Contacts of the helix formed by residues 292 - 306 (chain A) in PDB entry 2WW9
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 292 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU 3.1 15.5 + - - -
289A LEU 4.0 0.2 - - - -
290A TYR 3.4 0.2 - - - -
291A THR* 1.4 74.3 - - - +
293A CYS* 1.4 61.4 + - - +
294A LEU 3.4 1.1 - - - -
295A SER* 3.4 13.0 + - - -
296A VAL* 3.1 27.2 + - - +
427A ALA 5.8 1.1 - - - -
430A GLY 5.5 0.2 - - - -
431A ALA* 4.6 14.3 - - - +
434A LEU* 3.4 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A MET* 4.4 17.7 - - - -
289A LEU 3.3 16.9 + - - +
290A TYR* 3.4 21.8 - - + +
291A THR 3.2 1.4 - - - -
292A GLY* 1.4 76.3 - - - +
294A LEU* 1.4 66.8 + - + +
296A VAL* 4.4 0.2 - - - -
297A LEU* 3.1 44.1 + - - +
434A LEU* 4.6 0.4 - - - -
455A VAL* 3.4 36.1 - - - +
459A GLY* 4.1 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A MET* 6.3 1.1 - - - -
290A TYR* 4.4 22.0 - - + +
291A THR 4.2 2.3 + - - +
293A CYS* 1.4 93.8 - - + +
295A SER* 1.4 59.7 + - - +
297A LEU* 3.8 13.7 - - + -
298A PHE* 3.0 50.0 + - + -
385A TRP* 3.7 41.5 - - + -
----------------------------------------------------------
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 THR 4.4 4.5 + - - -
292A GLY* 3.6 19.0 - - - -
293A CYS 3.3 0.4 - - - -
294A LEU* 1.4 79.7 - - - +
296A VAL* 1.4 57.3 + - - +
298A PHE* 3.6 6.6 + - - +
299A SER* 3.2 22.0 + - - -
377A THR 4.8 0.3 - - - +
378A GLY* 3.2 24.4 + - - -
381A PHE* 3.5 27.0 - - - +
382A ALA* 3.5 8.1 + - - -
385A TRP* 5.7 7.2 - - - -
431A ALA* 4.0 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLY 3.1 17.3 + - - +
295A SER* 1.4 73.6 - - - +
297A LEU* 1.4 60.6 + - - +
298A PHE 3.4 0.2 - - - -
299A SER* 3.7 11.0 - - - +
300A TYR* 3.1 27.3 + - + +
374A ILE* 6.4 0.7 - - + -
378A GLY* 6.0 0.4 - - - -
431A ALA* 5.1 2.5 - - + +
434A LEU* 3.6 17.5 - - + -
435A SER* 3.6 29.2 - - - +
438A THR* 4.0 24.5 - - + +
455A VAL* 3.4 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.3 13.8 - - + +
88A ILE* 3.9 19.5 - - + -
182A MET* 5.4 9.0 - - + -
185A ASN* 3.6 24.7 - - - +
293A CYS* 3.1 42.6 + - - +
294A LEU* 3.9 16.6 - - + +
296A VAL* 1.4 77.8 - - - +
298A PHE* 1.4 56.5 + - + +
300A TYR* 3.5 4.5 + - + +
301A THR* 2.9 33.9 + - - -
452A GLY* 5.7 1.3 - - - -
455A VAL* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.0 23.3 - - + -
91A GLY* 4.7 11.7 - - - -
92A LEU* 3.5 35.6 - - + +
95A GLN* 3.8 30.5 - - + -
294A LEU* 3.0 40.1 + - + +
295A SER* 3.7 1.8 - - - +
297A LEU* 1.4 75.7 - - - +
299A SER* 1.4 60.5 + - - +
301A THR 3.5 0.3 + - - -
302A ILE* 3.2 21.3 + - - +
381A PHE* 3.6 43.6 - + + -
385A TRP* 4.2 20.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER 3.2 18.3 + - - -
296A VAL* 3.8 17.4 - - - +
297A LEU 3.3 0.2 - - - -
298A PHE* 1.4 76.2 - - - +
300A TYR* 1.4 59.1 + - - +
302A ILE* 3.5 10.6 - - - +
303A LEU* 3.4 19.6 - - - +
374A ILE* 3.4 31.3 + - - +
377A THR* 3.5 29.2 - - - +
378A GLY* 4.7 2.5 - - - -
381A PHE* 4.0 0.2 - - - -
435A SER* 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE 3.7 11.6 + - - -
70A GLY* 5.7 0.2 - - - -
71A VAL* 3.5 37.2 - - + -
296A VAL* 3.1 20.5 + - + +
297A LEU* 4.0 6.1 - - + +
299A SER* 1.4 72.4 - - - +
301A THR* 1.4 63.9 + - - +
303A LEU* 3.5 23.4 + - + +
304A PHE* 3.1 42.3 - + - -
352A PRO* 4.5 1.6 - - + -
370A TYR* 4.3 5.4 - - - -
438A THR* 5.5 2.0 - - + -
442A GLU* 3.3 14.5 + - - -
447A LYS* 3.1 23.6 + - - +
449A LYS* 4.9 4.3 + - - -
450A ALA 4.5 4.5 + - - -
451A ALA* 3.5 41.8 + - + +
452A GLY* 4.0 10.3 - - - -
455A VAL* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.4 19.9 - - - +
85A PHE* 3.8 11.5 - - + -
88A ILE* 3.7 24.3 - - + +
89A SER* 4.9 0.4 - - - -
92A LEU* 3.9 22.7 - - + -
297A LEU 2.9 20.9 + - - -
298A PHE 3.7 5.4 - - - -
299A SER 3.4 0.2 - - - -
300A TYR* 1.4 75.6 - - - +
302A ILE* 1.4 60.9 + - - +
304A PHE* 3.3 18.1 + - - +
305A TYR* 3.6 32.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.7 14.8 - - + -
96A LEU* 6.1 6.3 - - + -
298A PHE 3.2 13.2 + - - +
299A SER 3.5 14.1 - - - +
300A TYR 3.4 0.2 - - - -
301A THR* 1.4 76.0 - - - +
303A LEU* 1.4 65.3 + - + +
304A PHE 3.1 1.1 - - - -
305A TYR* 3.3 15.4 + - + +
306A ILE* 3.2 45.6 + - + +
373A PHE* 4.8 4.3 - - + -
377A THR* 3.9 22.9 - - + +
380A TRP* 6.1 3.4 - - + +
381A PHE* 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A SER 3.4 18.2 - - - +
300A TYR* 3.6 32.1 - - + +
301A THR 3.2 0.8 - - - -
302A ILE* 1.4 76.0 - - + +
304A PHE* 1.4 65.5 + - + +
305A TYR 3.5 0.2 - - - -
306A ILE* 4.8 3.6 - - - -
309A PHE 4.2 1.2 - - - +
310A ALA* 3.2 21.3 - - - +
311A PHE* 4.0 4.5 + - - -
350A LEU* 3.7 38.7 - - + +
351A ALA* 5.4 0.5 + - - -
352A PRO* 5.0 3.3 - - + +
370A TYR* 3.8 15.0 - - + +
373A PHE* 3.9 18.2 - - + -
374A ILE* 3.7 31.4 - - + -
377A THR* 6.3 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
67A PHE* 3.2 31.0 - - + -
68A LEU* 3.6 22.9 - - + -
71A VAL* 3.7 26.0 - - + -
85A PHE* 3.7 19.3 - + + -
300A TYR* 3.1 60.1 - + - -
301A THR 3.3 4.0 + - - +
302A ILE 3.1 0.6 - - - -
303A LEU* 1.4 80.1 - - + +
305A TYR* 1.4 60.6 + - - +
310A ALA* 3.4 4.5 - - - +
311A PHE* 3.6 33.7 - + - +
312A VAL* 3.1 32.4 + - - +
352A PRO* 4.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.2 62.9 + + - -
89A SER* 3.2 33.0 + - - -
92A LEU* 5.3 2.7 - - + -
127A GLN* 3.8 21.3 + - - +
131A LEU* 3.5 20.6 - - + +
134A ILE* 5.9 1.6 - - + -
301A THR* 3.6 21.0 + - + -
302A ILE* 3.3 15.0 + - + +
304A PHE* 1.4 79.6 - - - +
306A ILE* 1.4 67.8 + - + +
310A ALA* 3.7 0.2 - - - -
312A VAL* 4.3 5.8 - - + -
313A LEU* 3.2 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 3.2 41.3 - - + +
305A TYR* 1.4 74.6 - - + +
307A HIS* 1.4 65.3 + - - +
308A ILE* 3.5 20.9 - - + +
309A PHE* 3.6 31.9 - - + +
310A ALA* 3.0 26.5 + - - +
313A LEU* 4.3 1.6 - - - +
314A ILE* 4.0 3.3 - - - +
350A LEU* 4.1 24.5 - - + -
373A PHE* 4.3 12.6 - - + -
----------------------------------------------------------
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