Contacts of the helix formed by residues 287 - 308 (chain A) in PDB entry 3D7T
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 287 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG 4.1 4.0 + - - -
285A VAL 3.4 7.1 + - - -
286A LEU* 1.3 75.7 - - - +
288A GLY* 1.3 69.9 + - - +
289A ASP* 3.2 3.6 - - - -
290A CYS* 2.8 16.2 + - - +
291A LEU* 3.2 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY* 1.3 70.4 - - - +
289A ASP* 1.3 64.5 + - - +
291A LEU* 3.1 8.3 + - - +
292A LEU* 2.9 23.9 + - - +
380A TYR* 4.8 4.1 + - - -
412A PRO* 6.2 1.1 - - - -
449A HIS* 3.6 31.0 - - - -
450A LEU* 4.3 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY 3.0 1.7 + - - -
288A GLY* 1.3 73.8 - - - +
290A CYS* 1.3 60.6 + - - +
292A LEU* 3.3 2.4 + - - +
293A LYS* 2.9 30.8 + - - +
449A HIS* 2.9 26.6 + - - -
450A LEU* 3.4 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A VAL* 4.3 15.3 - - - -
286A LEU* 3.8 28.7 - - + -
287A GLY 2.8 15.9 + - - +
289A ASP* 1.3 78.3 - - - +
291A LEU* 1.3 58.8 + - - +
293A LYS* 3.6 6.3 - - - +
294A PHE* 2.9 38.8 + - + -
326A ASN* 5.1 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 4.0 22.0 - - + -
286A LEU* 4.0 20.6 - - + +
287A GLY 3.7 12.6 - - - +
288A GLY* 3.1 6.6 + - - +
290A CYS* 1.3 74.8 - - - +
292A LEU* 1.3 61.6 + - - +
294A PHE* 3.3 9.0 + - + +
295A SER* 2.9 33.2 + - - -
379A ILE* 3.7 22.7 - - + +
380A TYR* 3.6 41.1 - - + +
382A PHE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLY 2.9 17.0 + - - +
289A ASP* 3.7 3.4 - - - +
291A LEU* 1.3 74.6 - - - +
293A LYS* 1.3 65.9 + - - +
295A SER* 3.2 7.9 + - - -
296A LEU* 2.9 31.7 + - + +
380A TYR* 3.7 14.9 + - - +
415A VAL* 5.3 4.0 - - + -
440A LEU* 4.5 25.4 - - + +
443A ILE* 4.4 9.9 - - + -
444A LYS* 3.4 44.9 - - + +
449A HIS* 3.5 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASP 2.9 17.8 + - - +
290A CYS* 3.6 8.5 - - - +
291A LEU 3.2 0.2 - - - -
292A LEU* 1.3 75.7 - - - +
294A PHE* 1.3 65.1 + - + +
296A LEU* 3.0 13.1 + - + +
297A ASP* 2.9 54.8 + - - +
326A ASN* 3.9 16.6 - - + +
327A VAL* 5.3 6.7 - - - -
444A LYS* 4.7 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 4.0 24.2 - - + -
277A TYR* 4.3 20.0 - + - -
278A LEU* 5.0 1.6 - - + -
286A LEU* 4.1 24.9 - - + -
290A CYS* 2.9 30.0 + - + -
291A LEU* 3.6 15.7 - - + +
293A LYS* 1.3 80.9 - - + +
295A SER* 1.3 65.0 + - - +
297A ASP* 3.3 13.1 + - - +
298A VAL* 3.3 19.6 - - - +
322A VAL* 4.0 23.6 - - + -
326A ASN* 4.1 27.1 - - + -
328A ALA* 3.8 18.6 - - + +
379A ILE* 4.4 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU 2.9 23.8 + - - -
292A LEU* 3.4 13.0 - - - -
293A LYS 3.1 0.2 - - - -
294A PHE* 1.3 78.2 - - - +
296A LEU* 1.3 60.2 + - - +
298A VAL* 3.6 3.2 + - - +
299A CYS* 3.3 17.8 + - - +
372A PHE* 3.6 12.9 - - - -
375A LEU* 6.1 0.2 - - - -
376A LEU* 3.5 27.9 - - - +
379A ILE* 3.7 13.7 - - - +
380A TYR* 3.9 10.4 - - - -
440A LEU* 3.9 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 2.9 26.2 + - + +
293A LYS* 3.7 10.1 - - + +
295A SER* 1.3 73.3 - - - +
297A ASP* 1.3 56.8 + - - +
298A VAL 2.6 17.1 + - - -
299A CYS* 3.2 1.5 + - + +
300A GLU* 3.0 40.5 + - + +
437A ARG* 4.0 24.7 - - + +
440A LEU* 3.5 36.1 - - + -
441A GLU* 3.9 12.6 - - - +
444A LYS* 3.7 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 2.9 42.0 + - - +
293A LYS* 2.9 56.9 + - - +
294A PHE* 3.3 7.6 + - - +
296A LEU* 1.3 73.6 - - - +
298A VAL* 1.3 58.4 + - - +
300A GLU* 5.3 1.8 - - - +
301A ALA* 3.8 1.9 - - - +
326A ASN 3.9 0.5 - - - +
327A VAL* 3.7 11.4 - - - +
328A ALA* 3.1 45.4 + - + +
330A VAL* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 6.0 2.2 - - + -
294A PHE 3.3 17.0 - - - +
295A SER* 3.7 7.2 - - - +
296A LEU 2.6 6.7 + - - -
297A ASP* 1.3 78.9 - - - +
299A CYS* 1.3 51.0 + - - +
300A GLU 2.9 4.5 - - - -
301A ALA* 2.8 6.2 + - - +
302A MET* 2.6 47.7 + - + +
315A LEU* 4.6 11.4 - - + -
320A VAL* 5.0 15.3 - - + -
328A ALA* 4.6 11.2 - - + +
330A VAL* 5.1 11.2 - - + -
372A PHE* 3.2 25.4 - - + -
375A LEU* 4.6 15.0 - - + -
379A ILE* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER 3.3 8.9 + - - +
296A LEU* 3.2 4.4 + - + +
298A VAL* 1.3 76.8 - - - +
300A GLU* 1.3 54.1 + - - +
302A MET* 4.1 5.2 - - - -
303A GLU* 2.8 32.8 + - - +
372A PHE* 3.6 21.5 - - + -
433A PHE* 3.4 10.4 - - - +
436A LEU* 3.4 21.8 - - - -
437A ARG* 3.2 38.8 - - + -
440A LEU* 3.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A HIS* 3.7 14.5 + - - +
247A ASN* 2.9 26.5 + - - +
296A LEU* 3.0 23.8 + - + +
297A ASP* 5.5 1.8 - - - +
298A VAL 2.9 0.8 - - - -
299A CYS* 1.3 75.6 - - - +
301A ALA* 1.3 54.3 + - - +
302A MET 2.9 4.5 - - - -
303A GLU* 3.7 6.2 - - - +
304A TYR* 2.8 31.9 + - - +
437A ARG* 2.7 58.4 + - + +
441A GLU* 5.1 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A HIS* 4.0 6.3 - - - -
247A ASN* 3.2 33.1 - - + +
248A LEU* 3.4 26.0 - - + +
297A ASP 3.8 4.3 - - - +
298A VAL 2.8 8.9 + - - +
300A GLU* 1.3 77.4 - - - +
302A MET* 1.3 60.1 + - - +
304A TYR* 3.9 3.8 - - - +
305A LEU* 3.2 28.1 + - - +
330A VAL* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 2.6 31.2 + - + +
299A CYS* 4.0 1.3 - - - +
301A ALA* 1.3 83.1 - - + +
303A GLU* 1.3 67.2 + - - +
304A TYR 2.9 2.4 + - - -
305A LEU* 3.1 19.4 + - + +
306A GLU* 3.0 23.4 + - - +
312A HIS* 5.1 11.7 - - + +
315A LEU* 4.1 22.2 - - + -
330A VAL* 5.6 7.2 - - - -
368A ASP* 3.7 22.4 - - + +
372A PHE* 4.6 0.4 - - + -
433A PHE* 3.2 63.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A CYS 2.8 17.4 + - - +
300A GLU* 3.7 6.3 - - - +
302A MET* 1.3 72.4 - - - +
304A TYR* 1.3 64.0 + - - +
306A GLU* 3.4 13.9 - - - +
307A GLY* 3.7 3.8 + - - -
433A PHE* 3.0 36.7 - - - +
434A LEU* 3.2 31.6 - - + +
437A ARG* 3.1 40.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLN 4.7 0.3 + - - -
243A LEU* 3.3 8.6 - - + +
244A ARG 2.6 41.8 + - - -
245A HIS* 3.1 41.3 - + + +
248A LEU* 3.6 13.7 - - + -
300A GLU 2.8 13.5 + - - +
301A ALA 3.9 3.1 - - - +
302A MET 2.9 0.2 - - - -
303A GLU* 1.3 74.4 - - - +
305A LEU* 1.3 86.5 + - + +
306A GLU 2.8 14.7 + - - -
307A GLY* 2.9 14.6 + - - -
308A ASN* 2.9 37.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
243A LEU* 4.5 19.1 - - + -
248A LEU* 3.7 20.4 - - + -
301A ALA 3.2 17.5 - - - +
302A MET* 3.1 23.9 + - + +
304A TYR* 1.3 105.3 - - + +
306A GLU* 1.3 56.1 + - - +
307A GLY 3.4 0.2 - - - -
308A ASN* 4.0 5.4 - - - +
309A ASN 3.6 1.2 + - - -
310A PHE* 2.7 63.1 + - + +
312A HIS* 5.3 11.0 - - + +
330A VAL* 6.3 0.9 - - + -
333A PHE* 5.0 9.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
302A MET 3.0 15.4 + - - +
303A GLU* 3.4 8.8 - - - +
304A TYR 2.8 0.4 + - - -
305A LEU* 1.3 78.7 - - - +
307A GLY* 1.3 61.8 + - - +
309A ASN* 3.7 9.4 + - - -
310A PHE 4.7 0.4 - - - -
365A THR* 3.3 42.3 + - + +
366A LYS* 4.8 0.2 + - - -
432A SER* 3.0 28.7 - - - -
433A PHE* 3.3 30.2 + - + +
434A LEU* 3.8 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU 3.7 3.9 + - - -
304A TYR 2.9 8.0 + - - -
306A GLU* 1.3 77.5 - - - +
308A ASN* 1.3 57.0 + - - +
309A ASN* 3.0 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.1 32.6 - - + +
304A TYR* 2.9 60.3 + - - +
305A LEU* 3.8 5.1 + - - +
306A GLU 3.5 0.2 - - - -
307A GLY* 1.3 74.0 - - - +
309A ASN* 1.3 69.5 + - - +
310A PHE* 3.4 2.8 + - - +
----------------------------------------------------------
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