Contacts of the helix formed by residues 303 - 317 (chain A) in PDB entry 5Y7G
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 ARG 303 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE 6.3 0.2 - - - -
276A ASP* 2.5 56.2 + - - +
279A GLN* 3.8 21.6 + - - +
280A ARG* 5.6 0.8 - - - +
298A LEU* 3.1 31.5 + - + +
301A GLY* 3.5 13.0 - - - +
302A GLU* 1.3 76.1 - - - +
304A PHE* 1.3 65.1 + - - +
305A ALA* 3.5 2.0 - - - +
306A GLU* 2.7 47.1 + - + +
307A ALA* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLU* 3.9 30.3 - - + -
302A GLU* 3.0 50.2 + - + -
303A ARG* 1.3 73.7 - - - +
305A ALA* 1.3 66.8 + - - +
307A ALA* 3.3 6.0 + - - +
308A HIS* 2.9 26.0 + - - +
334A LEU* 4.2 10.5 - - + +
337A LYS* 3.6 38.1 - - + -
338A LEU* 3.6 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ARG* 4.5 0.6 - - + +
304A PHE* 1.3 80.4 - - - +
306A GLU* 1.3 67.1 + - + +
308A HIS* 3.3 9.0 + - - +
309A ALA* 3.3 13.9 + - - +
338A LEU* 4.2 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLN* 5.0 3.2 + - - -
283A ARG* 4.9 6.9 + - - +
298A LEU* 3.5 20.3 - - + +
303A ARG* 2.7 58.7 + - - +
305A ALA* 1.3 75.3 - - + +
307A ALA* 1.3 67.3 + - - +
309A ALA* 3.2 7.5 + - - +
310A LEU* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 4.0 16.8 - - + +
298A LEU* 3.7 19.4 - - + +
299A GLU* 4.2 3.6 - - - +
303A ARG 3.4 18.1 + - - +
304A PHE* 3.3 5.6 + - - +
306A GLU* 1.3 79.4 - - - +
308A HIS* 1.3 63.6 + - - +
310A LEU* 3.0 3.4 + - - +
311A ALA* 2.9 22.0 + - - +
334A LEU* 3.6 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE 2.9 8.7 + - - +
305A ALA 3.3 2.4 + - - +
307A ALA* 1.3 75.8 - - - +
309A ALA* 1.3 60.9 + - - +
311A ALA* 3.4 2.6 + - - +
312A ARG* 3.0 52.1 + - + +
331A LEU* 3.8 11.0 - - + +
334A LEU* 3.6 15.4 - - + +
335A GLN* 3.5 38.8 + - + +
338A LEU* 3.6 28.3 - - + +
340A LEU* 3.2 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA 3.3 9.3 + - - +
306A GLU* 3.2 10.6 + - - +
308A HIS* 1.3 80.6 + - - +
310A LEU* 1.3 66.6 + - - +
312A ARG* 3.4 6.2 + - - +
313A GLU* 3.0 23.4 + - - +
340B LEU* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 3.9 45.8 - - - +
291A ARG* 4.4 17.3 - - + +
294A ALA* 4.2 14.1 - - + -
295A ILE* 3.5 28.0 - - + +
298A LEU* 4.5 5.2 - - + -
306A GLU 2.9 12.4 + - - +
307A ALA* 3.6 7.9 - - - +
309A ALA* 1.3 77.8 - - - +
311A ALA* 1.3 56.6 + - - +
313A GLU* 3.0 25.3 + - + +
314A ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 3.6 21.0 - - + +
307A ALA 2.9 14.1 + - - +
308A HIS 3.7 1.3 - - - +
310A LEU* 1.3 77.3 - - - +
312A ARG* 1.3 57.3 + - - +
314A ALA* 3.1 2.6 + - - +
315A SER* 2.9 30.5 + - - -
327A LEU* 4.1 12.1 - - + +
330A LEU* 5.3 0.2 - - + -
331A LEU* 3.6 30.1 - - + +
334A LEU* 4.3 11.2 - - + -
----------------------------------------------------------
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 HIS* 3.0 43.2 + - + +
309A ALA* 3.8 6.3 - - - +
311A ALA* 1.3 75.6 - - - +
313A GLU* 1.3 63.9 + - - +
315A SER* 3.2 21.7 + - - -
316A CYS* 2.9 26.1 - - - -
331A LEU* 3.4 27.4 - - - +
335A GLN* 4.7 3.8 - - - +
343A GLN* 4.3 14.8 - - - +
338B LEU 4.2 13.5 + - - +
339B GLY* 4.3 28.9 + - - +
340B LEU* 5.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 4.2 12.2 + - - +
309A ALA 3.0 14.5 + - - +
310A LEU* 3.4 25.0 - - + +
312A ARG* 1.3 78.1 - - - +
314A ALA* 1.3 60.1 + - - +
316A CYS* 3.3 21.5 - - - +
317A ALA* 4.0 2.4 + - - +
305B ALA* 3.2 34.0 - - + +
338B LEU* 4.8 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 3.3 43.0 - - - +
295A ILE* 4.6 0.9 - - + -
310A LEU 2.9 12.0 + - - +
311A ALA* 3.1 8.5 + - - +
313A GLU* 1.3 71.3 - - - +
315A SER* 1.3 59.2 + - - +
316A CYS 2.9 11.1 + - - -
317A ALA 3.1 11.6 + - - -
318A PRO* 3.2 17.2 - - - +
327A LEU* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA 2.9 13.5 + - - -
312A ARG* 3.2 30.5 + - - -
313A GLU 3.4 0.2 - - - -
314A ALA* 1.3 74.7 - - - +
316A CYS* 1.3 60.2 + - - +
317A ALA 3.6 0.2 - - - -
318A PRO* 4.0 11.5 - - - +
327A LEU* 4.0 16.8 - - - +
331A LEU* 4.1 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 2.9 30.5 - - - -
313A GLU 3.3 11.0 - - - +
314A ALA 2.9 0.4 + - - -
315A SER* 1.3 81.2 - - - +
317A ALA* 1.3 61.6 + - + +
318A PRO* 4.0 1.9 - - - +
304B PHE* 4.7 12.7 - - + -
337B LYS 3.0 28.7 - - - +
338B LEU* 3.4 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 3.6 17.0 + - - +
313A GLU 4.0 2.7 + - - +
314A ALA 3.1 3.1 + - - -
316A CYS* 1.3 80.3 - - + +
318A PRO* 1.3 69.2 - - - +
319A GLU* 4.7 0.3 - - - -
302B GLU* 3.6 25.1 - - + +
303B ARG* 5.3 0.7 - - - -
304B PHE* 4.4 12.6 - - + +
305B ALA 6.0 0.9 - - - +
----------------------------------------------------------
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