Contacts of the strand formed by residues 267 - 280 (chain B) in PDB entry 1AF6
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 GLY 267 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B THR* 3.6 3.1 + - - -
237B ASP* 2.8 31.7 + - - +
240B THR* 4.3 3.1 - - - -
265B ASN 3.3 0.6 + - - -
266B ASN* 1.3 76.4 - - - +
268B HIS* 1.3 66.9 + - - +
296B ASN* 3.2 12.1 - - - -
297B TRP* 4.2 0.9 - - - -
298B ASP* 3.8 12.4 + - - -
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Residues in contact with HIS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TYR* 3.6 36.1 + + + +
235B ALA 3.1 13.5 - - - +
236B THR* 4.7 2.2 - - - +
240B THR* 3.8 7.2 - - - +
267B GLY* 1.3 77.3 - - - +
269B MET* 1.3 69.3 + - - +
270B LEU* 4.3 6.6 - - + +
294B ASP* 4.4 10.7 + - - -
295B ILE* 3.7 1.9 - - - +
296B ASN* 2.8 63.4 + - + +
297B TRP* 4.9 0.4 - - - -
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Residues in contact with MET 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 5.9 0.2 - - - -
214B LEU* 4.6 7.0 - - + -
233B GLN* 3.9 2.6 - - + +
234B TYR* 3.3 8.3 - - - -
235B ALA* 2.7 53.9 + - + +
239B MET 4.9 0.2 - - - +
240B THR* 3.8 13.7 - - + +
243B GLY* 3.6 32.5 - - - +
268B HIS* 1.3 78.3 - - - +
270B LEU* 1.3 69.3 - - - +
271B ARG* 3.6 31.4 - - + +
293B GLN* 3.9 15.5 - - + +
294B ASP 3.1 11.4 - - - +
295B ILE* 3.8 22.2 - - + -
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 4.5 11.0 - - + -
233B GLN 3.6 12.1 - - - +
234B TYR* 4.4 17.3 - - + -
268B HIS* 4.3 7.8 - - + +
269B MET* 1.3 75.5 - - - +
271B ARG* 1.3 62.1 + - - +
272B ILE* 4.1 31.4 - - + -
292B TYR* 3.8 14.6 - - + +
293B GLN* 3.4 2.3 - - - -
294B ASP* 2.9 40.5 + - + +
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Residues in contact with ARG 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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29B GLN* 4.3 5.1 - - - +
117B PHE* 3.8 20.0 - - - -
119B TYR* 3.2 21.0 + - - +
231B VAL* 3.8 1.8 - - + +
232B VAL* 3.4 5.0 - - - +
233B GLN* 2.8 82.5 + - + +
243B GLY* 2.8 33.1 + - - -
244B LYS* 5.1 1.4 - - - +
269B MET* 3.6 23.4 - - + +
270B LEU* 1.3 74.3 - - - +
272B ILE* 1.3 66.8 + - - +
273B LEU* 4.1 7.0 - - + -
291B MET* 3.8 27.6 - - + -
292B TYR 3.5 3.1 - - - +
293B GLN* 2.7 32.7 + - + +
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Residues in contact with ILE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 4.0 28.3 - - + -
231B VAL 3.5 4.3 - - - +
232B VAL* 4.6 9.6 - - + -
270B LEU* 4.1 30.1 - - + -
271B ARG* 1.3 77.8 - - - +
273B LEU* 1.3 62.7 + - - +
290B GLY 4.2 0.2 - - - +
291B MET* 3.3 3.5 - - - +
292B TYR* 2.8 52.5 + - + +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 3.9 5.2 - - + -
115B ILE* 6.1 0.2 - - + -
117B PHE* 5.5 0.4 - - + -
119B TYR* 3.6 48.0 - - + -
229B LYS 4.0 0.3 - - - +
230B PHE* 3.5 4.9 - - - -
231B VAL* 2.6 55.0 + - + +
271B ARG* 4.7 5.2 - - + -
272B ILE* 1.3 77.5 - - - +
274B ASP* 1.3 81.3 - - - +
275B HIS* 3.9 12.6 - - + -
289B VAL* 3.9 18.2 - - + -
290B GLY 3.5 11.9 - - - +
291B MET* 3.8 23.8 - - + +
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Residues in contact with ASP 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASN* 2.6 40.6 + - - +
229B LYS 3.2 10.7 - - - +
230B PHE* 3.3 23.2 - - + +
273B LEU* 1.3 76.6 - - - +
275B HIS* 1.3 62.3 + - - +
288B TYR* 3.5 10.3 - - - -
289B VAL* 3.5 1.0 - - - -
290B GLY* 2.9 36.7 + - - +
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Residues in contact with HIS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP 3.6 20.9 - - - -
112B VAL* 3.9 25.1 - - + +
113B HIS 5.5 0.4 + - - -
119B TYR* 3.1 23.4 + - - -
227B PHE* 4.4 8.3 - + - -
228B ASN* 3.6 0.5 - - - -
229B LYS* 2.6 71.4 + - + +
231B VAL* 4.8 0.7 - - + -
273B LEU* 3.9 14.6 - - + -
274B ASP* 1.3 78.1 + - - +
276B GLY* 1.3 59.7 + - - +
288B TYR* 3.3 22.9 - - - +
289B VAL* 3.7 15.3 - - + -
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Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PHE* 3.2 26.9 - - - -
275B HIS* 1.3 79.7 + - - +
277B ALA* 1.3 65.1 + - - +
287B MET* 3.4 4.2 - - - +
288B TYR* 3.1 40.4 + - - +
358B TRP* 5.7 0.4 - - - -
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Residues in contact with ALA 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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226B GLY* 3.2 6.0 - - - -
227B PHE* 2.9 35.3 + - + -
276B GLY* 1.3 75.3 - - - +
278B ILE* 1.3 61.0 + - - +
286B MET 3.1 11.9 - - - +
287B MET* 4.0 9.6 - - + -
288B TYR* 4.0 1.0 - - - -
357B ILE* 4.7 4.9 - - + -
358B TRP* 3.5 40.2 - - + +
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Residues in contact with ILE 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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223B VAL* 4.0 21.1 - - + +
224B LEU* 3.9 31.9 - - + -
226B GLY* 4.6 2.0 - - - -
227B PHE 4.2 9.9 - - - +
277B ALA* 1.3 79.1 - - - +
279B SER* 1.3 62.9 + - - +
280B MET* 4.3 20.8 - - + +
285B ASP* 3.3 4.3 - - - +
286B MET* 2.9 54.8 + - + +
288B TYR* 4.2 20.0 - - + +
357B ILE* 5.8 0.6 - - - +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 3.0 39.3 + - - +
225B LYS* 4.0 32.1 + - - +
226B GLY 5.0 0.2 - - - +
278B ILE* 1.3 73.7 - - - +
280B MET* 1.3 65.0 + - - +
281B GLY 3.8 5.5 + - - -
284B TRP 3.4 4.7 - - - -
285B ASP* 2.5 24.8 + - - -
315B LYS* 4.7 2.4 + - - -
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Residues in contact with MET 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 5.5 4.7 - - + -
278B ILE* 4.3 19.3 - - + +
279B SER* 1.3 77.2 - - - +
281B GLY* 1.3 60.7 + - - +
282B ASP 3.9 0.3 + - - -
283B ASN 4.3 0.2 + - - -
284B TRP* 2.8 63.6 + - + +
285B ASP 5.6 0.2 - - - -
286B MET* 4.3 35.4 - - + -
312B PRO* 6.2 0.9 - - + -
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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