Contacts of the helix formed by residues 285 - 296 (chain A) in PDB entry 1PXV
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 PHE 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A TYR* 4.2 11.9 - + - -
283A ALA 5.5 0.4 - - - -
284A THR* 1.3 74.6 - - - +
286A PRO* 1.3 77.8 - - + +
287A ASN* 4.2 8.1 - - + +
288A GLN* 2.9 39.5 + - + +
289A MET* 3.2 15.2 + - - +
95C GLN* 3.7 50.3 - - + -
96C GLY* 4.6 3.8 - - - -
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Residues in contact with PRO 286 (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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285A PHE* 1.3 92.8 - - + +
287A ASN* 1.3 63.5 + - - +
289A MET* 3.0 31.4 + - - +
290A ILE* 3.2 11.5 + - + +
325A LEU* 4.8 4.0 - - + -
387A TYR* 5.2 1.8 - - - +
390A MET* 3.7 22.3 - - + +
95C GLN 5.7 1.8 - - - +
97C ILE* 3.7 24.0 - - + -
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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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285A PHE* 3.2 5.4 - - + +
286A PRO* 1.3 83.0 - - - +
288A GLN* 1.3 58.5 + - + +
290A ILE* 3.4 15.8 + - - +
291A GLU* 2.9 38.1 + - + +
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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 LEU* 3.7 36.0 + - + +
271A TYR* 3.2 40.3 + - - -
284A THR* 3.5 11.8 - - + -
285A PHE* 2.9 43.5 + - + +
287A ASN* 1.3 77.1 - - + +
289A MET* 1.3 60.3 + - - +
291A GLU* 4.4 5.4 - - - +
292A TYR* 2.8 33.6 + - - +
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Residues in contact with MET 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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244A ALA* 3.5 22.4 - - + -
248A MET* 3.9 11.3 - - + +
284A THR* 3.7 11.0 - - + -
285A PHE 3.2 11.4 + - - +
286A PRO* 3.0 20.2 + - - +
288A GLN* 1.3 76.1 - - - +
290A ILE* 1.3 63.3 + - - +
293A GLY* 3.2 15.4 + - - -
323A MET* 3.4 27.6 - - + -
325A LEU* 3.7 28.7 - - + -
341A ALA* 4.2 6.3 - - + -
390A MET* 4.0 10.5 - - + -
393A TYR* 2.8 29.3 + - - +
97C ILE* 4.4 14.8 - - + -
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Residues in contact with ILE 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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286A PRO* 3.2 12.5 + - + +
287A ASN* 3.7 19.7 - - - +
288A GLN 3.2 0.2 - - - -
289A MET* 1.3 75.9 - - - +
291A GLU* 1.3 80.7 + - - +
293A GLY* 3.3 1.7 + - - -
294A LYS* 3.0 38.2 + - + +
300A ILE* 3.9 29.2 - - + +
301A HIS 5.2 0.2 - - - +
302A TYR* 4.9 9.2 - - + +
390A MET* 3.7 31.0 - - + -
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Residues in contact with GLU 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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270A LEU* 6.2 1.1 - - + -
287A ASN* 2.9 26.0 + - + +
288A GLN* 4.2 4.9 - - - +
290A ILE* 1.3 83.7 - - - +
292A TYR* 1.3 64.1 + - - +
294A LYS* 2.8 39.8 + - - +
295A SER* 2.9 24.5 + - - -
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Residues in contact with TYR 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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248A MET* 4.0 21.5 - - + -
252A LEU* 3.7 12.1 - - + -
261A TYR* 3.4 22.5 - - - -
266A ILE* 3.5 46.6 - - + +
269A THR* 4.3 24.0 - - + -
270A LEU* 4.2 20.6 - - + +
288A GLN 2.8 19.3 + - - +
289A MET 4.2 2.2 - - - +
291A GLU* 1.3 76.0 - - - +
293A GLY* 1.3 65.3 + - - +
295A SER* 2.6 33.2 + - - -
296A GLN* 3.3 28.8 + - + +
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Residues in contact with GLY 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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252A LEU* 5.5 0.9 - - - -
289A MET 3.2 9.5 + - - -
290A ILE 3.3 0.2 + - - -
292A TYR* 1.3 81.4 - - - +
294A LYS* 1.3 62.9 + - - +
296A GLN* 3.0 13.6 + - - +
297A GLY 3.3 0.3 + - - -
298A ARG* 3.0 28.0 + - - +
300A ILE* 3.7 18.8 - - - -
393A TYR* 3.9 15.9 - - - -
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Residues in contact with LYS 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 ILE* 3.0 29.7 + - + +
291A GLU* 2.8 43.1 + - - +
293A GLY* 1.3 77.5 - - - +
295A SER* 1.3 59.8 + - - +
297A GLY* 2.9 20.1 + - - -
298A ARG 3.1 17.5 + - - +
299A ASP* 4.7 10.1 - - - +
300A ILE 4.4 9.0 - - - +
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Residues in contact with SER 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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269A THR* 6.0 0.3 - - - +
291A GLU 2.9 13.2 + - - -
292A TYR* 2.6 30.1 + - - -
294A LYS* 1.3 76.1 - - - +
296A GLN* 1.3 77.7 + - - +
297A GLY 3.3 1.1 + - - -
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Residues in contact with GLN 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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252A LEU* 4.3 14.8 - - + -
256A LYS* 2.7 33.3 + - - -
261A TYR* 2.7 35.4 + - + +
292A TYR* 3.6 45.3 + - + +
293A GLY 3.0 8.1 + - - +
294A LYS 3.0 1.2 - - - -
295A SER* 1.3 102.6 + - - +
297A GLY* 1.3 56.2 + - - +
298A ARG* 3.5 2.4 - - - +
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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