Contacts of the helix formed by residues 299 - 317 (chain A) in PDB entry 1YH7
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 ASP 299 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA* 3.0 16.1 + - + +
295A LEU* 5.4 0.2 - - - -
297A ARG* 3.2 11.9 - - + -
298A GLY* 1.3 74.8 - - - +
300A TYR* 1.3 62.2 + - - +
301A ARG* 3.2 13.7 + - - +
302A ALA* 3.0 34.2 + - + +
303A PHE* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A SER* 2.7 38.3 + - - -
215A ASP* 3.3 20.0 - - + -
216A PRO* 2.9 28.5 - - + +
218A LEU* 4.9 14.1 - - + -
295A LEU* 4.4 16.4 - - + -
298A GLY* 2.9 39.0 + - - -
299A ASP* 1.3 71.2 + - - +
301A ARG* 1.3 53.6 + - - +
303A PHE* 3.0 9.7 + - + +
304A GLY* 2.6 34.3 + - - -
339A TYR* 4.2 21.6 - + + +
355A LEU* 5.6 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASP* 3.2 9.8 + - - +
300A TYR* 1.3 79.5 - - - +
302A ALA* 1.3 65.2 + - - +
304A GLY* 3.0 1.9 + - - -
305A ARG* 2.9 33.8 + - + +
339A TYR* 3.7 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA* 4.1 10.3 - - + -
299A ASP* 3.0 33.8 + - + +
301A ARG* 1.3 76.6 - - - +
303A PHE* 1.3 63.7 + - - +
305A ARG* 3.0 31.6 + - - +
306A LEU* 2.9 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.4 8.3 - - + -
41A ILE* 5.0 4.3 - - + -
53A LEU* 4.3 20.6 - - + -
291A ALA* 3.3 38.1 - - + -
294A ALA* 4.1 7.1 - - + +
295A LEU* 3.7 32.8 - - + +
299A ASP 3.0 13.6 + - - +
300A TYR* 3.1 13.7 - + - +
302A ALA* 1.3 78.1 - - - +
304A GLY* 1.3 63.9 + - - +
306A LEU* 3.1 10.2 + - - +
307A MET* 2.9 58.9 + - + +
355A LEU* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR 2.6 18.3 + - - -
301A ARG 3.0 2.9 + - - -
303A PHE* 1.3 78.0 - - - +
305A ARG* 1.3 61.2 - - - +
307A MET* 3.0 18.9 + - - +
308A VAL* 3.0 10.0 + - - +
339A TYR* 3.6 28.7 - - - -
340A GLY* 3.5 10.3 - - - -
355A LEU* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 2.9 23.9 + - + +
302A ALA* 3.3 34.7 + - - +
304A GLY* 1.3 76.1 - - - +
306A LEU* 1.3 75.8 + - - +
308A VAL* 2.7 36.8 - - + +
309A GLU* 3.0 16.7 + - + +
339A TYR 4.0 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.4 6.0 - - + +
287A ARG* 3.8 19.9 - - + +
290A GLN* 4.0 14.6 - - + +
291A ALA* 2.9 50.9 - - + +
294A ALA* 4.8 3.8 - - + -
302A ALA* 2.9 22.8 + - + +
303A PHE* 3.4 10.1 - - - +
305A ARG* 1.3 99.6 - - - +
307A MET* 1.3 60.6 + - - +
309A GLU* 2.9 13.9 + - + +
310A SER* 2.8 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.1 41.3 - - + +
41A ILE* 5.1 5.2 - - + -
303A PHE* 2.9 48.8 + - + +
304A GLY* 3.0 11.6 + - - +
306A LEU* 1.3 75.4 - - - +
308A VAL* 1.3 63.6 + - - +
310A SER* 3.1 10.4 + - - -
311A HIS 3.1 8.5 + - - -
340A GLY 4.8 2.0 - - - +
341A SER* 4.1 13.9 - - - +
342A ARG* 3.4 27.5 - - + +
353A VAL* 5.5 6.7 - - + +
355A LEU* 3.1 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLY 3.0 5.9 + - - +
305A ARG* 2.7 32.1 - - + +
307A MET* 1.3 76.4 - - - +
309A GLU* 1.3 68.4 + - + +
311A HIS* 3.1 5.1 + - - +
312A ARG* 3.1 21.5 + - - +
329A VAL* 5.5 1.6 - - + -
333A LEU* 3.1 47.6 - - + -
339A TYR 4.8 0.2 - - - +
340A GLY* 3.6 15.3 - - - -
341A SER 3.7 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ARG* 3.6 22.7 + - - +
305A ARG* 3.0 26.0 + - + +
306A LEU* 2.9 24.3 + - + +
308A VAL* 1.3 86.8 - - + +
310A SER* 1.3 61.4 + - - +
312A ARG* 3.2 12.9 + - - +
313A SER* 3.1 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.4 4.5 - - - -
284A GLU* 2.6 39.4 + - - -
287A ARG* 3.8 8.7 - - - +
306A LEU 2.8 11.5 + - - -
307A MET 3.1 1.5 + - - -
309A GLU* 1.3 75.2 - - - +
311A HIS* 1.3 63.9 + - - +
313A SER* 3.2 4.0 + - - -
314A LEU* 3.0 26.7 + - - +
342A ARG* 3.5 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET 3.1 2.9 + - - +
308A VAL* 3.1 9.9 + - - +
310A SER* 1.3 79.5 - - - +
312A ARG* 1.3 56.0 + - + +
314A LEU* 3.2 8.6 + - - +
315A ARG* 2.6 35.0 + - + +
321A SER* 4.1 5.8 - - - -
325A LEU* 3.0 33.8 - - + +
326A ASP* 2.8 33.6 + - - -
329A VAL* 3.2 37.0 - - + +
330A GLU* 4.6 9.6 + - + +
341A SER 4.0 0.2 - - - +
342A ARG* 3.5 19.9 - - + +
343A MET* 3.5 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL 3.1 11.7 + - - +
309A GLU* 3.2 15.7 + - - +
311A HIS* 1.3 79.6 - - + +
313A SER* 1.3 52.1 + - - +
315A ARG* 2.8 42.7 + - - +
316A ASP* 2.5 58.8 + - - +
330A GLU* 4.9 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A HIS* 2.9 30.6 - - - -
283A GLY* 5.9 0.2 - - - -
284A GLU 5.4 0.2 + - - -
287A ARG* 2.9 36.3 + - - -
309A GLU 3.1 6.1 + - - -
310A SER 3.2 2.2 + - - -
312A ARG* 1.3 75.8 - - - +
314A LEU* 1.3 57.6 + - - +
316A ASP* 3.1 7.6 - - - -
317A ASP* 2.7 38.4 + - - +
318A TYR 3.1 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.7 10.5 - - + -
44A HIS* 3.8 22.4 - - + -
280A HIS* 2.9 38.4 - - + +
310A SER* 3.0 18.3 + - - +
311A HIS* 3.4 7.0 - - - +
313A SER* 1.3 76.5 - - - +
315A ARG* 1.3 61.9 + - - +
318A TYR* 3.9 4.7 - - + -
319A GLU 2.8 24.4 + - - -
320A VAL* 3.1 23.7 + - + -
321A SER* 4.6 0.9 - - - +
342A ARG* 3.7 20.4 - - - +
343A MET* 3.3 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A HIS* 2.6 23.4 + - + +
312A ARG* 2.8 44.0 + - - +
314A LEU* 1.3 77.4 - - - +
316A ASP* 1.4 87.0 + - - +
319A GLU* 3.1 18.9 - - - +
321A SER* 3.0 27.5 + - - +
326A ASP* 3.1 26.8 + - - +
330A GLU* 4.7 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ARG* 3.6 23.3 + - - +
279A ARG* 5.2 3.3 + - - -
312A ARG* 2.5 52.7 + - - +
313A SER* 3.0 11.0 - - - +
315A ARG* 1.4 99.2 + - - +
317A ASP* 1.4 90.0 + - - +
319A GLU* 4.1 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ARG* 3.1 57.5 + - - +
277A ARG* 3.4 12.5 + - - -
279A ARG* 2.9 48.9 + - - +
280A HIS* 3.8 11.8 + - + -
313A SER* 2.7 17.5 + - - +
316A ASP* 1.4 90.2 + - - +
318A TYR* 1.3 62.2 + - - +
----------------------------------------------------------
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