Contacts of the strand formed by residues 277 - 294 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASP* 4.0 5.1 + - - +
257C SER 3.6 0.9 - - - +
258C ASP* 3.4 0.9 - - - -
259C THR* 2.8 46.6 + - - +
261C TYR* 5.3 4.2 - - - -
275C ASP 3.0 7.5 + - - -
276C ASP* 1.3 70.5 - - - +
278C ASN* 1.3 69.5 + - - +
279C MET* 3.3 30.1 - - - +
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Residues in contact with ASN 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 3.0 47.6 + - - +
56B ASP* 3.1 26.7 + - - +
257C SER 3.6 4.5 - - - -
258C ASP* 3.4 21.3 - - - +
259C THR 4.9 1.2 - - - +
276C ASP* 3.7 21.1 + - - +
277C SER* 1.3 80.0 + - - +
279C MET* 1.3 59.0 + - - +
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Residues in contact with MET 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 3.0 19.9 + - - -
56B ASP* 4.2 13.5 - - - +
57B ALA* 3.5 29.4 - - + -
60B ILE* 6.3 0.7 - - + -
255C GLY 4.8 0.2 - - - -
256C ILE* 3.4 1.8 - - - -
257C SER* 3.0 40.0 + - - +
259C THR* 6.1 0.2 - - - +
277C SER* 3.3 22.0 - - - +
278C ASN* 1.3 73.1 - - - +
280C GLY* 1.3 60.2 + - - +
281C GLN* 4.5 12.8 - - + +
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Residues in contact with GLY 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY* 3.2 4.2 - - - -
54B TYR* 2.9 49.7 + - - -
55B ARG* 3.7 9.3 - - - +
57B ALA* 3.5 4.2 - - - +
255C GLY 3.7 3.8 - - - -
279C MET* 1.3 76.3 - - - +
281C GLN* 1.3 69.7 + - - +
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Residues in contact with GLN 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER* 3.8 14.4 - - - -
52B ASN 3.5 27.2 - - - +
53B GLY* 3.5 15.3 + - - +
54B TYR* 3.2 11.8 - - - -
57B ALA* 3.8 9.5 - - + +
60B ILE 5.0 0.9 - - - +
253C SER 4.6 0.2 - - - -
254C THR* 3.1 5.2 - - - -
255C GLY* 3.0 37.2 + - - +
279C MET* 4.5 12.4 - - + +
280C GLY* 1.3 82.2 - - - +
282C ASN* 1.3 61.9 + - - +
283C LYS* 3.9 25.7 - - + +
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Residues in contact with ASN 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 3.7 2.6 - - + +
51B SER* 3.6 2.1 - - - -
52B ASN* 3.0 58.4 + - + +
54B TYR* 2.9 29.7 - - - +
253C SER 3.4 5.4 - - - +
254C THR* 2.9 30.0 + - - -
281C GLN* 1.3 71.4 - - - +
283C LYS* 1.3 65.6 + - - +
284C VAL* 5.8 0.2 - - - -
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Residues in contact with LYS 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR* 4.6 13.9 - - + -
50B TYR* 3.5 8.7 - - - +
51B SER* 4.3 14.5 + - - +
251C THR 5.2 0.2 - - - -
252C ALA* 3.1 3.4 - - - +
253C SER* 2.9 49.2 + - - +
281C GLN* 3.9 31.3 - - + +
282C ASN* 1.3 84.1 - - - +
284C VAL* 1.3 70.0 + - - +
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 5.1 2.9 - - + -
49B THR* 3.7 5.8 - - - +
50B TYR* 3.2 44.8 + - + +
250C LEU* 5.7 3.1 - - + -
251C THR* 3.2 10.3 - - - +
252C ALA* 4.5 9.2 - - + -
282C ASN 5.8 0.4 - - - -
283C LYS* 1.3 81.7 - - - +
285C GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 3.0 15.5 - - - -
49B THR* 4.4 4.7 - - - -
250C LEU* 3.2 7.6 - - - +
251C THR* 2.9 40.2 + - - -
284C VAL* 1.3 77.5 - - - +
286C LEU* 1.3 68.9 + - - +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA 4.9 0.2 - - - -
47B ASP* 3.4 6.6 - - - +
48B TYR* 3.1 41.3 + - + +
75C ILE* 4.9 7.2 - - + -
248C LEU* 4.0 23.1 - - + -
249C ASP 3.3 4.3 - - - +
250C LEU* 3.9 25.8 - - + -
251C THR* 5.6 0.2 - - - -
285C GLY* 1.3 87.6 - - - +
287C SER* 1.3 61.0 + - - +
288C PHE 4.2 0.4 - - - -
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Residues in contact with SER 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 2.9 20.9 + - - -
247C THR 3.4 1.9 - - - +
248C LEU* 3.2 8.6 - - - -
249C ASP* 2.8 45.9 + - - +
251C THR* 5.8 6.1 - - - -
286C LEU* 1.3 73.4 - - - +
288C PHE* 1.3 62.9 + - - +
289C SER* 4.1 3.9 + - - -
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Residues in contact with PHE 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.4 16.4 - - + -
45B GLY* 3.5 3.9 - - - -
46B ALA* 2.9 51.4 + - + +
47B ASP* 4.9 0.2 - - - +
246C PRO* 3.9 20.0 - - + -
247C THR 3.4 11.0 - - - -
248C LEU* 4.4 15.3 - - + -
286C LEU 4.2 0.2 - - - -
287C SER* 1.3 77.1 + - - +
289C SER* 1.3 62.9 + - - +
290C LEU* 3.6 40.4 - - + -
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Residues in contact with SER 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU 3.6 4.9 + - - -
45B GLY* 5.5 1.6 - - - -
1431B PGE 3.9 28.6 + - - -
246C PRO* 3.0 3.8 - - - +
247C THR* 2.8 49.7 + - - +
287C SER* 5.4 4.3 - - - -
288C PHE* 1.3 76.5 - - - +
290C LEU* 1.3 62.6 + - - +
291C PRO* 4.1 3.3 - - - +
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY* 4.7 0.2 - - - -
44B LEU* 2.9 52.2 + - + +
1431B PGE 5.4 1.6 - - - -
244C HIS 3.7 12.8 - - - +
246C PRO* 3.5 23.1 - - + -
288C PHE* 3.6 27.8 - - + -
289C SER* 1.3 76.6 + - - +
291C PRO* 1.3 86.5 - - + +
292C ILE* 3.4 6.6 + - + +
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Residues in contact with PRO 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU 4.3 3.8 - - - +
1431B PGE 4.3 14.6 - - - +
243C GLY 3.6 19.7 - - - +
244C HIS* 4.1 7.7 - - + +
245C LEU 3.5 20.9 - - - +
289C SER* 4.1 4.7 - - - +
290C LEU* 1.3 102.5 - - + +
292C ILE* 1.3 60.2 + - - +
294C GLN* 3.6 31.2 - - + +
298C VAL* 5.8 0.4 - - + -
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Residues in contact with ILE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 2.9 37.7 + - + +
43B GLY 3.8 5.4 - - - -
44B LEU* 3.6 18.2 - - + +
69B LEU* 3.3 34.1 - - + -
290C LEU* 3.4 16.8 + - + +
291C PRO* 1.3 75.0 - - - +
293C TYR* 1.3 66.9 + - + +
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Residues in contact with TYR 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.5 15.4 - - - +
40B PRO* 3.2 45.3 - - + -
41B GLN* 3.5 2.6 - - - -
42B LEU* 2.7 47.0 + - + +
291C PRO 3.8 0.4 - - - -
292C ILE* 1.3 83.5 - - + +
294C GLN* 1.3 65.3 + - - +
295C GLY* 3.2 23.4 - - - -
296C GLY* 3.4 17.6 + - - -
1429C CL 4.5 4.3 - - + -
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Residues in contact with GLN 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 2.9 18.2 + - - -
41B GLN* 3.0 30.4 + - - +
42B LEU 5.0 2.0 - - - +
1431B PGE 4.0 18.8 - - - +
243C GLY* 3.7 5.9 + - - -
291C PRO* 3.6 30.7 - - + +
293C TYR* 1.3 79.9 - - - +
295C GLY* 1.3 61.0 + - - +
296C GLY 3.2 1.8 - - - -
297C MET* 3.1 25.2 + - + +
298C VAL* 3.5 22.5 - - + +
1429C CL 3.4 15.1 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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