Contacts of the helix formed by residues 281 - 296 (chain A) in PDB entry 1W57
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 ASN 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A GLY* 6.0 0.2 - - - -
245A ASP* 3.3 10.1 - - - +
279A ASN* 5.4 0.4 - - - +
280A ALA* 1.3 70.9 - - - +
282A SER* 1.3 57.1 + - - +
283A MET* 3.0 22.4 + - - +
284A GLU* 2.9 34.8 + - + +
285A LEU* 3.3 11.5 + - - +
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Residues in contact with SER 282 (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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244A SER* 3.6 6.8 + - - -
245A ASP* 2.9 26.9 + - - -
247A ASP* 3.6 15.9 - - - +
250A ALA* 3.9 6.3 - - - +
251A HIS* 2.6 38.2 + - - -
254A THR* 4.9 1.0 + - - -
280A ALA 3.3 1.6 + - - -
281A ASN* 1.3 72.6 - - - +
283A MET* 1.3 56.8 + - - +
285A LEU* 3.2 14.0 + - - +
286A LEU* 2.8 27.9 + - - +
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Residues in contact with MET 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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230A ALA* 3.4 32.3 - - - +
231A GLY* 3.7 23.6 - - - +
247A ASP* 4.3 2.9 + - - +
249A LEU* 5.7 0.4 - - - -
250A ALA* 3.8 15.5 - - - -
281A ASN* 3.0 12.5 + - - +
282A SER* 1.3 77.9 - - - +
284A GLU* 1.3 56.6 + - - +
286A LEU* 3.2 18.7 + - + +
287A LYS 2.9 22.9 + - - -
324A ASN* 4.1 6.5 - - - +
325A ILE* 4.0 18.4 - - + -
328A THR* 3.2 50.7 - - + +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 2.9 26.5 + - + +
283A MET* 1.3 77.2 - - - +
285A LEU* 1.3 66.4 + - + +
287A LYS* 3.1 31.2 + - - +
288A GLN* 2.6 53.9 + - - +
328A THR* 5.3 0.7 - - - -
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Residues in contact with LEU 285 (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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244A SER* 5.6 1.3 - - - -
251A HIS* 5.4 5.8 - - + +
254A THR* 4.6 2.7 - - - +
266A ILE* 5.6 6.5 - - + -
270A TYR* 3.3 51.4 + - + -
277A PHE* 4.1 25.6 - - + -
280A ALA* 4.2 22.7 - - + -
281A ASN 3.3 11.4 + - - +
282A SER* 3.2 15.7 + - - +
284A GLU* 1.3 79.9 - - + +
286A LEU* 1.3 55.6 + - - +
288A GLN* 3.5 11.8 + - - +
289A ALA* 3.0 23.2 + - - +
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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
----------------------------------------------------------
250A ALA* 4.0 7.4 - - + +
253A LEU* 3.9 28.0 - - + -
254A THR* 3.2 45.9 + - - +
257A ILE* 3.9 13.2 - - + -
282A SER 2.8 12.9 + - - +
283A MET* 3.3 40.6 - - + +
285A LEU* 1.3 72.8 - - - +
287A LYS* 1.3 66.0 + - - +
289A ALA* 3.0 6.0 + - + +
290A TYR* 3.0 20.3 + - - +
325A ILE* 5.1 0.9 - - + -
328A THR* 4.7 1.3 - - + -
329A LEU* 3.9 17.7 - - + -
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Residues in contact with LYS 287 (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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20A LYS* 5.4 4.3 - - - +
283A MET 2.9 12.4 + - - +
284A GLU* 3.3 31.4 - - - +
286A LEU* 1.3 75.2 - - - +
288A GLN* 1.3 58.9 + - + +
290A TYR* 3.1 5.5 + - + +
291A ASP* 2.9 50.5 + - - +
327A HIS 5.3 1.6 + - - -
328A THR* 3.3 36.9 + - + +
329A LEU* 4.3 10.7 - - + +
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Residues in contact with GLN 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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270A TYR* 3.1 29.5 + - - +
284A GLU* 2.6 48.6 + - - +
285A LEU* 3.7 8.2 - - - +
286A LEU 3.2 0.4 - - - -
287A LYS* 1.3 79.0 - - + +
289A ALA* 1.3 60.1 + - - +
291A ASP* 3.3 15.3 + - + +
292A LYS* 3.2 25.9 + - - +
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Residues in contact with ALA 289 (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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254A THR* 3.9 28.7 - - + +
257A ILE* 4.9 3.4 - - + -
258A LEU* 4.2 18.3 - - + +
269A LEU* 4.6 6.1 - - + -
270A TYR* 3.9 3.3 + - - -
285A LEU 3.0 12.9 + - - +
286A LEU* 3.0 10.9 + - + +
288A GLN* 1.3 77.0 - - - +
290A TYR* 1.3 61.8 + - - +
292A LYS* 3.1 20.7 + - - +
293A VAL* 3.3 14.9 + - - +
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Residues in contact with TYR 290 (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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257A ILE* 3.9 21.7 - - + +
286A LEU 3.0 6.8 + - - +
287A LYS* 3.1 8.5 + - + +
289A ALA* 1.3 75.9 - - - +
291A ASP* 1.3 58.6 + - - +
293A VAL* 3.0 15.4 + - + -
294A ARG* 2.8 63.1 + - + +
299A GLU* 3.9 9.4 - - - +
300A LEU* 3.0 50.9 + - + +
329A LEU* 3.3 55.0 - - + -
331A LEU* 3.5 11.4 - - + +
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Residues in contact with ASP 291 (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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20A LYS* 3.2 40.3 + - + +
287A LYS* 2.9 32.7 + - - +
288A GLN* 3.4 18.4 - - + +
289A ALA 3.2 0.2 - - - -
290A TYR* 1.3 78.3 - - - +
292A LYS* 1.3 60.6 + - - +
294A ARG* 3.6 14.3 + - - +
295A GLU* 3.2 34.6 + - - +
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Residues in contact with LYS 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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258A LEU* 5.3 2.2 - - + -
263A LEU* 4.2 17.5 - - + +
269A LEU* 4.5 21.5 - - + -
270A TYR* 5.7 0.9 - - - +
288A GLN 3.2 15.4 + - - +
289A ALA* 3.1 10.9 + - - +
291A ASP* 1.3 76.7 - - - +
293A VAL* 1.3 63.2 + - - +
294A ARG 3.1 0.2 - - - -
295A GLU* 3.2 46.7 + - - +
296A ILE* 3.5 13.3 + - - +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 3.6 25.8 - - + +
258A LEU* 4.5 3.8 - - + -
261A ALA* 3.5 22.9 - - + -
263A LEU* 3.9 7.6 - - + -
289A ALA 3.3 7.5 + - - +
290A TYR* 3.0 22.1 + - + +
292A LYS* 1.3 76.6 - - - +
294A ARG* 1.3 60.8 + - - +
296A ILE* 3.4 17.2 - - - +
298A PHE* 3.2 38.1 + - + +
363A LEU* 3.8 21.3 - - + -
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Residues in contact with ARG 294 (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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20A LYS* 3.1 60.7 - - + +
21A VAL* 3.4 16.7 - - + +
290A TYR* 2.8 54.8 + - + +
291A ASP* 3.9 13.5 + - - +
293A VAL* 1.3 79.1 - - - +
295A GLU* 1.3 60.3 + - - +
297A GLY* 3.1 13.7 + - - -
298A PHE 3.7 17.0 + - - +
299A GLU* 5.5 5.1 - - + +
329A LEU 5.4 2.8 + - - -
330A ASP* 5.2 13.2 + - - +
366A PHE* 5.8 3.5 - - - +
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Residues in contact with GLU 295 (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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20A LYS 3.3 18.1 + - - +
21A VAL* 4.0 2.0 - - - +
22A LYS* 3.1 57.2 + - + +
25A PHE* 3.3 14.0 - - - +
291A ASP* 3.2 24.7 + - - +
292A LYS* 3.2 34.9 + - - +
294A ARG* 1.3 76.5 - - - +
296A ILE* 1.3 60.3 + - + +
297A GLY 3.4 1.8 + - - -
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Residues in contact with ILE 296 (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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22A LYS* 5.3 2.2 - - - +
25A PHE* 3.7 31.4 - - + +
27A ARG* 2.9 26.5 + - - -
56A ASN* 5.6 2.7 - - - +
59A TYR* 3.4 43.9 + - + +
261A ALA* 3.8 11.7 - - + +
263A LEU* 3.7 26.7 - - + -
292A LYS 3.5 11.7 - - - +
293A VAL 3.4 13.5 - - - +
294A ARG 3.2 0.2 - - - -
295A GLU* 1.3 78.6 - - + +
297A GLY* 1.3 59.7 + - - +
298A PHE* 3.8 19.3 - - + -
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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