Contacts of the helix formed by residues 280 - 296 (chain A) in PDB entry 1YPN
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 PRO 280 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.9 38.9 - - + +
252A LEU* 4.5 7.4 - - + -
255A GLY* 3.4 28.0 - - - +
256A GLU* 4.4 0.2 - - - -
257A ILE* 4.0 19.5 - - + -
278A GLY 4.0 2.5 - - - +
279A ALA* 1.3 83.0 - - + -
281A GLN* 1.3 75.4 + - + +
282A ASP 3.0 1.6 + - - -
283A ALA* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 5.7 0.9 - - - -
279A ALA* 3.5 17.7 - - - +
280A PRO* 1.3 96.3 - - + +
282A ASP* 1.3 66.1 + - - +
283A ALA 3.3 2.2 + - - -
284A GLU* 5.1 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLY* 5.9 0.7 - - - -
279A ALA* 2.9 28.6 + - - +
281A GLN* 1.3 85.3 + - - +
283A ALA* 1.3 62.9 + - - +
284A GLU 3.4 2.0 - - - -
285A GLN* 3.4 16.5 + - + +
286A MET* 2.9 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.9 17.5 - - + +
229A THR* 4.6 7.4 - - + -
230A ALA* 3.5 32.7 - - + +
257A ILE* 4.8 5.4 - - + -
279A ALA 4.0 0.4 + - - -
280A PRO 3.0 16.7 + - - +
281A GLN 3.3 2.6 + - - -
282A ASP* 1.3 77.5 - - - +
284A GLU* 1.3 63.7 + - - +
286A MET* 3.3 12.9 - - - +
287A GLY 3.1 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 4.4 17.3 - - + +
233A ALA* 3.1 28.4 - - + +
281A GLN 5.1 0.6 + - - -
282A ASP 3.4 0.6 - - - -
283A ALA* 1.3 78.2 - - - +
285A GLN* 1.3 67.2 + - + +
288A ILE* 3.0 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASP* 3.4 19.1 + - + +
284A GLU* 1.3 86.6 + - + +
286A MET* 1.3 61.3 + - - +
288A ILE* 3.2 35.6 + - - +
289A SER* 2.8 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA* 4.7 0.9 - - + -
257A ILE* 3.7 41.5 - - + +
259A LEU* 4.3 15.4 - - + +
276A ARG* 3.7 27.9 - - + +
277A ARG 5.9 0.4 - - - -
278A GLY* 3.7 35.7 - - - +
279A ALA 3.7 10.3 - - - +
282A ASP* 2.9 21.8 + - + +
283A ALA* 3.3 14.4 - - - +
285A GLN* 1.3 77.0 - - - +
287A GLY* 1.3 61.6 + - - +
289A SER* 3.4 6.1 + - - -
290A LEU* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA 3.8 14.8 - - - -
234A MET* 3.2 21.5 - - - +
259A LEU* 3.5 22.4 - - - -
283A ALA 3.1 9.9 + - - -
284A GLU 3.8 3.1 - - - -
286A MET* 1.3 76.8 - - - +
288A ILE* 1.3 63.0 + - - +
290A LEU 3.5 0.5 + - - -
291A ALA* 3.1 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA* 4.0 17.9 - - + +
237A ARG* 4.2 13.9 - - + +
284A GLU* 3.0 30.9 + - + +
285A GLN* 3.2 37.4 + - - +
287A GLY* 1.3 77.5 - - - +
289A SER* 1.3 61.4 + - - +
291A ALA* 3.5 4.9 + - - +
292A GLU* 3.2 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ARG* 3.5 23.8 + - - -
285A GLN* 2.8 23.4 + - - +
286A MET* 3.7 6.4 - - - -
288A ILE* 1.3 76.7 - - - +
290A LEU* 1.3 66.3 + - - +
292A GLU* 3.2 10.8 + - - +
293A GLU* 3.0 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A MET* 4.2 5.2 - - + -
259A LEU* 3.7 34.3 - - + +
261A ALA* 3.7 27.4 - - + -
274A GLY* 3.6 18.8 - - - +
275A GLU* 3.5 30.5 - - - +
276A ARG* 3.7 17.5 - - + +
286A MET 2.9 17.3 + - - +
287A GLY 3.8 4.5 - - - +
289A SER* 1.3 75.5 - - - +
291A ALA* 1.3 63.9 + - - +
293A GLU* 3.0 10.9 + - - +
294A LEU* 3.0 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A MET* 3.4 39.7 - - - +
237A ARG* 3.6 16.8 - - + -
238A LEU* 3.5 11.6 - - + +
287A GLY 3.1 15.7 + - - +
288A ILE 3.6 5.8 - - - +
290A LEU* 1.3 77.5 - - - +
292A GLU* 1.3 56.8 + - - +
294A LEU* 3.3 3.6 + - - +
295A LEU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ARG* 3.2 41.8 + - - +
288A ILE* 3.2 26.5 - - - +
289A SER* 3.2 11.0 + - - +
291A ALA* 1.3 73.4 - - - +
293A GLU* 1.3 64.2 + - - +
295A LEU* 3.2 8.6 + - - +
296A ASN* 3.0 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG 4.7 2.9 - - - +
274A GLY* 4.1 19.9 - - - -
275A GLU 4.8 0.7 + - - -
276A ARG* 3.0 34.8 + - - +
289A SER 3.0 11.5 + - - +
290A LEU* 3.0 12.4 + - + +
292A GLU* 1.3 76.5 - - - +
294A LEU* 1.3 65.6 + - + +
296A ASN* 3.3 7.5 + - - +
297A ASN* 3.1 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A MET* 4.9 6.3 - - - -
238A LEU* 4.9 2.7 - - + -
261A ALA* 4.2 12.6 - - + -
262A LEU* 4.0 14.4 - - - +
263A VAL* 3.8 24.7 - - + -
272A ILE* 3.5 33.9 - - + +
273A ARG 3.8 21.5 - - - +
274A GLY* 4.0 6.7 - - - +
290A LEU* 3.0 21.8 + - + +
291A ALA* 3.6 7.6 - - - +
293A GLU* 1.3 82.2 - - - +
295A LEU* 1.3 63.3 + - - +
297A ASN* 3.0 10.3 + - + +
298A GLY 3.4 0.9 + - - -
299A ALA* 3.0 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ARG* 3.6 43.5 - - + +
238A LEU* 4.0 19.1 - - + -
291A ALA 2.9 18.5 + - - +
292A GLU* 3.2 13.0 + - - +
294A LEU* 1.3 78.3 - - - +
296A ASN* 1.3 64.4 + - - +
297A ASN 3.3 0.3 + - - -
298A GLY* 3.3 8.0 + - - -
299A ALA* 3.9 4.9 - - + -
300A ARG* 3.6 68.6 + - + +
301A GLU* 4.8 1.2 - - - +
303A LEU* 5.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU* 3.0 24.9 + - - +
293A GLU* 3.9 6.6 - - - +
295A LEU* 1.3 79.2 - - - +
297A ASN* 1.3 60.2 + - - +
298A GLY 3.3 1.8 + - - -
300A ARG* 5.2 5.4 + - - -
----------------------------------------------------------
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