Contacts of the helix formed by residues 264 - 281 (chain A) in PDB entry 2AFW
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 SER 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A LEU* 4.1 16.8 - - - -
259A ASN* 4.7 1.7 + - - -
261A PHE* 3.1 15.1 + - - +
263A ASN* 1.3 81.8 + - - +
265A ALA* 1.3 66.6 + - - +
266A ARG* 3.2 3.1 - - - -
267A TRP* 2.9 22.6 + - - +
268A PHE* 3.0 10.6 + - - +
316A PRO* 5.1 0.2 - - - -
317A VAL 2.7 33.7 + - - -
318A LEU* 4.0 11.5 - - - +
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Residues in contact with ALA 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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259A ASN* 3.5 26.6 - - - +
261A PHE 3.1 8.6 + - - +
262A PRO* 3.3 19.5 + - + +
264A SER* 1.3 78.2 - - - +
266A ARG* 1.3 58.1 + - - +
268A PHE* 3.2 2.6 + - - +
269A GLU* 2.9 41.0 + - - +
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Residues in contact with ARG 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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40A LYS 3.1 24.4 + - - -
41A ASN* 3.3 19.2 + - - +
43A HIS 2.9 30.1 + - - +
44A GLN* 3.6 20.4 + - - +
45A PRO* 5.2 0.6 - - - +
262A PRO 4.9 0.6 + - - -
263A ASN 5.5 4.4 + - - +
264A SER* 4.9 2.0 - - - -
265A ALA* 1.3 79.3 - - - +
267A TRP* 1.3 94.7 + - + +
269A GLU* 3.5 17.7 + - - +
270A ARG* 3.2 27.0 + - - +
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Residues in contact with TRP 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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40A LYS 5.0 1.6 + - - -
43A HIS* 3.4 27.6 - - + -
45A PRO* 3.7 44.6 - - + -
243A LEU* 3.9 23.7 - - + +
263A ASN 5.1 2.0 - - - -
264A SER* 2.9 16.1 + - - +
266A ARG* 1.3 108.5 - - + +
268A PHE* 1.3 66.6 + - - +
270A ARG* 3.1 16.6 + - + +
271A LEU* 3.0 18.7 + - - +
318A LEU* 4.1 10.8 - - + -
354A PHE* 3.6 36.1 - + + -
358A TYR* 3.3 40.4 + + + -
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Residues in contact with PHE 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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257A PHE* 3.2 29.8 - - + -
258A PRO 3.4 14.1 - - - -
259A ASN* 3.5 45.5 - - + +
264A SER 3.0 8.3 + - - +
265A ALA 3.5 7.9 - - - +
267A TRP* 1.3 79.3 - - - +
269A GLU* 1.3 61.6 + - - +
271A LEU* 3.0 10.3 + - + +
272A GLN* 3.0 43.4 + - + +
294A PHE* 3.8 25.6 - + + -
295A GLN 3.3 23.8 - - - -
296A ASN* 5.3 0.9 - - - -
318A LEU* 3.9 20.0 - - + +
320A LEU* 5.5 2.5 - - + -
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Residues in contact with GLU 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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259A ASN* 5.1 3.4 - - - +
265A ALA* 2.9 25.2 + - - +
266A ARG* 3.6 17.1 - - - +
267A TRP 3.1 0.2 - - - -
268A PHE* 1.3 78.6 - - + +
270A ARG* 1.3 58.2 + - - +
272A GLN* 3.3 24.8 + - - +
273A ALA* 2.9 27.7 + - - +
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Residues in contact with ARG 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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45A PRO* 4.0 16.9 - - + +
47A ILE* 3.6 31.3 - - - +
266A ARG 3.2 14.7 + - - +
267A TRP* 3.1 31.5 + - + +
269A GLU* 1.3 74.9 - - - +
271A LEU* 1.3 58.6 + - - +
273A ALA* 3.1 25.3 + - - +
274A ILE* 2.8 50.8 + - + +
354A PHE* 4.3 12.3 - - + -
357A GLU* 2.8 33.5 + - - -
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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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267A TRP 3.0 12.8 + - - +
268A PHE* 3.0 10.8 + - + +
270A ARG* 1.3 76.4 - - - +
272A GLN* 1.3 57.9 + - - +
274A ILE* 3.4 4.5 + - - +
275A GLU* 2.9 30.7 + - - +
294A PHE* 3.8 28.5 - - + -
318A LEU* 3.7 21.3 - - + -
320A LEU* 3.7 37.5 - - + -
350A ILE* 3.8 23.3 - - + +
351A LEU* 5.1 4.7 - - + -
354A PHE* 3.5 31.4 - - + -
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Residues in contact with GLN 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 PHE* 3.0 30.8 + - + +
269A GLU* 3.4 30.4 - - - +
271A LEU* 1.3 76.1 - - - +
273A ALA* 1.3 55.7 + - - +
275A GLU* 3.7 5.6 - - - +
276A HIS* 2.9 29.3 + - - +
292A ARG* 5.1 0.9 + - - -
294A PHE* 3.1 38.0 - - + +
295A GLN 3.6 4.0 - - - -
296A ASN* 3.4 33.5 + - - +
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Residues in contact with ALA 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 GLU 2.9 15.5 + - - +
270A ARG* 3.1 31.2 + - - +
272A GLN* 1.3 72.9 - - - +
274A ILE* 1.3 62.7 + - - +
276A HIS* 3.6 6.9 - - - +
277A GLU* 2.9 30.0 + - - +
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Residues in contact with ILE 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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53A LEU* 5.4 1.6 - - + -
270A ARG* 2.8 43.5 + - + +
271A LEU* 3.7 6.1 - - - +
273A ALA* 1.3 72.7 - - - +
275A GLU* 1.3 68.2 + - - +
277A GLU* 3.9 3.5 - - - +
278A LEU* 2.9 44.0 + - + +
350A ILE* 3.8 13.9 - - + +
353A VAL* 3.7 23.1 - - + -
354A PHE* 3.7 36.8 - - + +
357A GLU* 3.5 17.7 - - - +
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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 LEU 2.9 17.4 + - - +
272A GLN* 3.7 4.8 - - - +
274A ILE* 1.3 78.7 - - - +
276A HIS* 1.3 58.9 + - - +
278A LEU* 4.7 1.1 - - - -
279A HIS* 2.9 30.5 + - - +
284A LEU* 3.8 3.3 - - + +
287A HIS* 2.7 33.4 + - + +
289A LEU* 5.5 1.1 - - + -
292A ARG* 3.4 13.3 - - + +
293A TYR* 2.8 33.5 + - - -
294A PHE* 3.1 32.7 + - + +
350A ILE* 3.9 24.2 - - + -
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Residues in contact with HIS 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 GLN 2.9 18.8 + - - +
273A ALA* 3.6 7.6 - - - +
274A ILE 3.2 0.2 - - - -
275A GLU* 1.3 78.7 - - - +
277A GLU* 1.3 66.1 + - - +
279A HIS* 3.2 7.0 + - - +
280A GLU* 2.9 53.5 + - + +
289A LEU* 3.8 36.5 - - + +
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Residues in contact with GLU 277 (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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50A SER* 4.3 6.8 + - - -
53A LEU* 3.7 26.2 - - + -
273A ALA 2.9 17.3 + - - +
274A ILE* 4.1 3.6 - - - +
276A HIS* 1.3 81.6 - - + +
278A LEU* 1.3 65.3 + - - +
280A GLU* 3.2 10.8 + - - +
281A LEU* 3.0 40.9 + - + +
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Residues in contact with LEU 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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53A LEU* 4.0 28.7 - - + +
57A ALA* 5.0 5.2 - - + +
274A ILE* 2.9 38.9 + - + +
275A GLU 4.0 1.6 - - - +
277A GLU* 1.3 78.9 - - - +
279A HIS* 1.3 62.4 + - - +
281A LEU* 3.4 2.3 + - - -
282A GLY 3.4 2.4 + - - -
283A LEU* 3.0 54.8 + - + +
284A LEU* 3.8 17.0 + - + -
349A LYS* 4.0 14.8 - - + +
350A ILE* 3.8 29.2 - - + +
353A VAL* 4.4 4.5 - - + -
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Residues in contact with HIS 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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275A GLU 2.9 20.0 + - - +
276A HIS 3.3 5.2 - - - +
278A LEU* 1.3 76.3 - - - +
280A GLU* 1.3 76.4 + - - +
282A GLY* 2.9 21.3 + - - -
284A LEU* 3.8 11.1 - - + +
287A HIS* 2.8 55.3 + + + +
288A SER* 3.8 7.4 - - - -
289A LEU* 3.6 28.6 - - + +
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Residues in contact with GLU 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 HIS* 2.9 42.8 + - + +
277A GLU* 3.2 14.8 + - - +
279A HIS* 1.3 99.8 + - - +
281A LEU* 1.3 58.3 + - + +
282A GLY 3.1 3.2 + - - -
289A LEU* 3.8 13.0 - - - +
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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
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50A SER* 3.9 28.5 - - - +
53A LEU* 3.7 37.0 - - + -
54A ARG* 4.3 17.5 + - + +
277A GLU* 3.0 34.6 + - + +
278A LEU 3.9 0.2 - - - +
279A HIS 3.2 0.2 - - - -
280A GLU* 1.3 77.2 - - + +
282A GLY* 1.3 63.3 + - - +
283A LEU* 3.5 26.8 + - + +
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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