Contacts of the helix formed by residues 276 - 282 (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 SER 276 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186P ILE* 4.1 4.9 - - - -
274P ARG 3.6 2.3 + - - -
275P ILE* 1.3 79.6 - - - +
277P ALA* 1.3 58.0 + - - +
278P LYS* 3.6 8.8 + - - +
279P ALA* 3.1 24.6 + - - +
280P ALA* 2.9 28.1 + - - +
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Residues in contact with ALA 277 (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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112P LEU* 3.5 30.1 - - + +
115P LEU* 3.9 13.0 - - + -
116P ALA* 3.5 18.8 - - - +
119P HIS* 4.5 7.3 + - - +
186P ILE* 3.6 19.3 - - + +
276P SER* 1.3 72.2 - - - +
278P LYS* 1.3 64.5 + - - +
280P ALA* 3.2 3.5 + - - +
281P LEU* 3.0 29.3 + - - +
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Residues in contact with LYS 278 (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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116P ALA* 4.1 21.8 + - + +
120P SER* 6.4 1.8 - - - -
276P SER* 3.2 7.8 - - - +
277P ALA* 1.3 79.5 - - - +
279P ALA* 1.3 61.6 + - - +
281P LEU* 3.3 30.3 + - - +
282P ALA* 3.8 6.2 + - - +
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Residues in contact with ALA 279 (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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275P ILE* 3.7 23.0 - - + +
276P SER* 3.1 19.5 + - - +
278P LYS* 1.3 73.9 - - - +
280P ALA* 1.3 66.0 + - - +
282P ALA* 3.0 17.9 + - - +
283P HIS* 3.5 6.9 + - - -
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Residues in contact with ALA 280 (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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112P LEU* 3.7 26.5 - - + -
186P ILE* 5.7 0.4 - - + -
262P LEU* 4.0 17.3 - - + -
266P MET* 5.4 1.3 - - + -
275P ILE* 3.7 17.6 - - + +
276P SER 2.9 17.9 + - - +
277P ALA 3.2 5.6 + - - +
279P ALA* 1.3 76.2 - - - +
281P LEU* 1.3 62.1 + - - +
283P HIS* 3.0 14.4 + - - +
286P PHE* 3.2 18.4 - - - -
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Residues in contact with LEU 281 (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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109P PHE* 3.5 54.8 - - + +
112P LEU* 3.6 15.7 - - + +
113P GLN* 3.8 16.6 - - + -
116P ALA* 4.2 22.2 - - + -
277P ALA 3.0 19.9 + - - +
278P LYS* 3.4 19.3 - - + +
279P ALA 3.1 0.6 - - - -
280P ALA* 1.3 77.4 - - - +
282P ALA* 1.3 58.3 + - - +
283P HIS 3.3 1.2 + - - -
286P PHE* 3.8 16.8 - - - +
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Residues in contact with ALA 282 (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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278P LYS 3.8 5.4 + - - +
279P ALA* 3.0 13.1 + - - +
281P LEU* 1.3 77.6 - - - +
283P HIS* 1.3 65.5 + - - +
284P PRO* 3.5 4.2 - - - +
287P GLN* 5.0 5.0 + - - -
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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