Contacts of the helix formed by residues 263 - 272 (chain A) in PDB entry 2Z82
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A THR* 1.3 73.0 - - - +
264A GLU* 1.3 73.9 + - - +
266A PHE* 3.8 7.7 - - - +
267A ASN* 3.4 17.8 + - - +
289A LEU* 4.1 5.1 - - - +
290A ASN 3.0 4.8 + - - -
291A GLY* 3.2 5.0 - - - -
292A LEU* 2.6 58.0 + - - +
295A PHE* 4.0 26.1 - - + +
324A LEU 4.1 2.4 - - - +
325A PHE* 4.2 20.8 - - + -
326A TYR* 5.7 3.5 - - + -
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Residues in contact with GLU 264 (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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235A ALA 4.8 8.7 - - - +
237A PHE 5.7 1.9 - - - +
238A GLN* 6.3 0.7 - - - -
262A THR* 3.0 5.7 + - - +
263A ASP* 1.3 82.5 + - - +
265A SER* 1.3 66.8 + - - +
266A PHE 3.1 1.8 - - - -
267A ASN* 3.1 15.4 + - - +
268A GLU* 3.1 22.5 + - + +
295A PHE* 3.7 33.9 - - + -
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Residues in contact with SER 265 (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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234A LEU* 3.1 27.1 + - - -
235A ALA 3.6 7.6 - - - -
237A PHE* 4.2 9.9 - - - -
261A LEU* 3.0 12.3 - - - +
262A THR* 2.7 43.0 + - - -
264A GLU* 1.3 74.9 + - - +
266A PHE* 1.3 60.4 + - - +
268A GLU* 3.1 13.6 + - - +
269A LEU* 3.0 25.8 + - - +
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Residues in contact with PHE 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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1A PDJ 3.7 63.7 - - + -
261A LEU* 3.5 17.5 - - + -
262A THR 2.9 19.5 + - - +
263A ASP* 3.8 7.2 - - - +
265A SER* 1.3 77.2 + - - +
267A ASN* 1.3 65.7 + - + +
269A LEU* 3.1 19.4 + - + +
270A LEU* 3.2 44.8 + - + +
284A PHE* 4.0 19.7 - + - -
289A LEU* 4.4 7.2 - - + -
331A VAL* 5.4 5.8 - - + -
334A LEU* 5.3 7.0 - - + -
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Residues in contact with ASN 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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263A ASP 3.4 9.0 + - - +
264A GLU 3.1 10.8 + - - +
266A PHE* 1.3 80.7 - - + +
268A GLU* 1.3 67.3 + - - +
270A LEU* 3.4 22.1 + - + +
271A LYS* 3.5 12.5 + - - +
295A PHE* 4.1 17.0 - - + -
301A ASP* 3.4 20.7 + - - +
302A VAL* 3.6 20.6 + - - +
303A VAL* 3.5 32.3 - - - +
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Residues in contact with GLU 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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237A PHE* 3.5 39.0 - - + +
238A GLN* 3.8 10.1 - - + +
239A PHE* 3.0 35.8 + - - +
264A GLU* 3.1 28.5 + - + +
265A SER* 3.2 9.9 - - - +
266A PHE 3.1 0.2 - - - -
267A ASN* 1.3 82.3 - - - +
269A LEU* 1.3 63.3 + - - +
271A LYS* 3.1 47.0 + - - +
272A LEU* 3.9 1.4 + - - +
295A PHE* 5.9 1.2 - - - -
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Residues in contact with LEU 269 (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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1A PDJ 5.2 10.9 - - + +
213A LEU* 4.8 10.3 - - + -
217A PHE* 6.0 1.6 - - + -
234A LEU* 3.9 14.6 - - + -
237A PHE* 4.0 17.9 - - + -
254A LEU* 6.0 1.3 - - + -
256A PHE* 3.6 40.6 - - + -
261A LEU* 4.1 19.3 - - + -
265A SER 3.0 12.4 + - - +
266A PHE* 3.1 15.0 + - + +
268A GLU* 1.3 75.9 - - - +
270A LEU* 1.3 54.0 + - - +
272A LEU* 2.7 57.8 + - + +
273A LEU* 4.1 1.9 + - - +
284A PHE* 5.2 2.9 - - + -
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Residues in contact with LEU 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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1A PDJ 3.5 38.6 - - + -
266A PHE* 3.2 38.1 + - + +
267A ASN* 3.5 19.3 - - - +
268A GLU 3.3 0.2 - - - -
269A LEU* 1.3 77.8 - - - +
271A LYS* 1.3 63.1 + - - +
273A LEU* 3.1 35.5 + - + +
302A VAL* 5.7 2.0 - - + -
303A VAL* 4.0 34.8 - - + +
306A LEU* 4.2 8.5 - - + -
330A THR* 5.9 1.1 - - - +
334A LEU* 4.4 15.0 - - + -
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Residues in contact with LYS 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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239A PHE* 3.9 34.4 - - + +
267A ASN* 3.5 13.6 + - - +
268A GLU* 3.1 34.6 + - - +
269A LEU 3.0 1.0 + - - -
270A LEU* 1.3 75.4 - - - +
272A LEU* 1.3 61.9 + - - +
273A LEU 3.2 1.0 + - - -
274A ARG* 2.8 48.9 + - - +
301A ASP* 3.3 32.1 + - - +
303A VAL* 3.4 20.2 - - + -
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Residues in contact with LEU 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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213A LEU* 5.7 0.2 - - + -
214A LEU* 5.1 3.4 - - + -
217A PHE* 3.6 53.7 - - + -
237A PHE* 3.6 30.3 - - + -
239A PHE* 4.1 23.1 - - + -
242A LEU* 4.4 15.5 - - + -
269A LEU* 2.7 33.9 + - + +
271A LYS* 1.3 80.5 - - - +
273A LEU* 1.3 60.9 + - + +
274A ARG 3.1 1.2 + - - -
275A TYR* 3.1 22.4 + - + +
276A ILE* 3.8 8.7 - - + +
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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