Contacts of the helix formed by residues 300 - 315 (chain A) in PDB entry 3BMW
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
----------------------------------------------------------
293A VAL* 3.4 13.5 - - - +
299A ASP* 1.3 88.0 + - - +
301A MET* 1.3 64.2 + - - +
302A TYR* 3.2 26.0 + - - +
303A GLY* 3.0 12.6 + - - -
304A LEU 3.2 7.8 + - - -
416A ASN* 3.6 36.1 - - + +
436A ARG* 3.8 7.9 - - - +
709A GOL 4.0 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 3.7 19.0 - - + +
294A PHE* 3.8 25.6 - - + -
300A THR* 1.3 72.7 - - - +
302A TYR* 1.3 59.4 + - - +
304A LEU* 3.2 20.5 + - - +
305A ASP 2.9 24.8 + - - -
414A ILE* 3.3 11.2 - - + +
415A ASN 3.2 16.6 - - - +
416A ASN 3.0 17.4 + - - +
417A ASP* 3.4 29.4 - - - +
418A VAL 3.6 11.7 - - - +
419A TYR* 3.8 13.7 - - + +
434A ILE* 3.8 22.2 - - + +
436A ARG* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A THR* 3.1 9.1 - - - +
301A MET* 1.3 79.6 - - - +
303A GLY* 1.3 56.3 + - - +
305A ASP* 3.4 3.0 + - - +
306A SER* 2.9 34.2 + - - +
414A ILE* 3.4 42.7 + - + +
415A ASN* 3.5 26.1 - - + +
416A ASN* 3.4 27.6 - - - -
1B GLC 4.5 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 3.7 11.9 - - - +
299A ASP* 3.3 26.2 + - - -
300A THR* 3.0 10.4 + - - -
302A TYR* 1.3 74.3 - - - +
304A LEU* 1.3 63.8 + - - +
306A SER* 3.3 7.4 + - - -
307A MET* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 3.9 15.3 - - + +
290A VAL* 4.0 18.2 - - + -
293A VAL* 4.2 7.0 - - + -
294A PHE* 3.8 15.9 - - + -
300A THR 3.2 6.3 + - - +
301A MET* 3.2 37.8 + - - +
303A GLY* 1.3 76.4 - - - +
305A ASP* 1.3 62.9 + - - +
307A MET* 3.2 27.1 + - + +
308A ILE* 3.1 25.2 + - - +
348A PHE* 3.7 38.4 - - + -
419A TYR* 3.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A MET 2.9 6.6 + - - +
302A TYR 3.8 2.2 - - - +
304A LEU* 1.3 77.1 - - - +
306A SER* 1.3 59.2 + - - +
308A ILE* 3.2 1.8 + - - +
309A GLN* 2.9 47.9 + - - +
411A GLN* 3.4 25.6 - - - +
414A ILE* 3.6 26.5 - - + +
419A TYR* 2.7 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 2.9 23.5 + - - +
303A GLY* 3.6 8.5 - - - -
305A ASP* 1.3 78.1 + - - +
307A MET* 1.3 57.2 + - - +
309A GLN* 4.0 4.4 - - - +
310A SER* 3.0 31.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
285A ARG 3.7 20.9 - - - +
286A PHE* 3.6 48.2 - - + +
289A LYS* 3.9 14.4 - - + -
303A GLY 3.0 13.0 + - - +
304A LEU* 3.5 36.6 - - + +
305A ASP 3.2 0.2 - - - -
306A SER* 1.3 73.7 - - - +
308A ILE* 1.3 66.4 + - + +
311A THR* 2.7 52.6 + - + +
353A ARG* 4.2 0.2 - - - -
700A CL 3.7 22.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
286A PHE* 4.1 10.1 - - + -
304A LEU 3.1 18.4 + - - +
305A ASP 3.2 7.2 + - - +
307A MET* 1.3 91.9 - - + +
309A GLN* 1.3 78.1 + - - +
311A THR* 3.2 13.6 + - - -
312A ALA* 3.2 16.0 + - + +
348A PHE* 4.2 15.3 - - + -
352A SER* 5.0 3.1 - - - +
353A ARG* 3.8 30.1 + - - +
409A THR* 3.8 31.4 - - + +
419A TYR* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 2.9 37.7 + - - +
306A SER* 4.2 4.9 - - - +
308A ILE* 1.3 92.9 + - - +
310A SER* 1.3 58.1 + - - +
312A ALA* 3.5 9.2 + - - +
313A SER* 3.1 26.7 + - - -
409A THR* 3.6 21.7 + - - +
410A GLN* 4.9 0.3 - - - -
411A GLN* 4.8 5.9 + - + +
419A TYR* 4.9 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
285A ARG* 2.9 19.2 + - - -
306A SER 3.0 19.7 + - - -
307A MET 3.4 0.2 + - - -
309A GLN* 1.3 74.5 - - - +
311A THR* 1.3 60.3 + - - +
313A SER* 3.2 7.2 + - - -
314A ASP* 2.9 36.6 + - - -
700A CL 4.1 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 4.4 2.0 - - - +
285A ARG* 3.7 41.3 - - + +
307A MET* 2.7 33.1 + - + +
308A ILE* 3.2 6.8 + - - -
310A SER* 1.3 75.8 - - - +
312A ALA* 1.3 60.9 + - - +
314A ASP 4.5 0.2 - - - +
315A TYR* 2.9 46.1 + - + -
318A ILE* 3.5 7.7 - - - +
353A ARG* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 3.2 17.3 + - + +
309A GLN* 3.7 12.8 - - - +
310A SER 3.3 0.2 - - - -
311A THR* 1.3 80.3 + - - +
313A SER* 1.3 61.1 + - - +
315A TYR 3.4 13.7 - - - +
318A ILE* 3.7 23.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
309A GLN 3.1 15.4 + - - -
310A SER* 3.2 10.7 + - - -
312A ALA* 1.3 77.7 - - - +
314A ASP* 1.3 67.4 + - - +
315A TYR 4.6 1.4 - - - +
316A ASN* 5.3 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 3.5 21.7 + - + +
275A ASN* 3.1 22.0 + - - -
285A ARG* 2.8 39.3 + - - +
310A SER* 2.9 21.5 + - - +
311A THR 4.0 1.8 - - - +
313A SER* 1.3 85.1 + - - +
315A TYR* 1.3 61.8 + - + +
316A ASN* 3.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.9 0.5 - - - +
270A ASN* 2.7 30.7 + - - -
271A THR* 4.1 13.0 - - - -
274A ALA* 3.6 32.1 - - + -
275A ASN* 3.7 3.1 - - - +
281A LEU* 4.7 2.0 - - + +
282A LEU 5.7 0.3 + - - -
283A ASP* 4.6 3.3 + - - -
284A PHE 5.9 0.3 + - - -
285A ARG* 3.6 32.5 + - - +
311A THR* 2.9 42.2 + - + +
312A ALA 3.4 15.9 - - - +
313A SER 4.6 1.2 - - - +
314A ASP* 1.3 79.9 - - - +
316A ASN* 1.3 64.7 + - - +
317A PHE 3.2 5.7 + - - +
318A ILE* 4.1 13.6 + - + +
321A MET* 3.5 40.7 - - + +
----------------------------------------------------------
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