Contacts of the helix formed by residues 310 - 325 (chain A) in PDB entry 4OG2
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 GLY 310 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 3.3 37.4 + - - -
309A THR* 1.3 78.9 - - - +
311A GLU* 1.3 66.4 + - - -
312A ILE* 3.2 4.5 - - - -
313A ASN* 3.0 14.0 + - - +
314A LYS* 3.0 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR 3.4 3.7 + - - -
310A GLY* 1.3 70.8 - - - -
312A ILE* 1.3 62.5 + - - +
314A LYS* 3.2 14.5 + - - +
315A ALA* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.7 36.3 - - + +
85A PHE* 4.3 1.3 - - + -
310A GLY* 5.0 2.5 - - - +
311A GLU* 1.3 76.2 - - - +
313A ASN* 1.3 64.1 + - + +
315A ALA* 3.3 4.3 + - - +
316A PHE* 2.8 28.1 + - - +
336A PHE* 3.7 19.3 - - + -
340A GLN* 3.6 32.5 - - - +
344A GLU* 5.1 1.1 - - - +
377A ASN* 3.2 22.7 - - + +
378A THR 3.4 22.2 - - - +
379A PRO* 3.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 2.6 26.5 + - - -
305A SER 3.1 24.9 + - - -
306A PRO 3.4 10.2 + - - -
308A TYR* 2.8 40.6 + - + +
310A GLY 3.0 9.0 + - - +
312A ILE* 1.3 78.6 - - - +
314A LYS* 1.3 57.4 - - - +
316A PHE* 3.6 3.3 - - - -
317A ARG* 2.6 39.1 + - - +
379A PRO* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR 4.8 2.5 - - - +
309A THR* 3.3 38.4 - - - +
310A GLY 3.0 15.6 + - - +
311A GLU* 3.3 13.5 - - - +
313A ASN* 1.3 76.7 - - - +
315A ALA* 1.3 57.1 + - - +
317A ARG* 3.8 8.2 - - - +
318A GLN* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 4.0 27.1 - - + +
311A GLU 3.1 12.7 + - - +
312A ILE* 3.7 8.1 - - - +
314A LYS* 1.3 74.1 - - - +
316A PHE* 1.3 64.5 + - - +
318A GLN* 3.4 4.6 + - - +
319A ALA* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 4.7 2.5 - - - -
80A ILE* 3.8 24.9 - - + -
84A TYR* 5.5 2.1 - - - -
304A TYR* 3.6 8.1 - - - -
312A ILE* 2.8 21.7 + - - +
313A ASN* 3.6 16.4 - - - +
315A ALA* 1.3 73.8 - - - +
317A ARG* 1.3 58.6 + - - +
319A ALA* 3.3 6.3 + - - +
320A TYR* 2.9 30.2 + + - +
328A PRO* 3.5 29.4 - - + -
332A SER* 3.8 8.7 - - - -
333A ALA* 3.6 33.9 - - + -
336A PHE* 3.5 42.4 - + + -
379A PRO* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 4.5 2.2 - - - +
306A PRO* 3.2 28.5 + - - +
307A GLU* 4.1 24.2 + - - +
313A ASN 2.6 23.0 + - - +
314A LYS* 3.8 7.4 - - - +
316A PHE* 1.3 72.7 - - - +
318A GLN* 1.3 59.4 + - - +
320A TYR* 3.1 1.0 + - - +
321A VAL* 2.8 39.9 + - + +
327A GLU* 2.9 42.6 + - - +
328A PRO* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS 2.9 18.8 + - - +
315A ALA* 3.9 4.9 - - - +
316A PHE 3.3 0.2 - - - -
317A ARG* 1.3 76.4 - - - +
319A ALA* 1.3 63.4 + - - +
321A VAL* 4.7 9.4 - - - +
322A ASP* 2.9 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 4.3 21.2 - - + +
315A ALA 3.0 17.7 + - - +
316A PHE* 3.6 4.5 - - - +
318A GLN* 1.3 76.1 - - - +
320A TYR* 1.3 63.6 + - - +
322A ASP* 4.0 4.7 - - - +
323A GLN* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 5.7 1.6 - - - +
76A ALA* 4.7 5.9 - - + +
80A ILE* 3.6 27.5 - - + +
316A PHE* 2.9 19.8 + + + +
317A ARG 3.6 3.4 - - - +
319A ALA* 1.3 78.0 - - - +
321A VAL* 1.3 57.2 + - - +
323A GLN 3.1 1.9 + - - -
324A TYR* 2.8 65.2 + + + +
326A LYS* 3.2 40.8 - - + -
327A GLU 3.5 10.3 - - - -
328A PRO* 3.5 25.6 - - + -
329A PRO* 3.2 28.0 - - + +
332A SER* 3.7 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 2.8 30.8 + - + +
318A GLN* 4.1 10.8 - - - +
320A TYR* 1.3 71.2 - - - +
322A ASP* 1.3 64.9 + - - +
325A LYS* 2.9 30.7 + - - +
326A LYS 3.4 29.6 - - - +
327A GLU* 3.9 23.1 - - - +
328A PRO* 4.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLN* 2.9 51.0 + - - +
319A ALA* 4.0 5.6 - - - +
321A VAL* 1.3 78.7 - - - +
323A GLN* 1.3 57.8 + - - +
325A LYS* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 4.7 10.0 - - - +
319A ALA 3.3 13.9 + - - +
320A TYR 3.1 3.7 + - - +
322A ASP* 1.3 81.9 - - - +
324A TYR* 1.3 102.9 + - + +
325A LYS* 3.5 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA* 3.6 27.7 + - + +
79A LYS* 6.0 1.9 - - - +
80A ILE* 4.2 8.0 - - + +
320A TYR* 2.8 68.5 + + + +
323A GLN* 1.3 110.4 + - + +
325A LYS* 1.3 74.3 + - - +
326A LYS* 3.2 13.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 2.9 20.5 + - - +
322A ASP* 2.8 26.5 + - - +
323A GLN 3.9 9.4 - - - +
324A TYR* 1.3 81.1 - - - +
326A LYS* 1.3 59.0 + - - +
----------------------------------------------------------
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