Contacts of the helix formed by residues 286 - 299 (chain A) in PDB entry 2B6V
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 ALA 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 5.1 8.5 - - + +
282A LEU 4.1 1.2 + - - +
283A LEU* 3.0 29.1 + - + +
285A ALA* 1.4 73.9 - - - +
287A ASN* 1.4 55.9 + - - +
288A VAL* 3.0 11.7 - - - -
289A CYS* 2.9 34.7 + - - -
290A LEU* 3.1 20.7 + - + +
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Residues in contact with ASN 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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67A ASP* 3.1 15.0 + - - +
70A MET* 3.2 20.6 - - - +
101A PHE* 5.1 0.2 - - - -
104A ASN* 3.2 19.6 + - - +
105A MET* 3.7 23.3 - - + +
108A SER* 2.9 26.5 + - - -
242A PHE* 3.7 23.5 - - + -
245A CYS* 4.2 11.3 - - - -
284A SER 2.9 27.0 + - - +
286A ALA* 1.4 74.5 - - - +
288A VAL* 1.4 66.6 + - - +
289A CYS 3.5 0.2 + - - -
290A LEU* 3.8 12.3 + - - +
291A ASP* 4.7 2.4 + - - +
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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
----------------------------------------------------------
32A VAL* 3.8 26.2 - - + +
36A GLY* 3.9 19.1 - - - -
40A ASN* 2.8 26.9 + - - +
67A ASP* 3.3 41.2 - - - +
70A MET* 3.5 19.8 - - + -
71A SER* 4.3 8.5 - - - +
75A PRO* 5.5 1.1 - - + -
285A ALA 3.0 24.6 + - - +
286A ALA* 3.9 6.1 - - - -
287A ASN* 1.4 80.1 - - - +
289A CYS* 1.4 72.1 + - + +
290A LEU 3.9 0.2 + - - -
292A PRO* 4.4 1.6 - - - +
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Residues in contact with CYS 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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32A VAL* 5.8 3.8 - - - -
35A ALA* 4.6 8.1 - - + -
36A GLY* 4.6 10.1 - - - +
39A LEU* 4.1 17.5 - - + +
40A ASN* 4.4 5.6 - - - +
286A ALA* 2.9 36.8 + - - -
288A VAL* 1.4 85.4 - - + +
290A LEU* 1.4 71.4 + - - +
292A PRO* 3.2 17.8 - - - +
293A ILE* 3.3 19.5 - - - +
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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
----------------------------------------------------------
241A VAL* 3.8 25.1 - - + -
242A PHE* 4.1 16.2 - - + -
245A CYS* 3.8 31.2 - - + -
286A ALA* 3.1 22.5 + - + +
287A ASN* 3.8 4.1 + - + -
288A VAL 3.6 2.2 - - - -
289A CYS* 1.4 82.2 - - - +
291A ASP* 1.4 68.0 + - - +
293A ILE* 3.1 25.6 + - + +
294A ILE* 3.3 17.1 + - + +
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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
----------------------------------------------------------
60A LEU* 4.8 2.7 - - + +
63A ILE* 3.7 38.5 - - + +
67A ASP* 4.6 4.7 - - - +
108A SER* 4.3 5.9 + - - -
111A PHE* 4.3 5.5 - - - -
112A PHE* 4.1 8.1 - - - -
238A ILE* 4.0 20.4 - - - +
242A PHE* 3.2 31.9 - - - -
287A ASN 4.7 2.6 + - - +
290A LEU* 1.4 74.3 - - - +
292A PRO* 1.4 65.9 - - + +
294A ILE* 3.0 10.5 + - - +
295A TYR* 2.9 27.0 + - - +
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Residues in contact with PRO 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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39A LEU* 4.1 21.3 - - + +
40A ASN* 3.3 30.1 - - - +
43A SER* 3.9 19.9 - - - +
60A LEU* 4.9 3.6 - - + -
63A ILE* 3.7 6.1 - - + -
288A VAL 4.4 1.6 - - - +
289A CYS 3.2 25.8 - - - +
291A ASP* 1.4 95.5 - - + +
293A ILE* 1.3 56.0 + - + +
295A TYR* 3.7 6.6 - - + +
296A PHE* 3.0 32.2 + - - +
302A PHE* 6.1 0.3 - - - -
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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
----------------------------------------------------------
39A LEU* 4.1 23.8 - - + -
289A CYS* 3.3 31.4 - - - +
290A LEU* 3.4 17.0 - - + +
292A PRO* 1.3 73.8 - - - +
294A ILE* 1.4 69.1 + - + +
296A PHE* 4.0 5.8 - - + +
297A PHE* 3.1 27.3 + - + +
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Residues in contact with ILE 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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234A ASN* 4.8 4.0 - - - +
237A SER* 4.7 11.2 - - - -
238A ILE* 3.8 29.4 - - + -
241A VAL* 3.9 37.7 - - + -
242A PHE* 4.0 17.3 - - + -
290A LEU* 3.3 17.7 + - + +
291A ASP* 3.0 6.8 + - - +
293A ILE* 1.4 79.5 - - + +
295A TYR* 1.4 57.8 + - + +
297A PHE* 5.0 0.2 - - - -
298A LEU* 2.9 57.5 + - + +
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Residues in contact with TYR 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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56A PHE* 5.2 1.1 - - + +
57A ILE* 2.9 45.9 - - + +
60A LEU* 3.7 34.3 - - + -
231A SER* 4.1 4.9 + - - -
234A ASN* 3.4 40.4 + - - -
235A ILE* 5.7 0.7 - - + -
238A ILE* 5.7 3.4 - - + -
291A ASP 2.9 10.4 + - - +
292A PRO* 4.1 3.1 - - + +
293A ILE 3.2 0.4 - - - -
294A ILE* 1.4 76.2 - - + +
296A PHE* 1.3 66.5 + - - +
298A LEU* 4.9 0.2 - - - -
299A CYS* 3.0 60.1 + - + +
302A PHE* 3.8 26.6 - + + +
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Residues in contact with PHE 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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292A PRO 3.0 19.0 + - - +
293A ILE* 4.0 5.4 - - - +
295A TYR* 1.3 77.6 - - - +
297A PHE* 1.4 63.4 + + + +
299A CYS 3.9 0.3 - - - +
302A PHE* 4.6 10.0 - + + -
303A ARG* 3.1 62.5 - - + +
306A LEU* 3.6 49.8 - - + -
307A CYS* 4.4 9.2 - - - -
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Residues in contact with PHE 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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233A ARG* 4.9 3.9 + - - -
293A ILE* 3.1 21.5 + - + +
294A ILE* 4.1 1.6 - - - +
296A PHE* 1.4 84.0 - + + +
298A LEU* 1.4 81.8 + - + +
299A CYS 4.7 1.4 - - - -
300A GLN* 5.1 0.3 + - - -
303A ARG* 4.9 16.8 - - - +
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Residues in contact with LEU 298 (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 LYS* 4.6 8.8 - - - +
233A ARG* 3.1 57.5 + - + +
234A ASN* 3.8 33.7 - - + -
237A SER* 4.6 10.3 - - - +
294A ILE* 2.9 37.5 + - + +
295A TYR* 4.5 0.9 - - - +
297A PHE* 1.4 97.7 - - + +
299A CYS* 1.4 62.6 + - - +
300A GLN* 3.4 3.6 + - - +
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Residues in contact with CYS 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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56A PHE* 5.3 9.9 - - - -
227A VAL 6.2 0.2 - - - -
230A LYS* 5.2 13.2 - - - +
231A SER* 6.4 1.3 - - - -
234A ASN* 5.5 0.9 - - - +
295A TYR* 3.0 53.1 + - + +
296A PHE 3.9 0.6 - - - +
297A PHE 4.7 0.7 - - - -
298A LEU* 1.4 76.8 - - + +
300A GLN* 1.3 67.4 + - - +
301A PRO* 3.7 22.4 - - - -
302A PHE* 3.7 11.7 - - + -
303A ARG* 3.0 22.7 + - - +
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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