Contacts of the helix formed by residues 264 - 281 (chain B) in PDB entry 2AFU
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B LEU* 4.2 16.2 - - - -
259B ASN* 4.5 2.4 + - - -
261B PHE* 3.5 17.8 + - - +
262B PRO 3.3 0.2 - - - -
263B ASN* 1.3 80.9 + - - +
265B ALA* 1.3 55.2 + - - +
266B ARG 3.1 3.4 - - - -
267B TRP* 2.8 34.3 + - - +
268B PHE 3.3 6.9 + - - -
316B PRO* 5.0 2.5 - - - -
317B VAL 2.5 35.4 + - - -
318B LEU* 4.0 8.4 - - - +
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASN* 3.4 22.2 - - - +
261B PHE 3.2 10.1 + - - +
262B PRO* 3.5 17.9 - - + +
263B ASN 3.5 1.6 - - - -
264B SER* 1.3 77.6 - - - +
266B ARG* 1.3 57.7 + - - +
268B PHE* 3.0 4.5 + - - +
269B GLU* 2.8 39.3 + - + +
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS 3.2 22.6 + - - -
41B ASN* 3.4 16.6 + - - +
43B HIS 2.9 29.9 + - - -
44B GLN* 3.6 17.4 + - - +
45B PRO* 5.0 1.6 - - - +
263B ASN 5.0 8.6 + - - +
264B SER 3.0 2.0 + - - -
265B ALA* 1.3 78.7 - - - +
267B TRP* 1.3 100.6 + - + +
269B GLU* 3.4 19.4 + - - +
270B ARG* 3.3 25.8 + - - +
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Residues in contact with TRP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LYS 5.1 1.2 + - - -
43B HIS* 3.6 19.1 - - + -
45B PRO* 3.7 43.1 - - + -
243B LEU* 4.0 24.1 - - + +
263B ASN 5.2 1.6 - - - -
264B SER* 2.8 20.6 + - - +
266B ARG* 1.3 117.6 - - + +
268B PHE* 1.3 65.4 + - - +
270B ARG* 3.3 16.1 + - + +
271B LEU* 3.3 5.5 + - - +
316B PRO* 6.4 0.4 - - + -
318B LEU* 4.1 7.6 - - + -
354B PHE* 3.3 46.4 - + + -
358B TYR* 3.3 41.6 + + + -
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Residues in contact with PHE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PHE* 3.2 25.6 - - + -
258B PRO 3.3 25.4 - - - -
259B ASN* 2.9 43.7 - - + +
264B SER 3.3 3.2 + - - -
265B ALA 3.0 5.0 + - - +
267B TRP* 1.3 76.4 - - - +
269B GLU* 1.3 61.7 + - + +
271B LEU* 2.8 28.6 + - + +
272B GLN* 3.1 29.0 + - + -
294B PHE* 3.9 24.0 - + + -
295B GLN 3.1 24.0 - - - -
297B TYR 5.0 0.7 - - - -
318B LEU* 3.8 17.4 - - + +
319B HIS 6.0 0.7 - - - -
320B LEU* 5.2 5.4 - - + -
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Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ALA* 2.8 20.4 + - + +
266B ARG* 3.4 27.2 + - - +
268B PHE* 1.3 77.8 - - + +
270B ARG* 1.3 61.1 + - - +
272B GLN* 3.3 24.2 + - - +
273B ALA* 3.0 24.3 + - - +
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Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PRO* 4.1 17.1 - - + +
47B ILE* 3.7 34.9 - - - +
266B ARG 3.3 15.8 + - - +
267B TRP* 3.4 29.4 - - + +
268B PHE 3.1 0.6 - - - -
269B GLU* 1.3 80.4 - - - +
271B LEU* 1.3 57.0 + - - +
273B ALA* 3.5 24.0 - - - +
274B ILE* 2.9 48.7 + - + +
354B PHE* 4.2 12.8 - - + -
357B GLU* 3.0 27.7 + - - -
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B TRP 3.3 9.4 + - - +
268B PHE* 2.8 14.4 + - + +
270B ARG* 1.3 75.5 - - - +
272B GLN* 1.3 59.9 + - - +
274B ILE* 3.3 4.4 + - + +
275B GLU* 2.9 30.3 + - - +
294B PHE* 3.9 30.9 - - + -
318B LEU* 4.0 15.5 - - + -
320B LEU* 3.7 36.1 - - + -
350B ILE* 3.8 24.8 - - + +
351B LEU* 5.3 3.8 - - + -
354B PHE* 3.6 29.8 - - + -
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Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B PHE* 3.1 25.9 + - + +
269B GLU* 3.3 34.8 + - - +
271B LEU* 1.3 75.1 - - - +
273B ALA* 1.3 58.7 + - - +
275B GLU* 3.2 5.4 + - - +
276B HIS* 2.8 30.7 + - - +
292B ARG* 3.8 19.1 + - - +
294B PHE* 3.9 19.4 - - + +
295B GLN 3.3 18.1 - - - +
296B ASN* 3.2 30.2 + - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B GLU 3.0 14.9 + - - +
270B ARG* 3.5 29.2 - - - +
271B LEU 3.3 0.2 - - - -
272B GLN* 1.3 79.9 - - - +
274B ILE* 1.3 60.1 + - - +
276B HIS* 3.5 6.6 + - - +
277B GLU* 3.1 24.9 + - - +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 5.2 1.8 - - + -
270B ARG* 2.9 34.8 + - + +
271B LEU* 3.7 5.2 - - - +
272B GLN 3.3 0.2 - - - -
273B ALA* 1.3 72.8 - - - +
275B GLU* 1.3 66.9 + - - +
277B GLU* 3.5 4.0 + - - +
278B LEU* 3.0 40.9 + - + +
350B ILE* 4.0 13.0 - - + +
353B VAL* 3.6 34.5 - - + -
354B PHE* 3.6 28.5 - - + +
357B GLU* 3.4 26.2 - - - +
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LEU 2.9 17.2 + - - +
272B GLN* 3.5 2.9 - - - +
274B ILE* 1.3 77.6 - - - +
276B HIS* 1.3 62.9 + - - +
278B LEU* 3.4 1.3 + - - -
279B HIS* 3.0 23.2 + - - +
284B LEU* 3.7 3.7 - - + +
287B HIS* 2.9 30.0 + - + +
289B LEU* 5.9 0.2 - - + -
292B ARG* 3.6 16.9 + - + +
293B TYR* 2.6 35.6 + - - -
294B PHE* 3.1 36.5 + - + +
350B ILE* 3.9 22.0 - - + +
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLN 2.8 16.8 + - - +
273B ALA* 3.7 7.9 - - - +
274B ILE 3.3 0.2 - - - -
275B GLU* 1.3 75.4 - - - +
277B GLU* 1.3 64.4 + - + +
279B HIS* 3.2 7.1 + - - +
280B GLU* 2.9 52.8 + - + +
289B LEU* 3.9 26.7 - - + +
292B ARG* 3.0 30.7 + - - +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B SER* 4.3 7.4 + - - -
53B LEU* 3.5 26.8 - - + +
273B ALA 3.1 15.3 + - - +
274B ILE* 4.0 4.7 - - - +
276B HIS* 1.3 82.4 - - + +
278B LEU* 1.3 61.5 + - - +
280B GLU* 3.3 11.2 + - - +
281B LEU* 2.9 52.1 + - + +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.9 33.0 - - + +
57B ALA* 5.3 3.1 - - + +
274B ILE* 3.0 32.4 + - + +
275B GLU 3.9 2.0 - - - +
277B GLU* 1.3 77.1 - - - +
279B HIS* 1.3 60.7 + - - +
281B LEU* 3.4 2.9 + - - -
282B GLY 3.3 2.4 + - - -
283B LEU* 2.8 55.1 + - + +
284B LEU* 3.3 26.6 + - + -
349B LYS* 4.1 11.9 - - + +
350B ILE* 3.9 30.5 - - + +
353B VAL* 4.4 3.1 - - + -
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Residues in contact with HIS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLU 3.0 14.7 + - - +
276B HIS 3.3 8.1 - - - +
278B LEU* 1.3 77.0 - - - +
280B GLU* 1.3 69.6 + - - +
282B GLY* 2.7 27.7 + - - -
284B LEU* 3.6 17.0 - - + +
287B HIS* 2.9 49.3 + + + +
288B SER* 3.7 1.6 - - - -
289B LEU* 3.6 35.6 + - + +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B HIS* 2.9 47.2 + - + +
277B GLU* 3.6 14.1 - - - +
279B HIS* 1.3 85.0 + - - +
281B LEU* 1.3 58.8 + - + +
282B GLY 3.1 3.2 + - - -
289B LEU* 3.7 20.7 - - + +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B SER* 3.9 23.6 - - - +
53B LEU* 3.6 32.5 - - + -
54B ARG* 4.2 21.5 + - + +
277B GLU* 2.9 34.8 + - - +
278B LEU* 3.9 0.9 - - - +
279B HIS 3.1 0.6 - - - -
280B GLU* 1.3 75.2 - - - +
282B GLY* 1.3 63.4 + - - +
283B LEU* 3.2 33.2 + - + +
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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