Contacts of the helix formed by residues 283 - 289 (chain P) in PDB entry 1JVP
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 HIS 283 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258P ASP* 3.0 34.3 - - + -
261P SER* 2.8 24.5 + - - -
262P LEU* 3.4 22.5 + - + -
265P GLN* 3.6 22.4 - - - -
275P ILE* 4.9 2.0 - - + -
279P ALA 3.5 3.9 + - - +
280P ALA* 3.0 19.9 + - - +
281P LEU 3.3 0.4 - - - +
282P ALA* 1.3 80.2 - - - +
284P PRO* 1.3 81.6 - - + +
285P PHE* 3.0 31.8 + - + +
286P PHE* 3.1 20.9 + - + +
287P GLN* 4.2 3.3 + - - -
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Residues in contact with PRO 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258P ASP* 3.8 24.5 - - - +
282P ALA 3.5 3.8 - - - +
283P HIS* 1.3 101.3 - - + +
285P PHE* 1.3 61.5 + - - +
286P PHE 3.1 0.4 - - - -
287P GLN* 2.9 38.0 + - + +
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Residues in contact with PHE 285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P LEU* 4.1 17.3 - - + -
105P LYS* 3.1 67.7 + - + +
108P LEU* 4.2 3.1 - - + -
193P PHE* 3.7 29.6 - + - -
256P ASP* 4.0 14.1 - - - -
258P ASP* 3.8 13.4 - - + +
259P GLY* 3.3 30.3 - - - -
262P LEU* 3.9 16.8 - - + -
283P HIS* 3.0 24.1 + - + +
284P PRO* 1.3 77.8 - - - +
286P PHE* 1.3 78.9 + + + +
287P GLN 3.5 0.9 + - - -
288P ASP* 3.5 2.1 - - - +
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Residues in contact with PHE 286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P LYS* 3.7 31.2 - - + -
108P LEU* 3.7 18.8 - - + -
109P PHE* 3.6 39.3 - + + -
112P LEU* 3.6 28.7 - - + -
262P LEU* 3.8 13.9 - - + -
280P ALA 3.2 28.7 - - - -
281P LEU* 3.8 11.7 - - - +
283P HIS* 3.1 12.8 + - + +
285P PHE* 1.3 86.4 - + + +
287P GLN* 1.3 65.6 + - - +
288P ASP 3.1 2.9 - - - -
289P VAL* 3.2 24.7 + - + +
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Residues in contact with GLN 287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282P ALA 5.0 4.4 + - - -
283P HIS 4.6 2.4 + - - -
284P PRO* 2.9 35.3 + - + +
285P PHE 3.3 0.4 - - - -
286P PHE* 1.3 78.7 - - - +
288P ASP* 1.3 60.1 + - + +
289P VAL* 3.8 1.2 + - - +
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Residues in contact with ASP 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P LYS* 2.6 34.4 + - - +
285P PHE 3.5 4.0 - - - +
287P GLN* 1.3 80.3 - - + +
289P VAL* 1.3 64.4 + - - +
290P THR* 3.6 12.1 + - - +
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Residues in contact with VAL 289 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P LYS* 4.1 17.3 - - + +
106P SER* 4.0 11.7 - - - +
109P PHE* 4.0 50.5 - - + -
286P PHE* 3.2 24.7 + - + +
287P GLN 3.5 2.0 + - - +
288P ASP* 1.3 80.2 + - - +
290P THR* 1.3 75.4 + - - +
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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