Contacts of the strand formed by residues 277 - 294 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A SER 3.6 2.0 - - - +
258A ASP* 3.4 1.0 - - - -
259A THR* 2.8 48.0 + - - -
261A TYR* 5.3 4.9 - - - -
275A ASP 3.1 7.3 + - - -
276A ASP* 1.3 72.3 - - - +
278A ASN* 1.3 64.4 + - - +
279A MET* 3.5 27.5 - - - +
56C ASP* 3.7 6.7 + - - +
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A SER 3.6 4.3 - - - -
258A ASP* 3.4 20.8 - - - +
259A THR 4.6 1.0 + - - +
276A ASP* 3.6 22.7 + - - +
277A SER* 1.3 79.1 + - - +
279A MET* 1.3 59.9 + - - +
55C ARG* 2.9 47.8 - - + +
56C ASP* 3.0 27.7 + - - +
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Residues in contact with MET 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLY 4.8 0.4 - - - -
256A ILE* 3.4 0.9 - - - -
257A SER* 3.0 38.7 + - - +
259A THR* 6.0 1.1 - - - +
277A SER* 3.5 22.7 - - - +
278A ASN* 1.3 73.9 - - - +
280A GLY* 1.3 60.4 + - - +
281A GLN* 4.5 13.2 - - + +
55C ARG* 3.1 21.0 + - - -
56C ASP* 4.2 12.6 - - - +
57C ALA* 3.4 29.4 - - + -
60C ILE* 6.2 1.1 - - + -
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLY 3.7 2.7 - - - -
279A MET* 1.3 75.7 - - - +
281A GLN* 1.3 65.2 + - - +
53C GLY* 3.0 8.0 - - - -
54C TYR* 2.7 54.0 + - - -
55C ARG* 3.7 7.5 - - - +
57C ALA* 3.5 3.8 - - - +
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A SER 4.6 0.2 - - - -
254A THR* 3.1 5.5 - - - -
255A GLY 3.1 37.0 + - - +
279A MET* 4.5 12.8 - - + +
280A GLY* 1.3 82.6 - - - +
282A ASN* 1.3 66.2 + - - +
283A LYS* 3.9 24.9 - - - +
51C SER* 3.7 14.9 - - - -
52C ASN 3.4 28.7 - - - +
53C GLY* 3.5 14.9 + - - -
54C TYR* 3.2 7.5 - - - -
57C ALA* 3.9 8.8 - - + +
60C ILE* 4.9 1.6 - - - +
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Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A SER 3.4 4.5 - - - +
254A THR* 2.9 30.0 + - - -
281A GLN* 1.3 74.1 - - - +
283A LYS* 1.3 66.7 + - - +
50C TYR* 3.6 2.7 - - + +
51C SER* 3.5 2.1 - - - -
52C ASN* 2.8 60.7 + - + +
54C TYR* 3.1 25.0 - - - +
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA* 3.1 4.7 - - - +
253A SER* 2.8 47.4 + - - +
281A GLN* 3.9 31.7 - - + +
282A ASN* 1.3 83.2 - - - +
284A VAL* 1.3 69.3 + - - +
49C THR* 4.4 14.8 - - + -
50C TYR* 3.3 9.2 - - - +
51C SER* 4.1 14.9 + - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 5.7 3.6 - - + -
251A THR* 3.2 11.7 - - - +
252A ALA* 4.4 9.4 - - + -
282A ASN 5.8 0.2 - - - -
283A LYS* 1.3 81.8 - - - +
285A GLY* 1.3 61.0 + - - +
48C TYR* 4.9 3.9 - - + -
49C THR* 3.6 5.6 - - - +
50C TYR* 3.0 45.4 + - + +
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 3.2 8.1 - - - +
251A THR* 2.9 39.8 + - - +
284A VAL* 1.3 78.2 - - - +
286A LEU* 1.3 69.5 + - - +
48C TYR* 2.9 16.2 - - - -
49C THR* 4.4 4.0 - - - -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 4.8 7.0 - - + -
248A LEU* 4.0 25.4 - - + -
249A ASP 3.3 4.3 - - - +
250A LEU* 4.0 25.4 - - + -
251A THR* 5.6 0.9 - - - -
285A GLY* 1.3 86.2 - - - +
287A SER* 1.3 60.6 + - - +
288A PHE 4.2 0.7 - - - -
46C ALA 4.7 0.2 - - - -
47C ASP* 3.3 7.4 - - - +
48C TYR* 3.0 42.4 + - + +
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A THR 3.4 2.1 - - - +
248A LEU* 3.2 8.3 - - - -
249A ASP* 2.8 45.6 + - - +
251A THR* 5.8 6.3 - - - -
286A LEU* 1.3 73.7 - - - +
288A PHE* 1.3 64.2 + - - +
289A SER* 5.3 3.5 - - - -
47C ASP* 2.9 20.6 + - - -
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO* 3.9 20.6 - - + -
247A THR 3.4 10.5 - - - -
248A LEU* 4.4 15.3 - - + -
286A LEU 4.2 0.2 - - - -
287A SER* 1.3 76.2 + - - +
289A SER* 1.3 62.8 + - - +
290A LEU* 3.6 37.0 - - + -
44C LEU* 4.3 19.7 - - + -
45C GLY* 3.4 4.3 - - - -
46C ALA* 2.9 50.1 + - + +
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 3.1 4.0 - - - +
247A THR* 2.8 46.2 + - - -
287A SER* 5.3 4.5 - - - -
288A PHE* 1.3 76.7 - - - +
290A LEU* 1.3 59.3 + - - +
291A PRO* 4.2 3.0 - - - +
44C LEU 3.4 4.5 - - - -
45C GLY* 4.7 0.7 - - - -
1431C PGE 3.2 33.1 + - - -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A HIS 3.6 13.7 - - - +
246A PRO* 3.5 23.6 - - + -
288A PHE* 3.6 26.2 - - + -
289A SER* 1.3 76.8 + - - +
291A PRO* 1.3 86.0 - - + +
292A ILE* 3.4 5.2 + - + +
43C GLY* 3.6 0.2 - - - -
44C LEU* 2.8 53.8 + - + +
1431C PGE 4.6 3.1 - - - -
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Residues in contact with PRO 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLY 3.7 18.8 - - - +
244A HIS* 4.0 8.2 - - + +
245A LEU 3.6 16.4 - - - +
289A SER* 4.2 3.4 - - - +
290A LEU* 1.3 107.3 - - + +
292A ILE* 1.3 60.1 + - - +
294A GLN* 3.5 30.7 - - + +
42C LEU 4.2 3.1 - - - +
1431C PGE 4.3 16.4 - - - +
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU* 3.7 14.6 - - + +
291A PRO* 1.3 77.2 - - - +
293A TYR* 1.3 64.1 + - + +
42C LEU* 2.8 44.6 + - + +
43C GLY 3.8 5.4 - - - -
44C LEU* 3.7 15.0 - - + +
69C LEU* 3.3 33.9 - - + -
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Residues in contact with TYR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A PRO 3.8 0.4 - - - -
292A ILE* 1.3 84.4 - - + +
294A GLN* 1.3 65.6 + - - +
295A GLY* 3.3 11.9 - - - -
296A GLY* 3.6 17.6 + - - -
1429A CL 4.3 7.2 - - + -
39C LEU* 3.2 27.4 - - - +
40C PRO* 3.0 47.7 - - + +
41C GLN* 3.3 3.5 - - - -
42C LEU* 2.6 46.8 + - + +
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLY* 3.6 6.5 + - - -
291A PRO* 3.5 32.1 - - + +
293A TYR* 1.3 79.7 - - - +
295A GLY* 1.3 59.9 + - - +
296A GLY 3.2 2.2 - - - -
297A MET* 3.1 25.6 + - + +
298A VAL* 3.4 22.7 - - + +
1429A CL 3.2 16.2 - - + +
36C SER* 2.9 17.8 + - - -
41C GLN* 2.9 28.5 + - - +
1431C PGE 4.3 17.0 - - - +
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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) + - + + + + + -
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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