Contacts of the helix formed by residues 271 - 286 (chain A) in PDB entry 1ZGA
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 ASN 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A TRP* 1.3 77.2 - - - +
272A ASP* 1.3 58.3 + - - +
273A GLU* 2.7 35.9 + - - +
274A GLN* 2.8 27.9 + - - +
275A SER* 2.8 25.8 + - - -
331A ARG* 3.5 3.4 - - - +
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Residues in contact with ASP 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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271A ASN* 1.3 74.6 - - - +
273A GLU* 1.3 58.5 + - - +
275A SER* 4.3 0.2 - - - -
276A LEU* 2.8 32.8 + - - +
329A LYS* 5.4 3.6 + - - -
331A ARG* 3.4 25.4 + - - +
335A GLU* 5.4 4.9 - - - +
339A LEU* 3.6 24.6 - - + +
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Residues in contact with GLU 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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271A ASN* 2.7 18.3 + - - +
272A ASP* 1.3 77.6 - - - +
274A GLN* 1.3 78.4 + - - +
276A LEU* 3.3 13.7 + - - +
277A LYS* 3.3 27.5 + - - +
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Residues in contact with GLN 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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252A PHE* 3.2 31.0 - - + -
270A TRP* 3.6 36.0 - - + -
271A ASN* 2.8 30.7 + - - +
273A GLU* 1.3 85.5 + - - +
275A SER* 1.3 64.1 + - - +
277A LYS* 3.3 30.8 + - - +
278A ILE* 3.2 27.2 + - - +
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Residues in contact with SER 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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267A LEU* 3.3 32.3 + - - +
270A TRP* 3.2 19.6 + - - +
271A ASN 2.8 19.4 + - - -
272A ASP 3.8 3.1 - - - -
274A GLN* 1.3 77.3 - - - +
276A LEU* 1.3 62.8 + - - +
278A ILE* 3.4 2.5 + - - +
279A LEU* 3.0 28.8 + - - +
331A ARG* 3.3 13.6 + - - -
336A TRP* 6.0 0.4 - - - -
339A LEU* 4.3 10.5 - - - -
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Residues in contact with LEU 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 ASP 2.8 18.6 + - - +
273A GLU* 3.5 7.4 - - - +
274A GLN 3.2 0.2 - - - -
275A SER* 1.3 75.6 - - - +
277A LYS* 1.3 60.5 + - + +
279A LEU* 3.2 3.8 + - + +
280A LYS* 2.8 57.7 + - + +
339A LEU* 3.8 17.0 - - + +
342A ASP* 3.7 21.5 - - + +
343A ALA* 3.6 36.3 - - + +
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PHE* 4.0 36.5 - - + +
273A GLU* 3.3 22.9 + - + +
274A GLN* 3.4 34.1 + - - +
275A SER 3.3 0.2 - - - -
276A LEU* 1.3 78.1 - - + +
278A ILE* 1.3 58.2 + - - +
280A LYS* 3.1 10.3 + - - +
281A ASN* 2.9 35.8 + - - +
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Residues in contact with ILE 278 (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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251A MET* 3.2 49.1 - - + +
252A PHE* 3.8 24.2 - - + -
255A ILE* 3.8 4.2 - - + +
263A LEU* 3.9 17.0 - - + -
266A VAL* 4.5 0.2 - - + -
267A LEU* 3.8 22.2 - - + -
270A TRP* 3.9 25.6 - - + -
274A GLN 3.2 16.2 + - - +
275A SER 3.7 6.3 - - - +
277A LYS* 1.3 75.1 - - - +
279A LEU* 1.3 57.9 + - - +
281A ASN* 3.4 2.9 + - - +
282A SER* 2.8 31.5 + - - +
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Residues in contact with LEU 279 (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 LEU* 3.8 24.5 - - + -
267A LEU* 3.9 15.0 - - + -
275A SER 3.0 21.2 + - - +
276A LEU* 3.7 4.5 - - - +
278A ILE* 1.3 73.9 - - - +
280A LYS* 1.3 60.5 + - - +
282A SER* 3.2 4.9 + - - -
283A LYS 3.0 22.0 + - - -
295A VAL* 4.5 9.0 - - + -
297A ILE* 3.9 21.5 - - + -
336A TRP* 5.5 1.1 - - + -
339A LEU* 3.8 40.8 - - + +
340A ILE* 4.5 4.5 - - + +
343A ALA* 3.8 12.8 - - + -
345A PHE* 3.5 19.2 - - + -
362A VAL* 5.6 2.0 - - + -
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Residues in contact with LYS 280 (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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276A LEU* 2.8 42.6 + - + +
277A LYS* 3.6 7.9 - - + +
279A LEU* 1.3 73.0 - - - +
281A ASN* 1.3 69.7 + - - +
283A LYS* 3.2 8.5 + - - +
284A GLU* 3.1 21.7 + - - +
342A ASP 3.8 20.1 + - - -
343A ALA* 3.9 20.2 - - - +
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Residues in contact with ASN 281 (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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251A MET 2.7 29.9 + - - +
252A PHE* 2.9 28.2 + - - +
253A LYS 3.5 16.5 - - - +
254A SER* 4.2 4.9 - - - -
255A ILE* 4.0 15.3 + - + +
277A LYS* 2.9 19.5 + - - +
278A ILE 3.8 3.1 - - - +
280A LYS* 1.3 78.8 - - - +
282A SER* 1.3 57.3 + - - +
284A GLU* 3.6 7.9 + - - +
285A ALA* 3.0 26.9 + - - +
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Residues in contact with SER 282 (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 ILE* 3.3 14.8 - - - +
261A VAL* 3.4 21.3 - - - +
263A LEU* 4.0 9.0 - - - +
278A ILE 2.8 22.6 + - - -
279A LEU* 3.4 10.1 - - - -
280A LYS 3.1 0.2 - - - -
281A ASN* 1.3 77.3 - - - +
283A LYS* 1.3 64.3 + - - +
285A ALA* 3.2 11.1 + - - +
286A ILE* 3.3 19.1 + - - +
295A VAL* 3.8 23.2 - - - +
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Residues in contact with LYS 283 (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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279A LEU 3.0 8.0 + - - +
280A LYS* 3.2 10.0 + - - +
282A SER* 1.3 76.1 - - - +
284A GLU* 1.3 58.6 + - - +
286A ILE* 3.1 10.6 - - - +
287A SER* 3.0 25.8 + - - -
343A ALA 3.8 19.1 - - - +
344A GLY* 3.7 21.5 + - - +
345A PHE* 3.4 26.4 - - + -
364A PRO* 3.4 38.4 + - + +
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Residues in contact with GLU 284 (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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254A SER* 6.5 1.6 - - - -
257A SER* 5.4 1.2 - - - -
280A LYS 3.1 12.6 + - - +
281A ASN* 3.8 11.4 - - - +
283A LYS* 1.3 73.3 - - - +
285A ALA* 1.3 65.6 + - - +
286A ILE 3.1 2.2 - - - -
287A SER* 2.8 36.8 + - - -
288A HIS* 4.7 1.0 + - - -
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Residues in contact with ALA 285 (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 ILE* 3.4 28.0 - - + +
256A PRO 3.5 10.1 - - - +
257A SER* 3.0 27.6 - - - +
258A ALA 3.0 7.5 + - - +
261A VAL* 3.8 15.0 - - + -
281A ASN 3.0 17.7 + - - +
282A SER 3.2 7.8 + - - +
284A GLU* 1.3 79.3 - - - +
286A ILE* 1.3 56.9 + - - +
288A HIS* 3.1 6.0 - - - -
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Residues in contact with ILE 286 (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 ALA 3.5 20.6 - - - +
259A ASP 3.9 2.7 - - - +
260A ALA* 4.1 1.1 - - - -
261A VAL* 3.7 16.6 - - + -
282A SER 3.5 10.5 - - - +
283A LYS* 3.1 18.8 - - + +
285A ALA* 1.3 77.1 - - - +
287A SER* 1.3 67.4 + - - +
288A HIS* 3.3 5.6 - - - -
289A LYS* 3.0 18.1 + - + +
290A GLY 3.6 5.6 + - - +
293A GLY* 3.7 13.0 - - - +
294A LYS* 3.5 36.8 - - - +
295A VAL* 3.9 15.0 - - + -
345A PHE* 4.3 3.6 - - + -
364A PRO* 4.2 18.2 - - + -
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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