Contacts of the helix formed by residues 260 - 276 (chain A) in PDB entry 3ZRH
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 LYS 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 ARG 3.9 14.6 + - - +
259A MET* 1.3 77.2 - - - +
261A LYS* 1.3 69.5 + - + +
262A THR* 3.2 14.4 - - + +
263A ASP* 2.6 50.2 + - - +
264A TRP* 3.1 17.0 + - - -
1693A EDO 4.3 2.0 - - - -
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Residues in contact with LYS 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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260A LYS* 1.3 75.0 - - - +
262A THR* 1.3 58.9 + - - +
264A TRP* 2.9 6.0 + - + +
265A LEU* 2.9 57.9 + - + +
1693A EDO 3.6 37.8 + - - +
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Residues in contact with THR 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 LYS* 4.7 11.7 - - + -
261A LYS* 1.3 77.9 - - - +
263A ASP* 1.3 68.8 + - - +
265A LEU* 3.4 13.6 + - - +
266A PHE* 2.9 27.7 + - - +
284A TYR* 4.3 12.8 + - - -
287A SER* 4.5 6.7 + - - -
289A GLY* 4.9 5.4 - - - -
293A ARG* 4.2 9.2 + - - +
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Residues in contact with ASP 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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258A ARG 4.1 0.6 - - - +
259A MET* 3.4 27.1 - - + -
260A LYS* 2.6 54.5 + - - +
262A THR* 1.3 80.7 - - - +
264A TRP* 1.3 56.2 + - - +
266A PHE* 3.2 2.3 + - - +
267A LEU* 2.9 33.5 + - + +
293A ARG* 3.0 33.1 + - - +
299A GLU* 5.5 1.3 - - + +
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Residues in contact with TRP 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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256A LYS* 3.8 37.3 + - + -
259A MET* 3.4 33.4 + - + +
260A LYS 3.1 21.5 + - - -
261A LYS 2.9 10.1 + - - +
263A ASP* 1.3 76.0 - - - +
265A LEU* 1.3 54.1 + - - +
267A LEU* 4.1 7.4 - - + +
268A ASN* 2.7 56.9 + - - +
302A LEU* 4.4 20.9 - - + -
1693A EDO 3.6 37.7 + - - +
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Residues in contact with LEU 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 LYS* 2.9 41.8 + - + +
262A THR* 3.6 12.6 - - - +
264A TRP* 1.3 77.9 - - + +
266A PHE* 1.3 61.8 + - - +
268A ASN* 3.8 11.5 - - + +
269A ALA* 3.1 23.7 + - - +
280A ALA 4.7 1.7 - - - +
283A ALA* 4.1 28.9 - - + +
284A TYR* 3.9 14.6 - - + +
287A SER* 3.5 30.3 - - - +
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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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262A THR 2.9 14.3 + - - +
263A ASP 3.2 5.8 + - - +
265A LEU* 1.3 77.4 - - - +
267A LEU* 1.3 74.4 + - + +
269A ALA* 3.1 5.7 + - - +
270A CYS* 3.0 38.2 + - - -
284A TYR* 3.8 31.1 - + + -
290A ASP 5.2 0.4 - - - -
291A ILE 6.1 0.4 - - - -
293A ARG* 3.3 66.6 - - + +
295A LEU* 3.4 31.4 - - + -
299A GLU* 3.9 6.1 - - - -
313A TYR 4.7 2.0 - - - -
315A LEU* 4.0 19.3 - - + -
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Residues in contact with LEU 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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259A MET* 4.3 12.3 - - + -
263A ASP* 2.9 21.7 + - + +
264A TRP* 4.1 9.6 - - + +
266A PHE* 1.3 83.3 - - + +
268A ASN* 1.3 65.0 + - - +
270A CYS* 3.1 14.1 + - - +
271A VAL* 3.1 17.7 + - - +
295A LEU* 3.6 30.7 - - + -
299A GLU* 3.8 25.8 - - + +
302A LEU* 3.9 36.6 - - + -
303A LEU* 3.8 18.0 - - + +
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Residues in contact with ASN 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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264A TRP* 2.7 48.7 + - - +
265A LEU* 3.8 13.2 - - + +
267A LEU* 1.3 73.6 - - - +
269A ALA* 1.3 56.6 + - - +
271A VAL* 3.4 8.8 + - - +
272A GLY* 2.8 25.5 + - - -
280A ALA* 3.8 14.0 - - + +
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Residues in contact with ALA 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 LEU 3.1 14.8 + - - +
266A PHE 3.1 8.9 + - - +
268A ASN* 1.3 73.8 - - - +
270A CYS* 1.3 68.0 + - - +
272A GLY* 2.9 1.5 + - - +
273A VAL* 2.8 27.4 + - - +
280A ALA 3.8 16.1 + - - +
281A ILE* 4.5 7.0 - - + +
284A TYR* 3.7 21.5 - - + -
315A LEU* 3.7 19.3 - - + -
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Residues in contact with CYS 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 PHE* 3.0 49.1 + - - -
267A LEU* 3.1 9.6 + - - +
269A ALA* 1.3 77.6 - - - +
271A VAL* 1.3 62.6 + - - +
273A VAL* 3.5 3.8 + - - +
274A VAL* 3.3 22.5 + - - +
295A LEU* 3.8 19.3 - - - -
303A LEU* 4.6 4.7 - - + -
309A PHE* 3.7 22.2 - - + -
313A TYR 5.7 0.4 - - - -
315A LEU* 3.8 12.6 - - - -
318A LEU* 3.8 12.6 - - + +
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Residues in contact with VAL 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 LEU 3.1 12.6 + - - +
268A ASN* 3.7 9.4 - - - +
270A CYS* 1.3 71.9 - - - +
272A GLY* 1.3 69.7 + - - +
274A VAL* 2.9 7.8 + - + +
275A GLU* 2.9 36.2 + - + +
303A LEU* 4.6 13.5 - - + -
305A ARG* 5.6 4.0 - - - +
309A PHE* 4.3 19.3 - - + -
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Residues in contact with GLY 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 ASN 2.8 16.2 + - - -
269A ALA 2.9 5.3 + - - -
271A VAL* 1.3 77.4 - - - +
273A VAL* 1.3 57.4 + - - +
275A GLU* 3.1 2.6 + - - -
276A GLY 2.8 25.5 + - - -
277A ASP* 3.0 20.8 + - - -
280A ALA* 3.9 19.5 - - - -
281A ILE* 4.8 0.9 - - - -
327A MET* 4.1 1.3 - - - +
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Residues in contact with VAL 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 ALA 2.8 18.1 + - - +
270A CYS* 3.6 5.8 - - - +
272A GLY* 1.3 69.8 - - - +
274A VAL* 1.3 71.2 + - + +
276A GLY 3.6 0.2 + - - -
281A ILE* 4.7 5.7 - - + +
315A LEU* 3.6 26.9 - - + +
318A LEU* 3.3 45.1 - - + +
319A ALA* 3.8 7.9 - - + +
322A PHE* 4.4 2.3 - - + +
324A ARG* 3.0 24.6 + - + +
327A MET* 3.9 22.7 - - - -
331A LEU* 6.0 2.0 - - + -
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Residues in contact with VAL 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 CYS 3.3 14.5 + - - +
271A VAL* 2.9 8.8 + - - +
273A VAL* 1.3 79.3 - - + +
275A GLU* 1.3 58.9 + - - +
305A ARG* 3.2 30.1 - - - +
308A ALA* 4.1 4.7 - - + -
309A PHE* 3.6 26.9 - - + -
318A LEU* 5.0 0.9 - - + -
322A PHE* 3.9 44.6 - - + -
324A ARG* 2.6 28.1 + - - -
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Residues in contact with GLU 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 VAL* 2.9 31.8 + - + +
272A GLY* 3.9 3.8 - - - +
274A VAL* 1.3 85.5 - - + +
276A GLY* 1.3 59.6 + - - +
277A ASP* 3.5 7.1 + - + +
305A ARG* 2.8 35.3 + - - -
324A ARG* 3.9 6.6 + - - +
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Residues in contact with GLY 276 (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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272A GLY 2.8 8.4 + - - -
273A VAL 3.6 1.6 + - - -
274A VAL 3.5 3.4 + - - -
275A GLU* 1.3 75.0 - - - +
277A ASP* 1.3 58.0 + - - +
278A LEU* 3.5 6.1 + - - +
324A ARG* 3.7 20.2 - - - -
327A MET* 3.6 17.7 - - - +
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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