Contacts of the strand formed by residues 277 - 294 (chain B) in PDB entry 2WMZ
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 SER 277 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 3.9 5.3 + - - +
257B SER 3.6 1.3 - - - +
258B ASP* 3.3 1.4 - - - -
259B THR* 2.8 47.2 + - - +
261B TYR* 5.3 4.5 - - - -
275B ASP 3.1 7.0 + - - -
276B ASP* 1.3 72.3 - - - +
278B ASN* 1.3 65.2 + - - +
279B MET* 3.3 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 2.9 45.5 - - - +
56A ASP* 3.0 30.4 + - - +
257B SER 3.6 4.0 - - - -
258B ASP* 3.4 22.2 - - - +
259B THR 4.7 1.2 + - - +
276B ASP* 3.6 22.4 + - - +
277B SER* 1.3 79.3 + - - +
279B MET* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 3.1 20.9 + - - -
56A ASP* 4.3 13.5 - - - +
57A ALA* 3.4 28.7 - - + -
60A ILE* 6.1 1.6 - - + -
255B GLY 4.7 0.4 - - - -
256B ILE* 3.4 1.1 - - - -
257B SER* 3.0 40.0 + - - +
259B THR* 6.0 0.7 - - - +
277B SER* 3.3 22.4 - - - +
278B ASN* 1.3 71.5 - - - +
280B GLY* 1.3 60.1 + - - +
281B GLN* 4.5 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY* 2.9 8.5 - - - -
54A TYR* 2.6 54.2 + - - -
55A ARG* 3.7 7.7 - - - +
57A ALA* 3.3 5.4 - - - +
255B GLY 3.7 3.4 - - - -
279B MET* 1.3 75.3 - - - +
281B GLN* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER* 3.7 15.5 - - - -
52A ASN 3.4 28.5 - - - +
53A GLY* 3.4 15.8 + - - -
54A TYR* 3.2 11.4 - - - -
57A ALA* 3.8 9.9 - - + +
60A ILE* 4.8 2.1 - - - +
253B SER 4.6 0.2 - - - -
254B THR* 3.2 5.5 - - - -
255B GLY 3.0 36.8 + - - +
279B MET* 4.5 12.2 - - + +
280B GLY* 1.3 82.1 - - - +
282B ASN* 1.3 60.2 + - - +
283B LYS* 3.9 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.7 2.7 - - + +
51A SER* 3.5 1.7 - - - -
52A ASN* 2.9 60.7 + - + +
54A TYR* 3.0 28.7 - - - +
253B SER 3.4 5.2 - - - +
254B THR* 3.1 25.6 + - - -
281B GLN* 1.3 71.8 - - - +
283B LYS* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 4.5 15.0 - - + -
50A TYR* 3.4 9.0 - - - +
51A SER* 4.1 16.5 + - - +
251B THR 4.5 0.2 - - - -
252B ALA* 3.2 1.7 - - - +
253B SER* 2.8 47.8 + - - +
281B GLN* 3.9 30.4 - - + +
282B ASN* 1.3 82.4 - - - +
284B VAL* 1.3 71.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 5.0 3.5 - - + -
49A THR* 3.7 5.4 - - - +
50A TYR* 3.1 45.3 + - + +
250B LEU* 5.7 3.4 - - + -
251B THR 3.1 11.2 - - - +
252B ALA* 4.4 10.3 - - + -
283B LYS* 1.3 82.0 - - - +
285B GLY* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 3.0 17.0 - - - -
49A THR* 4.4 4.0 - - - -
250B LEU* 3.2 8.4 - - - +
251B THR* 2.8 40.1 + - - +
284B VAL* 1.3 77.7 - - - +
286B LEU* 1.3 68.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 4.8 0.2 - - - -
47A ASP* 3.4 6.6 - - - +
48A TYR* 3.1 42.7 + - + +
75B ILE* 4.9 7.0 - - + -
248B LEU* 4.0 24.2 - - + -
249B ASP 3.3 3.6 - - - +
250B LEU* 3.9 26.5 - - + -
251B THR* 5.6 0.4 - - - -
285B GLY* 1.3 86.0 - - - +
287B SER* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 2.8 21.6 + - - -
247B THR 3.4 2.3 - - - +
248B LEU* 3.3 8.2 - - - +
249B ASP* 2.7 43.8 + - - +
251B THR* 5.8 6.7 - - - -
286B LEU* 1.3 73.6 - - - +
288B PHE* 1.3 64.1 + - - +
289B SER* 4.1 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.4 16.4 - - + -
45A GLY* 3.5 3.7 - - - -
46A ALA* 2.9 50.3 + - + +
47A ASP* 5.0 0.2 - - - +
246B PRO* 3.8 20.9 - - + -
247B THR 3.4 9.9 - - - -
248B LEU* 4.4 14.6 - - + -
286B LEU 4.2 0.4 - - - -
287B SER* 1.3 75.6 + - - +
289B SER* 1.3 63.6 + - - +
290B LEU* 3.6 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU 3.5 6.6 + - - -
45A GLY* 5.4 1.3 - - - -
1430A PGE 4.1 19.9 + - - -
246B PRO* 3.1 3.1 - - - +
247B THR* 2.8 49.1 + - - -
287B SER* 5.3 4.5 - - - -
288B PHE* 1.3 77.0 - - - +
290B LEU* 1.3 62.3 + - - +
291B PRO* 4.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 4.8 0.7 - - - -
44A LEU* 2.9 53.2 + - + +
1430A PGE 5.1 1.1 - - - -
244B HIS 3.6 13.5 - - - +
246B PRO* 3.5 22.2 - - + -
288B PHE* 3.6 27.6 - - + -
289B SER* 1.3 77.5 + - - +
291B PRO* 1.3 86.8 - - + +
292B ILE* 3.4 4.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 4.3 0.2 - - - +
1430A PGE 4.3 23.3 - - - -
243B GLY 3.7 18.8 - - - +
244B HIS* 4.0 7.8 - - + +
245B LEU 3.5 21.3 - - - +
289B SER* 4.2 3.4 - - - +
290B LEU* 1.3 101.8 - - + +
292B ILE* 1.3 61.1 + - - +
294B GLN* 3.6 30.5 - - + +
298B VAL* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.0 38.8 + - + +
43A GLY 3.8 5.6 - - - +
44A LEU* 3.7 16.8 - - + +
69A LEU* 3.4 33.4 - - + -
290B LEU* 3.8 14.1 - - + +
291B PRO* 1.3 78.2 - - - +
293B TYR* 1.3 65.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.4 17.8 - - - +
40A PRO* 3.1 45.0 - - + +
41A GLN* 3.5 0.7 - - - -
42A LEU* 2.7 46.9 + - + +
291B PRO 3.8 0.4 - - - -
292B ILE* 1.3 84.6 - - + +
294B GLN* 1.3 65.0 + - - +
295B GLY* 3.3 21.2 - - - -
296B GLY* 3.5 17.6 + - - -
1429B CL 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 3.0 14.9 + - - -
41A GLN* 3.0 27.9 + - - +
42A LEU 5.1 1.6 - - - +
1430A PGE 4.5 16.3 - - - +
243B GLY* 3.5 13.5 + - - -
291B PRO* 3.6 24.6 - - + +
293B TYR* 1.3 78.8 - - - +
295B GLY* 1.3 63.4 + - - +
296B GLY 3.1 2.9 + - - -
297B MET* 3.1 24.2 + - + +
298B VAL* 3.3 23.2 - - + +
1429B CL 3.1 16.6 - - + +
----------------------------------------------------------
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