Contacts of the helix formed by residues 264 - 268 (chain A) in PDB entry 1JD7
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 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TRP* 3.8 14.7 - - - -
172A ARG* 4.6 1.4 + - - -
174A ASP* 5.8 0.2 - - - +
200A GLU* 3.9 16.0 - - - +
202A ILE* 6.0 3.4 - - + -
223A PHE* 5.5 2.2 - - + -
262A ASN* 3.1 16.1 + - - +
263A HIS* 1.3 108.6 + - - +
265A ASN* 1.3 64.0 + - - +
267A ARG* 3.2 11.5 + - - +
268A GLY 3.6 0.3 + - - -
269A HIS* 2.9 46.7 + - + +
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Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 4.4 6.0 - - + -
226A SER* 3.1 29.9 + - - -
227A THR* 5.5 0.8 + - - -
259A PHE* 4.2 8.5 - - - -
261A ASP* 3.4 8.7 - - - +
262A ASN* 2.6 41.4 + - - +
264A ASP* 1.3 70.3 - - - +
266A GLN* 1.3 62.0 + - - +
267A ARG 2.9 6.8 + - - -
268A GLY 3.5 6.6 + - - -
269A HIS 3.3 13.5 - - - +
270A GLY 3.8 6.9 + - - +
271A GLY* 3.6 29.0 - - - +
272A ALA 4.6 1.9 - - - +
275A VAL* 3.5 20.4 - - + +
277A THR* 5.2 0.3 - - - +
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Residues in contact with GLN 266 (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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9A PHE* 4.5 0.5 - - - -
261A ASP* 3.3 18.9 + - - +
262A ASN 3.1 17.6 + - - +
263A HIS* 3.4 3.6 - - - +
265A ASN* 1.3 84.6 + - - +
267A ARG* 1.3 93.7 + - + +
268A GLY 3.7 0.4 - - - -
277A THR* 3.9 26.4 - - + +
278A PHE* 4.0 13.6 - - + -
279A GLU* 5.5 0.3 - - - +
302A MET* 4.0 8.5 - - - +
304A SER* 3.4 36.1 + - - -
307A PHE* 3.7 18.2 - - + -
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Residues in contact with ARG 267 (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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9A PHE* 3.7 21.8 - - - -
46A TRP* 3.5 24.8 - - - +
263A HIS* 2.7 48.9 + - - +
264A ASP 3.6 4.5 - - - +
265A ASN 2.9 0.8 - - - -
266A GLN* 1.3 105.5 + - - +
268A GLY* 1.3 59.5 + - - +
269A HIS* 3.4 17.1 + - + -
305A TYR* 3.8 17.4 + - - -
307A PHE* 3.5 33.3 - - + +
311A THR* 3.4 57.6 + - + +
313A ALA 4.8 0.6 + - - -
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Residues in contact with GLY 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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265A ASN 3.5 6.7 + - - -
266A GLN 3.7 0.4 - - - -
267A ARG* 1.3 76.9 - - - +
269A HIS* 1.3 63.0 + - - +
270A GLY 3.7 2.8 + - - -
271A GLY 3.8 19.6 + - - +
272A ALA 6.2 0.2 - - - -
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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