Contacts of the helix formed by residues 267 - 275 (chain A) in PDB entry 2JIH
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 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ALA* 1.3 74.5 - - - +
268A GLN* 1.3 67.0 + - - +
269A SER* 2.4 28.8 + - - -
270A MET* 3.0 13.7 + - - +
271A ALA* 3.0 19.6 + - - +
312A ILE* 3.6 16.2 - - + -
321A VAL* 3.6 30.3 - - + +
355A LEU* 4.1 7.9 - - + +
356A PHE 3.3 5.9 + - - +
357A THR* 2.7 30.5 + - - -
359A GLN* 5.0 0.3 - - - +
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Residues in contact with GLN 268 (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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267A ASP* 1.3 76.2 - - - +
269A SER* 1.3 56.6 + - - +
271A ALA* 3.6 3.5 - - + +
272A GLU* 2.9 53.4 + - + +
312A ILE* 3.1 17.6 + - - +
313A HIS* 3.7 20.7 + - - +
315A GLU* 3.7 37.0 - - + +
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 2.4 30.0 + - - -
268A GLN* 1.3 78.8 + - - +
270A MET* 1.3 56.5 + - - +
272A GLU* 3.6 6.3 + - - +
273A PHE* 3.0 30.5 + - - +
357A THR* 3.4 1.7 + - - -
358A ARG* 3.0 33.7 + - - +
359A GLN* 4.7 3.1 - - - -
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Residues in contact with MET 270 (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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266A ALA* 3.7 13.0 - - + -
267A ASP* 3.0 14.7 + - - +
269A SER* 1.3 79.7 + - - +
271A ALA* 1.3 58.8 + - - +
274A HIS* 2.9 41.0 + - + +
278A LEU* 3.5 19.6 - - + +
281A TYR* 4.3 4.7 - - + -
282A LEU* 4.0 10.8 - - + -
356A PHE* 3.2 47.1 - - + +
357A THR* 3.9 4.0 - - - -
358A ARG* 3.7 16.4 - - - -
390A ASP* 3.6 40.2 - - + +
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Residues in contact with ALA 271 (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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267A ASP 3.0 9.4 + - - +
268A GLN* 3.6 12.6 - - + +
270A MET* 1.3 74.1 - - - +
272A GLU* 1.3 60.2 - - + +
275A GLY* 2.9 30.0 + - - +
278A LEU* 3.9 11.8 - - - +
311A VAL* 3.8 24.2 - - + -
312A ILE 4.2 2.7 - - - +
313A HIS* 3.9 22.5 - - + +
1559B NI 4.5 0.2 - - + -
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Residues in contact with GLU 272 (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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268A GLN* 2.9 40.3 + - + +
269A SER* 3.9 5.7 - - - +
271A ALA* 1.3 77.7 - - + +
273A PHE* 1.3 65.4 + - - +
275A GLY* 4.0 3.8 + - - -
272B GLU 5.3 2.1 - - - +
275B GLY* 4.3 8.1 - - - -
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Residues in contact with PHE 273 (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 SER 3.0 20.0 + - - +
270A MET 4.0 2.2 - - - +
271A ALA 3.4 0.2 - - - -
272A GLU* 1.3 77.7 - - - +
274A HIS* 1.3 84.2 + + - +
358A ARG* 3.6 43.7 - - + +
489A GLN 3.5 22.7 - - - -
490A PHE* 4.2 8.3 - + - -
493A GLY* 4.3 3.6 - - - -
494A GLU* 4.3 15.0 - - + -
275B GLY* 3.7 0.2 - - - -
276B SER* 3.0 61.7 + - - -
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Residues in contact with HIS 274 (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 MET* 2.9 32.4 + - + +
273A PHE* 1.3 101.7 - + + +
275A GLY* 1.3 65.7 + - - +
276A SER 3.3 0.5 + - - -
277A GLY* 3.3 13.5 + - - -
278A LEU* 3.6 35.7 - - + +
281A TYR* 3.4 45.2 - + - +
390A ASP* 3.0 23.0 + - - -
486A ARG* 5.4 2.5 + - - -
490A PHE* 4.0 9.7 - + - -
274B HIS 3.6 12.5 - - - +
276B SER* 4.6 3.7 + - - -
277B GLY* 5.2 1.6 + - - +
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Residues in contact with GLY 275 (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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271A ALA 2.9 22.0 + - - +
272A GLU 4.0 1.9 + - - -
273A PHE 3.6 2.0 + - - -
274A HIS* 1.3 77.8 - - - +
276A SER* 1.3 63.5 + - - -
277A GLY 3.2 0.3 + - - -
278A LEU* 3.3 14.2 + - - +
272B GLU 4.4 9.4 - - - -
273B PHE 3.6 10.1 - - - -
275B GLY* 4.4 5.4 - - - -
494B GLU* 4.4 0.9 - - - +
1559B NI 4.3 13.8 - - - +
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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