.1 - - + +
210A LEU* 3.8 20.9 - - + -
258A VAL 3.1 7.1 + - - +
259A ASP* 2.3 43.2 + - - +
261A LEU* 1.3 74.8 - - - +
263A ILE* 1.3 79.1 + - - +
265A PHE* 4.4 2.7 - - - -
266A ASP* 3.0 47.8 + - - +
448A SER* 3.2 16.7 + - - +
449A TYR* 5.6 3.2 - - - -
440C GLU* 4.8 12.9 + - - -
441C PHE* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 3.1 36.9 + - - +
260A GLY* 3.7 7.4 - - - +
262A ARG* 1.3 94.7 - - - +
264A THR* 1.3 66.5 + - - +
266A ASP* 3.3 8.7 + - + +
267A TYR* 3.2 21.0 + - + +
574E VAL* 3.9 27.4 - - + -
575E VAL 3.7 21.8 - - - +
576E ALA* 4.4 3.6 - - + -
581E LEU* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLY 2.6 29.4 + - - -
261A LEU* 3.8 5.6 - - - -
263A ILE* 1.3 75.0 - - - +
265A PHE* 1.3 53.4 + - - +
267A TYR* 3.4 2.7 + - + +
268A THR* 2.3 44.9 + - - +
459A LEU* 4.3 15.0 - - + -
463A LEU* 4.7 6.5 - - + -
466A ILE* 4.7 15.5 - - + -
470A MET* 5.2 1.6 - - + -
576E ALA* 3.4 7.6 - - - +
577E PHE* 3.2 23.6 - - + -
581E LEU* 4.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 3.4 34.1 - - + -
261A LEU 2.8 18.8 + - - +
262A ARG* 4.0 4.7 - - - +
264A THR* 1.3 73.8 - - - +
266A ASP* 1.3 67.2 + - - +
268A THR* 3.0 4.1 + - - -
269A LEU* 2.9 56.0 + - + +
273A LEU* 3.9 15.0 - - + -
447A PRO* 3.7 31.6 - - + -
448A SER* 4.0 11.9 - - - -
451A TYR* 3.7 8.7 - - + -
455A HIS* 3.7 25.6 - - + -
456A LEU* 4.3 11.0 - - + -
459A LEU* 4.1 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ARG* 3.0 34.3 + - - +
263A ILE* 3.6 7.7 - - - +
265A PHE* 1.3 75.6 - - - +
267A TYR* 1.3 60.2 + - - +
270A PRO* 3.8 7.1 - - - +
446A PRO* 3.3 16.6 - - + +
447A PRO* 3.1 32.6 - - + +
448A SER* 2.8 44.3 + - - -
449A TYR* 6.1 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE 3.2 4.4 + - - +
264A THR 3.8 2.0 - - - +
265A PHE 3.1 0.6 - - - -
266A ASP* 1.3 79.7 - - - +
268A THR* 1.3 70.8 + - - +
270A PRO* 3.6 9.7 - - - +
271A LEU* 3.6 32.0 - - + +
466A ILE* 6.6 0.2 - - + -
581E LEU* 3.7 35.0 - - + -
582E PRO* 3.3 28.1 + - + -
583E LYS* 4.1 2.8 - - - -
584E LEU* 3.7 27.5 + - + -
567F LEU* 4.4 12.7 - - + +
572G LEU* 3.6 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A THR* 2.3 39.2 + - - +
265A PHE 3.9 1.8 - - - -
267A TYR* 1.3 82.2 - - - +
269A LEU* 1.3 66.6 + - - +
271A LEU* 2.8 16.8 + - - -
272A VAL* 2.9 49.2 + - + -
273A LEU* 3.8 12.6 - - + -
459A LEU* 3.9 16.9 - - + +
466A ILE* 4.1 13.2 - - + +
584E LEU* 4.3 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 2.9 47.0 + - + +
268A THR* 1.3 78.4 - - - +
270A PRO* 1.3 65.8 - - + +
271A LEU 3.0 3.3 + - - -
273A LEU* 3.2 30.8 + - + +
274A LEU* 3.7 16.8 + - + +
282A TYR* 3.8 20.0 - - + -
447A PRO* 3.9 12.1 - - + -
451A TYR* 3.5 35.0 - - + +
455A HIS* 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP 3.8 11.7 - - - +
267A TYR 3.6 12.3 - - - +
268A THR 3.5 3.4 - - - -
269A LEU* 1.3 99.4 - - + +
271A LEU* 1.3 67.2 + - + +
274A LEU* 4.5 16.4 - - + +
279A GLN* 5.0 6.2 + - - +
282A TYR* 3.3 42.8 - - + +
447A PRO* 4.5 2.2 - - + -
586E PRO* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A TYR* 3.6 50.0 - - + +
268A THR* 2.8 8.9 + - - +
270A PRO* 1.3 89.7 - - + +
272A VAL* 1.3 63.3 + - + +
273A LEU 3.8 0.2 - - - -
274A LEU* 5.3 1.5 + - - -
584E LEU* 3.8 24.2 - - + +
586E PRO* 3.4 32.9 - - + +
587E GLN 3.0 27.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
268A THR* 2.9 41.2 + - + -
271A LEU* 1.3 81.1 - - + +
273A LEU* 1.3 62.8 + - + +
274A LEU 3.7 1.6 - - - -
462A LYS* 3.5 42.3 - - + +
465A GLU* 5.0 2.9 - - - +
466A ILE* 4.9 0.7 - - + -
584E LEU* 4.3 19.5 - - + -
585E ALA 4.9 4.3 - - - +
587E GLN* 3.6 25.9 - - + +
589E PHE* 3.6 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 3.9 20.9 - - + -
268A THR* 3.8 18.4 - - + -
269A LEU* 3.2 32.6 + - + +
272A VAL* 1.3 80.7 - - + +
274A LEU* 1.3 62.4 + - - +
455A HIS* 4.2 3.6 - - + +
458A ARG* 3.2 37.3 + - + +
459A LEU* 3.7 42.4 - - + +
462A LYS* 3.7 31.0 - - + -
589E PHE* 3.7 11.3 - - + +
----------------------------------------------------------
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