Contacts of the helix formed by residues 260 - 274 (chain A) in PDB entry 4ZZ7
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ASP 3.6 2.0 + - - -
259A ALA* 1.3 68.5 - - - +
261A MET* 1.3 64.8 + - - +
262A ASP* 3.5 15.3 + - - +
263A ASN* 3.4 26.3 + - + +
264A ALA* 3.1 22.5 + - - +
415A PHE* 5.6 0.5 - - - -
417A ARG* 4.8 6.2 - - - +
437A ASN* 5.7 1.6 + - - -
482B PRO* 4.7 11.9 - - + +
483B SER* 4.4 25.2 - - - +
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Residues in contact with MET 261 (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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255A VAL* 3.6 33.4 - - + -
256A MET 4.7 3.4 - - - +
257A PRO 5.2 3.6 - - - +
259A ALA* 3.1 13.5 + - - +
260A ASP* 1.3 70.8 + - - +
262A ASP* 1.3 60.6 + - - +
264A ALA* 3.3 4.4 + - - +
265A VAL* 3.0 36.1 + - + +
293A ALA* 4.0 24.7 - - + +
296A ALA* 4.1 17.9 - - + +
297A LEU* 4.0 26.2 - - - -
300A LYS* 4.1 28.3 - - + +
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Residues in contact with ASP 262 (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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260A ASP* 3.3 9.2 + - - +
261A MET* 1.3 76.6 - - - +
263A ASN* 1.3 63.2 + - - +
265A VAL* 4.1 3.9 - - - +
266A ASN* 3.2 25.1 + - - +
300A LYS* 2.7 38.1 + - - +
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Residues in contact with ASN 263 (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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260A ASP* 3.4 30.5 + - + +
262A ASP* 1.3 77.2 - - - +
264A ALA* 1.3 59.9 + - - +
266A ASN* 3.9 7.4 - - - +
267A GLN* 2.8 55.7 + - - +
415A PHE* 5.0 2.4 - - - -
437A ASN* 4.5 1.7 - - - +
480B ARG* 3.5 24.7 + - - +
482B PRO* 3.7 21.6 - - - +
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Residues in contact with ALA 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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255A VAL* 5.0 4.3 - - + -
259A ALA* 5.5 0.2 - - + -
260A ASP 3.1 17.5 + - - +
261A MET* 3.3 15.9 + - - +
263A ASN* 1.3 74.3 + - - +
265A VAL* 1.3 55.1 + - + +
267A GLN* 3.2 2.4 + - - +
268A LEU* 2.6 46.8 + - + +
297A LEU* 5.4 0.2 - - + -
415A PHE* 3.9 43.0 - - + -
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Residues in contact with VAL 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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261A MET* 3.0 24.6 + - + +
262A ASP* 4.1 4.3 - - - +
264A ALA* 1.3 72.8 - - - +
266A ASN* 1.3 66.1 + - - +
268A LEU* 3.0 18.2 + - - +
269A LEU* 3.1 13.7 + - - +
297A LEU* 4.2 21.8 - - + +
300A LYS* 3.8 41.3 - - + +
301A MET* 3.9 23.4 - - + +
304A ALA* 4.0 15.9 - - + -
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Residues in contact with ASN 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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262A ASP 3.2 17.4 + - - +
263A ASN* 3.9 9.0 - - - +
265A VAL* 1.3 82.7 - - - +
267A GLN* 1.3 62.9 + - + +
269A LEU* 3.6 29.4 - - - +
270A GLY 4.2 1.6 + - - -
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Residues in contact with GLN 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 ASN* 2.8 43.8 + - - +
264A ALA* 3.7 2.9 - - - +
266A ASN* 1.3 80.2 - - + +
268A LEU* 1.3 61.4 + - - +
269A LEU 3.3 0.5 + - - -
270A GLY* 3.5 3.3 + - - -
271A ALA* 3.3 21.3 + - - +
415A PHE* 4.0 7.9 - - + -
437A ASN 2.9 25.7 + - - +
438A ILE* 4.4 7.6 - - - +
439A PRO* 3.5 26.7 - - + +
480B ARG* 3.3 18.5 + - - +
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Residues in contact with LEU 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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253A ALA* 4.4 1.8 - - + -
255A VAL* 4.8 5.2 - - + -
264A ALA* 2.6 30.6 + - + +
265A VAL* 3.0 6.2 + - - +
267A GLN* 1.3 69.0 - - - +
269A LEU* 1.3 59.1 + - - +
270A GLY 3.4 0.2 - - - -
271A ALA* 3.8 3.6 - - - -
272A ALA* 3.0 33.1 + - - +
273A PHE* 4.4 0.9 - - - -
283A LEU* 3.8 42.8 - - + +
286A ALA* 4.8 11.2 - - + -
297A LEU* 4.0 26.9 - - + -
301A MET* 4.4 11.0 - - - -
388A LEU* 4.7 10.3 - - + +
415A PHE* 4.0 26.5 - - + -
439A PRO* 4.3 1.3 - - + -
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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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265A VAL 3.1 10.9 + - - +
266A ASN* 3.6 28.0 - - - +
268A LEU* 1.3 76.3 - - - +
270A GLY* 1.3 58.5 + - - +
273A PHE* 3.1 42.9 + - + +
274A GLY 3.7 0.7 + - - -
301A MET* 3.4 27.1 - - + +
304A ALA* 4.1 31.2 - - + +
305A MET* 4.5 0.9 - - - -
308A LEU* 3.9 30.7 - - + +
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Residues in contact with GLY 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 ASN 4.2 2.4 + - - -
267A GLN 3.5 5.5 + - - -
269A LEU* 1.3 79.4 - - - +
271A ALA* 1.3 52.6 + - - +
274A GLY* 3.1 19.8 + - - -
279A ARG* 2.7 28.5 + - - -
440A LEU* 4.7 3.1 - - - -
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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 GLN 3.3 11.3 + - - +
268A LEU* 4.2 3.8 - - - +
269A LEU 3.3 0.2 - - - -
270A GLY* 1.3 76.8 - - - +
272A ALA* 1.3 61.2 + - - +
274A GLY 4.9 0.7 + - - +
279A ARG* 4.1 3.3 + - - +
282A ALA* 3.4 11.3 - - - +
283A LEU* 2.9 30.0 + - + -
439A PRO* 3.6 31.6 - - + -
440A LEU* 3.7 28.2 - - + +
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Residues in contact with ALA 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 LEU* 3.0 18.8 + - + +
271A ALA* 1.3 79.8 - - - +
273A PHE* 1.3 76.7 + - + +
274A GLY 3.6 0.2 - - - -
277A GLY* 3.4 22.2 - - - -
282A ALA* 4.6 2.1 - - - +
283A LEU* 3.3 22.8 + - + +
385A GLY 4.4 1.6 - - - +
386A PRO* 4.4 2.8 - - - +
387A VAL 4.5 4.1 + - - +
388A LEU* 3.7 24.9 - - + -
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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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268A LEU 4.4 1.8 - - - -
269A LEU* 3.1 26.0 + - + +
272A ALA* 1.3 82.3 - - + +
274A GLY* 1.3 68.7 + - - +
276A SER* 3.0 13.5 + - - -
277A GLY 3.8 3.4 - - - +
301A MET* 4.1 13.2 - - + -
305A MET* 3.8 31.0 - - + -
308A LEU* 4.2 14.8 - - + -
320A PHE* 3.1 35.0 - - + -
366A GLY* 4.0 7.0 - - - -
367A THR 3.4 26.7 - - - -
386A PRO* 3.6 25.8 - - + -
387A VAL 4.1 0.4 - - - -
388A LEU* 3.6 29.8 - - + -
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Residues in contact with GLY 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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96A ASP* 4.6 4.9 - - - -
269A LEU 3.7 2.8 + - - -
270A GLY* 3.1 25.8 + - - -
271A ALA 5.3 0.3 - - - +
272A ALA 3.6 0.9 - - - +
273A PHE* 1.3 74.2 - - - +
275A SER* 1.3 73.0 + - - -
277A GLY* 2.8 16.3 + - - -
278A GLU 4.3 0.2 + - - -
279A ARG* 3.8 13.7 + - - +
319A ASP 5.2 2.5 - - - -
320A PHE* 4.9 2.0 - - - -
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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