Contacts of the helix formed by residues 285 - 299 (chain A) in PDB entry 2WP9
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 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY 5.4 1.3 - - - -
121A GLY* 4.8 5.8 - - - +
284A ALA* 1.3 78.9 - - - +
286A ARG* 1.3 63.7 + - - -
287A ASP* 3.4 8.3 - - - -
288A VAL* 3.3 4.9 + - - +
289A VAL* 3.1 18.1 + - - +
398A ASN* 4.6 5.4 - - - -
400A LEU* 5.3 4.0 - - - -
588A TYR* 3.7 33.5 - - - -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.7 13.7 - - - -
240A GLN* 2.7 47.2 + - + +
241A PHE 4.8 2.0 - - - +
242A HIS* 3.3 31.4 + - - -
243A PRO* 3.5 26.7 - - + +
255A GLU* 2.7 33.4 + - - +
258A ARG* 5.0 0.4 - - - +
284A ALA 4.6 1.1 - - - +
285A GLY* 1.3 68.3 - - - -
287A ASP* 1.3 67.1 + - - +
289A VAL* 4.0 0.8 - - - +
290A ALA* 2.9 28.1 + - - +
354A HIS* 4.1 2.0 + - - -
398A ASN* 3.7 14.5 + - - +
399A ARG* 3.5 25.4 + - - +
400A LEU* 6.0 0.2 - - - +
401A GLY* 3.5 29.5 - - - +
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Residues in contact with ASP 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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241A PHE 5.8 0.4 - - - -
285A GLY 3.7 2.1 - - - -
286A ARG* 1.3 75.2 + - - +
288A VAL* 1.3 62.0 + - - -
290A ALA* 3.8 4.0 - - - +
291A ARG* 2.9 57.0 + - - +
398A ASN* 3.1 19.8 + - - +
538A GLY* 3.5 25.1 - - - +
539A ALA* 3.7 12.3 - - + +
586A ARG* 2.6 47.4 + - - -
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A MET* 4.7 4.7 - - + -
276A TYR* 4.7 12.6 - - + +
277A ALA* 4.9 2.0 - - + -
284A ALA* 4.6 13.2 - - + -
285A GLY 3.6 7.0 - - - +
286A ARG 3.2 0.6 - - - -
287A ASP* 1.3 78.5 + - - +
289A VAL* 1.3 64.4 + - - +
291A ARG* 3.3 14.6 + - - +
292A SER* 2.8 36.5 + - - +
586A ARG* 3.7 26.9 - - - +
587A THR* 6.2 0.4 - - - -
588A TYR* 4.0 19.1 - - + +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PRO* 3.5 27.8 - - + -
258A ARG* 4.7 8.3 - - - +
264A LEU* 3.9 24.7 - - + -
273A MET* 3.8 23.8 - - + -
282A ASP 4.3 7.6 - - - +
284A ALA* 3.7 23.8 - - + +
285A GLY 3.1 17.0 + - - +
286A ARG* 4.0 3.4 - - - +
288A VAL* 1.3 74.8 - - - +
290A ALA* 1.3 63.1 + - - +
292A SER* 3.2 6.6 + - - -
293A ILE* 3.1 23.0 + - + +
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Residues in contact with ALA 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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241A PHE* 3.6 25.8 - - + +
243A PRO* 4.3 6.7 - - + +
286A ARG 2.9 17.8 + - - +
287A ASP* 3.8 5.2 - - - +
289A VAL* 1.3 77.9 - - - +
291A ARG* 1.3 62.0 + - - +
293A ILE 3.3 1.6 + - - -
294A MET* 3.2 27.7 + - - +
351A PRO* 3.5 23.5 - - + +
473A VAL* 4.6 7.0 - - + -
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 2.9 54.7 + - - +
288A VAL* 3.8 14.2 - - - +
290A ALA* 1.3 76.7 - - - +
292A SER* 1.3 64.5 + - - +
294A MET* 3.1 2.8 + - - +
295A ILE* 2.9 32.2 + - + +
473A VAL* 3.8 19.0 + - + +
474A PHE* 3.7 32.3 - - + -
538A GLY* 2.7 25.2 + - - -
539A ALA* 4.1 6.5 + - - +
540A HIS 4.9 0.2 + - - -
541A SER* 3.7 24.7 - - - -
586A ARG* 4.7 0.4 - - - +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 4.2 2.9 - - - -
273A MET* 3.7 16.6 - - - +
276A TYR* 3.3 49.8 + - - +
288A VAL* 2.8 25.5 + - - +
289A VAL 3.2 5.4 + - - -
291A ARG* 1.3 77.5 - - - +
293A ILE* 1.3 63.1 + - - +
295A ILE* 3.2 3.7 + - - +
296A GLU* 3.1 26.9 + - - +
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Residues in contact with ILE 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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243A PRO* 3.6 31.9 - - + +
264A LEU* 3.9 28.9 - - + -
272A PHE* 3.8 25.1 - - + -
289A VAL 3.1 14.1 + - - +
290A ALA 3.8 5.4 - - - +
291A ARG 3.2 0.2 - - - -
292A SER* 1.3 77.9 - - - +
294A MET* 1.3 61.8 + - - +
295A ILE 3.3 0.2 + - - -
296A GLU* 3.3 5.0 + - + +
297A ILE* 3.0 33.9 + - + +
311A ALA* 4.0 22.2 - - + +
349A VAL* 5.0 2.5 - - + -
350A ILE* 4.9 1.6 - - - -
351A PRO* 3.6 20.2 - - + -
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Residues in contact with MET 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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290A ALA 3.2 15.8 + - - +
291A ARG* 3.1 5.2 + - - +
293A ILE* 1.3 78.9 - - - +
295A ILE* 1.3 57.4 + - - +
297A ILE* 3.8 19.2 - - + +
298A ARG* 3.0 44.1 + - + +
350A ILE* 4.1 17.3 - - + -
351A PRO* 3.9 28.3 - - + +
473A VAL* 4.2 19.3 - - + -
474A PHE* 3.9 17.5 - - + -
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Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TYR* 3.1 37.0 - - + +
291A ARG* 2.9 27.3 + - + +
292A SER 3.8 0.9 - - - +
293A ILE 3.2 0.2 - - - -
294A MET* 1.3 75.0 - - - +
296A GLU* 1.3 66.2 + - - +
298A ARG* 3.1 9.6 + - - +
299A GLU* 2.9 49.7 + - + +
474A PHE* 3.8 23.6 - - + -
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Residues in contact with GLU 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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266A ASN* 2.7 33.6 + - + -
272A PHE* 3.7 33.7 - - + -
275A ARG* 2.7 32.1 + - - -
276A TYR* 2.7 10.4 + - - -
292A SER 3.1 16.4 + - - +
293A ILE* 3.4 11.2 - - + +
295A ILE* 1.3 78.4 - - - +
297A ILE* 1.3 59.4 + - + +
299A GLU* 3.6 1.4 + - - +
300A GLY 3.5 1.9 + - - -
301A ARG* 2.8 55.2 + - + +
302A GLY* 3.3 4.3 + - - +
311A ALA* 6.3 1.1 - - + -
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Residues in contact with ILE 297 (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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293A ILE* 3.0 32.3 + - + +
294A MET* 3.9 22.0 - - + +
295A ILE 3.1 0.2 - - - -
296A GLU* 1.3 71.8 - - + +
298A ARG* 1.3 69.4 + - + +
299A GLU 3.0 1.6 - - - -
300A GLY* 2.9 16.5 + - - -
302A GLY* 4.0 22.3 + - - +
309A PRO* 4.1 19.5 - - + -
310A HIS* 4.1 19.5 - - - +
311A ALA* 5.9 0.7 - - + -
350A ILE* 4.0 27.6 - - + -
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A MET* 3.0 38.0 + - + +
295A ILE* 3.7 8.1 - - - +
297A ILE* 1.3 76.9 - - + +
299A GLU* 1.3 63.1 + - + +
300A GLY 3.3 0.9 + - - -
474A PHE* 3.8 30.5 + - - +
476A GLU* 5.5 1.6 + - - -
543A PHE* 3.4 39.5 - - - -
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Residues in contact with GLU 299 (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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295A ILE* 2.9 31.5 + - - +
296A GLU 4.3 0.2 - - - +
298A ARG* 1.3 81.9 - - + +
300A GLY* 1.3 60.2 + - - +
301A ARG* 2.7 53.8 + - - +
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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