Contacts of the helix formed by residues 300 - 314 (chain A) in PDB entry 4O6M
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 THR 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASP 3.1 23.0 + - - +
149A GLY* 4.0 3.7 - - - -
275A ILE* 4.2 2.9 - - + -
297A ILE 5.8 1.1 - - - +
298A PRO* 5.3 0.9 - - + +
299A ILE* 1.3 86.2 + - - +
301A ARG* 1.3 68.5 + - - +
302A ASP* 2.8 16.3 + - - -
303A PHE* 3.0 22.7 + - - +
304A ARG* 3.0 8.8 + - - +
335A ARG* 4.0 22.7 - - - +
411A SO4 3.3 13.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
148A ASP* 3.8 18.5 + - - +
210A HIS* 3.0 36.3 + - - -
211A SER* 5.3 0.2 - - - +
214A ASP* 4.1 11.3 + - - +
239A ASP* 3.6 33.2 + - - +
240A ARG* 3.7 17.5 - - - +
242A SER* 3.3 19.0 - - - -
243A ASP* 2.9 31.2 + - - +
246A ILE* 5.0 0.4 - - - +
300A THR* 1.3 72.2 - - - +
302A ASP* 1.3 63.4 + - - +
304A ARG* 3.2 20.3 + - - +
305A LEU* 3.0 42.7 + - + +
411A SO4 2.7 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASP* 3.6 7.3 + - + +
149A GLY* 3.0 19.0 - - - -
150A TRP 3.3 0.5 + - - -
151A ILE* 2.9 26.2 + - + +
152A ALA* 2.8 42.6 + - + +
156A ASN* 4.4 4.3 - - - +
208A GLN* 5.0 1.0 - - - +
211A SER* 4.2 13.3 + - - +
300A THR* 2.8 26.2 + - - -
301A ARG* 1.3 74.1 - - - +
303A PHE* 1.3 65.2 + - - -
305A LEU* 3.7 1.6 + - - +
306A LEU* 3.2 23.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
149A GLY* 5.0 0.2 - - - -
150A TRP* 4.1 21.8 - + + -
151A ILE* 3.4 34.8 - - + -
298A PRO* 3.4 51.8 - - + +
299A ILE* 4.0 1.6 - - - -
300A THR* 3.0 26.2 + - - +
302A ASP* 1.3 92.9 + - - +
304A ARG* 1.3 64.9 + - - +
306A LEU* 3.3 8.4 + - + +
307A ILE* 2.9 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG* 3.9 1.4 - - - +
243A ASP* 2.9 28.5 + - - -
271A ALA 5.6 0.2 - - - -
272A SER* 3.7 38.6 + - - +
275A ILE* 3.5 14.8 - - - +
299A ILE* 2.9 47.4 + - + +
300A THR 3.0 6.0 + - - +
301A ARG* 3.2 28.7 + - - +
303A PHE* 1.3 77.0 - - - +
305A LEU* 1.3 62.3 + - + +
307A ILE* 3.3 8.5 + - - +
308A ILE* 3.0 32.5 + - + +
324A ILE* 3.9 22.8 - - + +
411A SO4 2.8 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 3.7 27.4 - - + +
208A GLN* 4.0 2.4 - - - +
210A HIS* 3.9 9.4 - - + -
211A SER* 3.5 39.7 - - - +
243A ASP* 4.3 12.6 - - - +
246A ILE* 4.3 16.4 - - + -
301A ARG* 3.0 45.7 + - + +
302A ASP 4.2 0.2 - - - +
304A ARG* 1.3 77.0 - - + +
306A LEU* 1.3 61.5 + - - +
308A ILE* 3.4 12.1 + - + +
309A PHE* 2.9 29.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
151A ILE* 3.8 37.2 - - + -
208A GLN* 3.7 19.2 + - - +
302A ASP 3.2 17.0 + - - +
303A PHE* 3.6 8.7 - - + +
305A LEU* 1.3 79.8 - - - +
307A ILE* 1.3 58.5 + - + +
309A PHE* 3.3 23.2 + - + +
310A ALA* 2.8 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PRO 5.0 2.2 - - - +
299A ILE* 3.8 28.3 - - + -
303A PHE* 2.9 28.6 + - + +
304A ARG* 3.5 5.6 - - - +
305A LEU 3.3 0.2 - - - -
306A LEU* 1.3 74.9 - - + +
308A ILE* 1.3 59.5 + - - +
310A ALA* 3.9 4.2 - - - +
311A CYS* 2.9 38.0 + - - -
320A ALA* 3.9 25.4 - - + +
323A ILE* 3.9 30.1 - - + -
324A ILE* 4.6 3.4 - - + -
327A LEU* 4.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PHE* 3.9 26.7 - - + -
204A GLY* 5.3 0.2 - - - -
207A ILE* 4.3 15.0 - - + -
246A ILE* 3.9 21.3 - - + -
247A VAL* 5.1 7.9 - - + -
250A ILE* 4.3 11.4 - - + -
304A ARG* 3.0 19.7 + - + +
305A LEU* 3.7 21.3 - - + +
307A ILE* 1.3 74.7 - - - +
309A PHE* 1.3 61.3 + - - +
311A CYS* 3.9 0.7 - - - +
312A SER* 2.7 33.8 + - - +
317A PRO* 6.2 0.2 - - + -
320A ALA* 3.8 16.7 - - + +
321A LEU* 6.0 1.6 - - + -
324A ILE* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY* 3.2 34.8 - - - +
205A VAL* 3.9 24.0 - - + -
207A ILE* 5.3 0.2 - - - +
208A GLN* 3.8 24.5 - - + +
305A LEU 2.9 17.7 + - - +
306A LEU* 3.3 24.9 + - + +
308A ILE* 1.3 76.3 - - - +
310A ALA* 1.3 66.9 + - + +
312A SER* 3.2 3.8 + - - -
313A VAL* 3.1 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 2.8 25.1 + - + +
307A ILE* 3.9 5.4 - - - +
309A PHE* 1.3 81.1 - - + +
311A CYS* 1.3 66.4 + - - +
313A VAL* 3.1 26.3 - - - +
314A VAL* 3.8 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 2.9 26.5 + - - +
308A ILE 4.2 0.4 - - - +
310A ALA* 1.3 80.0 - - - +
312A SER* 1.3 61.8 + - - +
314A VAL* 3.4 11.7 + - - +
315A ASN 3.3 3.1 + - - -
316A LEU* 2.8 42.2 + - + +
317A PRO* 4.4 0.2 - - + -
319A LEU* 3.9 23.3 - - - -
320A ALA* 3.6 31.2 - - + -
323A ILE* 4.3 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PHE* 3.4 25.1 - - - -
197A TYR* 3.9 5.0 - - - -
200A THR* 3.5 37.5 - - - +
201A LEU* 4.2 3.2 - - - -
204A GLY* 3.8 9.6 - - - -
308A ILE* 2.7 24.2 + - - +
309A PHE 3.2 4.9 + - - -
311A CYS* 1.3 77.9 - - - +
313A VAL* 1.3 55.4 - - - +
315A ASN* 2.9 18.9 + - - +
316A LEU 4.5 1.3 - - - +
317A PRO* 4.2 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 2.7 26.1 + - - -
201A LEU* 3.6 29.6 - - + +
309A PHE* 3.1 40.3 + - + +
310A ALA* 3.1 24.5 - - - +
312A SER* 1.3 75.7 - - - +
314A VAL* 1.3 67.9 + - + +
315A ASN 3.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 4.4 1.1 - - - -
310A ALA 4.0 7.9 - - - +
311A CYS* 3.4 15.0 - - - +
312A SER 3.2 0.2 - - - -
313A VAL* 1.3 89.5 - - + +
315A ASN* 1.3 68.0 + - - +
316A LEU* 3.3 26.9 + - + +
319A LEU* 6.2 1.3 - - + -
----------------------------------------------------------
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