Contacts of the helix formed by residues 267 - 286 (chain A) in PDB entry 4AYT
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 ARG 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS 4.3 1.4 + - - -
266A THR* 1.4 74.7 - - - +
268A THR* 1.4 64.7 + - - +
269A GLY* 3.3 6.3 - - - +
270A GLU* 3.3 23.3 + - + +
271A LEU* 3.3 14.3 + - - +
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Residues in contact with THR 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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263A PHE* 6.1 0.7 - - - -
266A THR 3.8 2.2 + - - -
267A ARG* 1.4 70.7 - - - +
269A GLY* 1.3 54.9 + - - +
271A LEU* 3.0 14.4 + - + +
272A ILE* 2.8 55.7 + - + +
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Residues in contact with GLY 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 3.3 5.6 - - - +
268A THR* 1.3 78.0 - - - +
270A GLU* 1.4 50.1 + - - +
272A ILE* 3.4 6.3 + - - +
273A ASN* 2.8 48.3 + - - -
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A THR* 4.9 7.6 - - + -
267A ARG* 3.3 23.0 + - + +
268A THR 3.3 0.6 - - - -
269A GLY* 1.4 72.7 - - - +
271A LEU* 1.3 58.6 + - - +
273A ASN* 3.9 14.2 + - - +
274A ARG* 3.0 76.0 + - - +
278A ASP* 4.9 0.3 - - - +
464A ARG* 4.2 9.4 - - - -
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Residues in contact with LEU 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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255A ILE* 4.2 22.9 - - + +
262A PHE* 3.9 17.0 - - + -
263A PHE* 4.1 29.4 - - + -
266A THR* 3.8 26.7 - - + +
267A ARG 3.3 12.9 + - - +
268A THR* 3.0 15.9 + - + +
270A GLU* 1.3 75.2 - - - +
272A ILE* 1.3 64.2 + - + +
274A ARG* 3.5 7.3 + - - +
275A LEU* 3.0 27.7 + - - +
468A LEU* 3.8 27.6 - - + -
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Residues in contact with ILE 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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252A PHE* 6.5 1.1 - - + -
268A THR* 2.8 35.6 + - + +
269A GLY* 3.9 5.8 - - - +
271A LEU* 1.3 78.0 - - + +
273A ASN* 1.4 57.4 + - - +
275A LEU* 3.0 20.6 + - + +
276A SER* 2.7 51.1 + - - +
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Residues in contact with ASN 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 GLY* 2.8 32.2 + - - +
270A GLU* 4.0 17.8 + - - +
272A ILE* 1.4 73.0 - - - +
274A ARG* 1.4 57.9 + - - +
276A SER* 4.7 2.7 - - - -
277A SER* 2.9 36.6 + - - +
278A ASP* 3.3 8.8 + - - -
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Residues in contact with ARG 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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251A LEU* 3.8 9.4 - - + -
266A THR* 6.1 3.6 - - - +
270A GLU* 3.0 53.0 + - - +
271A LEU* 3.7 8.2 - - - +
272A ILE 3.2 0.2 - - - -
273A ASN* 1.4 75.1 - - - +
275A LEU* 1.3 57.3 + - - +
278A ASP* 3.4 22.5 - - + +
279A THR* 3.4 23.9 + - - +
464A ARG* 2.9 43.5 + - + +
465A LEU* 3.5 12.7 - - + +
467A GLU* 2.8 29.3 + - - -
468A LEU* 3.7 28.6 - - + +
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Residues in contact with LEU 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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248A ARG* 3.6 45.5 + - + +
251A LEU* 3.6 24.0 - - + -
252A PHE* 4.1 26.9 - - + +
255A ILE* 5.2 4.0 - - + -
271A LEU 3.0 15.4 + - - +
272A ILE* 3.0 22.7 + - + +
274A ARG* 1.3 75.5 - - - +
276A SER* 1.4 57.0 + - - +
279A THR* 2.7 22.4 + - + +
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Residues in contact with SER 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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248A ARG* 5.0 6.9 + - - +
272A ILE* 2.7 32.7 + - - +
273A ASN* 4.3 3.4 - - - -
275A LEU* 1.4 75.6 - - - +
277A SER* 1.3 63.9 + - - +
279A THR* 3.2 13.9 + - - -
280A ALA* 3.4 13.5 + - - +
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASN* 2.9 23.6 + - - -
276A SER* 1.3 73.7 - - - +
278A ASP* 1.4 62.6 + - - -
280A ALA* 3.2 7.5 + - - +
281A LEU* 2.9 39.6 + - - +
284A ARG* 4.8 0.9 + - - -
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Residues in contact with ASP 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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270A GLU* 4.9 0.3 - - - +
273A ASN 3.3 6.0 + - - -
274A ARG* 3.4 35.0 + - - +
277A SER* 1.4 75.2 - - - +
279A THR* 1.4 59.7 + - - +
281A LEU* 3.8 9.0 - - - +
282A LEU* 3.1 23.7 + - - +
461A ALA* 3.7 15.4 - - + +
464A ARG* 2.8 47.7 + - - +
465A LEU* 3.3 22.9 - - + +
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Residues in contact with THR 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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244A VAL* 3.2 26.8 - - - +
247A LEU* 3.9 33.5 - - + +
248A ARG* 4.1 13.9 + - + -
251A LEU* 4.3 4.3 - - + -
274A ARG 3.4 16.9 + - - +
275A LEU* 2.7 29.4 + - - +
276A SER* 3.2 9.0 + - - -
278A ASP* 1.4 75.4 - - - +
280A ALA* 1.4 60.7 + - - +
283A GLY 3.3 10.0 + - - -
465A LEU* 3.8 18.6 - - + -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 4.3 11.4 - - + +
248A ARG* 5.7 2.9 - - - +
276A SER 3.4 12.5 + - - +
277A SER* 3.2 12.5 + - - +
279A THR* 1.4 78.3 + - - +
281A LEU* 1.4 64.3 + - - +
283A GLY* 3.4 1.9 + - - -
284A ARG* 3.1 39.7 + - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER* 2.9 24.6 + - - +
278A ASP* 3.8 26.5 - - - +
280A ALA* 1.4 73.6 - - - +
282A LEU* 1.3 53.8 + - - +
284A ARG* 3.2 36.6 + - - +
285A SER* 2.8 37.1 + - - -
454A GLU* 4.2 7.2 - - - +
457A LYS* 3.9 43.5 - - + +
458A GLY* 4.4 4.3 - - - +
461A ALA* 4.0 14.1 - - + -
464A ARG* 4.8 3.4 - - - +
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Residues in contact with LEU 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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160A LEU* 3.8 26.7 - - + -
163A LEU* 3.8 26.2 - - + -
247A LEU* 3.8 22.9 - - + -
278A ASP 3.1 15.8 + - - +
281A LEU* 1.3 77.2 - - - +
283A GLY* 1.3 62.9 + - - +
285A SER* 2.6 21.7 + - - +
286A VAL* 3.4 11.3 + - - +
458A GLY 3.3 24.2 - - - +
461A ALA* 4.7 1.5 - - + +
462A GLY* 3.9 14.6 - - - -
465A LEU* 3.8 18.6 - - + -
466A TRP* 4.5 10.5 - - - +
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Residues in contact with GLY 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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240A GLY* 4.3 6.1 - - - -
243A ILE* 4.0 16.9 - - - +
244A VAL* 3.7 25.4 - - - -
247A LEU* 4.4 1.2 - - - +
279A THR 3.3 7.9 + - - -
280A ALA 3.8 0.2 - - - -
281A LEU 3.3 0.6 - - - -
282A LEU* 1.3 80.3 - - - +
284A ARG* 1.4 52.4 + - - +
285A SER 3.5 0.3 + - - -
286A VAL* 3.6 5.9 - - - +
287A THR* 2.7 31.3 + - - +
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Residues in contact with ARG 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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240A GLY* 5.8 0.2 - - - -
244A VAL* 5.0 0.6 - - - +
277A SER* 4.8 0.8 + - - -
280A ALA* 3.1 28.0 + - - +
281A LEU* 3.5 53.3 - - + +
283A GLY* 1.4 72.1 - - - +
285A SER* 1.3 60.7 + - - +
286A VAL 3.5 0.2 - - - -
287A THR* 3.3 9.0 - - - -
288A GLU* 3.2 28.6 + - + +
289A ASN* 2.9 30.4 + - + +
454A GLU* 3.6 21.5 + - - +
457A LYS* 4.8 4.8 - - - +
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Residues in contact with SER 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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160A LEU* 4.5 3.8 - - - +
281A LEU 2.8 14.2 + - - -
282A LEU* 2.6 33.4 + - - +
284A ARG* 1.3 77.7 - - - +
286A VAL* 1.3 61.8 + - - +
287A THR 3.2 0.4 - - - -
289A ASN* 3.2 31.6 + - - -
290A LEU* 3.3 16.1 + - - +
454A GLU 4.8 5.4 - - - -
455A LEU* 5.3 8.6 - - - +
458A GLY* 4.1 18.3 - - - -
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Residues in contact with VAL 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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160A LEU* 3.5 52.5 - - + +
163A LEU* 4.3 14.4 - - + -
164A ALA* 4.3 10.9 - - + +
171A LEU* 4.4 8.7 - - - +
243A ILE* 4.2 20.0 - - + -
282A LEU 3.4 13.7 - - - +
283A GLY 3.6 8.7 - - - +
285A SER* 1.3 80.2 + - - +
287A THR* 1.3 61.5 + - - +
290A LEU* 3.6 28.9 - - + +
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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