Contacts of the helix formed by residues 256 - 267 (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 ASP 256 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101P LEU* 4.4 15.9 - - - +
105P LYS* 5.1 2.6 + - - -
257P GLU* 1.3 59.6 + - - +
258P ASP* 3.0 23.1 + - - +
259P GLY* 3.0 12.6 + - - -
260P ARG* 2.9 45.7 + - - +
285P PHE* 4.0 14.9 - - - -
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Residues in contact with GLU 257 (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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256P ASP* 1.3 75.0 - - - +
258P ASP* 1.3 58.1 + - - +
260P ARG* 3.6 32.4 + - - +
261P SER* 2.8 41.0 + - - -
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Residues in contact with ASP 258 (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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256P ASP* 3.0 10.4 + - - +
257P GLU* 1.3 78.7 - - - +
259P GLY* 1.3 57.8 + - - +
261P SER* 4.5 1.7 - - - -
262P LEU* 3.0 24.9 + - - +
283P HIS* 3.0 15.5 - - - -
284P PRO* 3.8 31.0 - - - +
285P PHE* 3.8 21.0 - - + +
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Residues in contact with GLY 259 (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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193P PHE* 3.8 11.6 - - - -
256P ASP* 3.0 15.2 + - - -
258P ASP* 1.3 76.2 - - - +
260P ARG* 1.3 57.2 + - - +
262P LEU* 3.3 2.8 + - - +
263P LEU* 2.8 30.9 + - - +
285P PHE* 3.3 29.0 - - - -
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Residues in contact with ARG 260 (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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248P PHE* 3.8 34.8 + - + +
249P SER* 3.7 36.2 + - - +
256P ASP* 2.9 30.0 + - - +
257P GLU* 3.6 35.6 + - - +
259P GLY* 1.3 73.4 - - - +
261P SER* 1.3 60.7 + - - +
263P LEU* 3.7 7.7 - - + +
264P SER* 2.9 31.4 + - - -
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Residues in contact with SER 261 (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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257P GLU* 2.8 29.7 + - - -
258P ASP* 3.7 4.3 - - - -
260P ARG* 1.3 73.4 - - - +
262P LEU* 1.3 62.9 + - - +
264P SER* 2.7 24.2 + - - -
265P GLN* 3.2 17.2 + - - +
283P HIS* 2.8 21.3 + - - -
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Residues in contact with LEU 262 (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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108P LEU* 3.8 17.5 - - + -
112P LEU* 5.0 0.4 - - + -
193P PHE* 4.3 2.9 - - + -
258P ASP 3.0 18.0 + - - +
259P GLY* 3.6 4.0 - - - +
261P SER* 1.3 77.3 + - - +
263P LEU* 1.3 63.5 + - - +
265P GLN* 3.1 5.6 + - - +
266P MET* 3.1 34.0 + - + +
275P ILE* 4.3 7.6 - - + -
280P ALA* 4.0 24.7 - - + -
283P HIS* 3.6 26.9 - - + +
285P PHE* 3.9 12.8 - - + -
286P PHE* 3.8 33.4 - - + -
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Residues in contact with LEU 263 (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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190P GLY* 3.3 36.8 - - - +
193P PHE* 4.1 17.9 - - + -
194P ALA* 4.3 19.7 - - + -
202P LEU* 5.4 1.1 - - + -
248P PHE* 3.5 23.8 - - + -
251P VAL* 4.9 8.3 - - + -
259P GLY 2.8 21.0 + - - +
260P ARG* 3.3 6.3 + - + +
262P LEU* 1.3 73.7 - - - +
264P SER* 1.3 63.0 + - - +
266P MET* 3.0 15.9 + - - +
267P LEU* 3.0 28.0 + - + +
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Residues in contact with SER 264 (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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245P ARG* 4.7 7.2 + - - -
248P PHE* 3.3 29.1 - - - -
260P ARG 2.9 14.4 + - - -
261P SER* 2.7 22.9 + - - -
263P LEU* 1.3 77.0 - - - +
265P GLN* 1.3 64.9 + - - +
267P LEU* 3.4 11.3 + - - +
268P HIS* 3.4 22.3 + - - -
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Residues in contact with GLN 265 (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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261P SER* 3.4 13.1 + - - +
262P LEU* 3.1 7.4 + - - +
264P SER* 1.3 79.5 + - - +
266P MET* 1.3 60.3 + - - +
267P LEU 3.2 0.4 + - - -
268P HIS* 3.6 26.2 + - + +
273P LYS 5.7 0.2 - - - +
274P ARG* 3.5 8.3 - - - +
275P ILE* 3.0 59.0 + - + +
283P HIS* 3.6 25.5 + - - -
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Residues in contact with MET 266 (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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108P LEU* 4.4 5.4 - - + -
112P LEU* 4.2 13.9 - - + -
186P ILE* 3.6 33.3 - - + +
187P TRP* 3.6 14.2 - - - -
189P LEU* 3.9 25.4 - - + -
190P GLY* 3.6 24.9 - - - +
193P PHE* 4.4 13.9 - - - -
262P LEU* 3.1 37.9 + - + +
263P LEU* 3.0 9.2 + - - +
265P GLN* 1.3 77.6 - - - +
267P LEU* 1.3 59.5 + - - +
268P HIS 3.5 0.9 - - - -
274P ARG* 3.2 20.8 - - - -
275P ILE* 3.7 15.7 - - + -
280P ALA* 5.4 0.2 - - + -
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Residues in contact with LEU 267 (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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187P TRP* 3.3 52.5 - - + +
190P GLY* 4.3 2.0 - - - -
191P CYS* 4.3 13.2 - - - +
202P LEU* 3.9 22.4 - - + -
203P PHE* 4.8 1.1 - - + -
219P LEU* 3.9 25.8 - - + +
245P ARG* 5.5 4.3 + - - +
248P PHE* 4.3 14.8 - - + -
263P LEU* 3.0 39.5 + - + +
264P SER 3.4 6.0 + - - +
265P GLN 3.2 0.4 - - - -
266P MET* 1.3 87.1 - - - +
268P HIS* 1.3 63.3 - - - -
269P TYR* 3.4 2.3 + - - -
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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