Contacts of the strand formed by residues 284 - 296 (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 TRP 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B SER* 3.4 1.0 - - - -
280B MET* 2.8 72.4 + - + +
281B GLY 4.9 0.9 - - - +
282B ASP 3.7 1.0 - - - -
283B ASN* 1.3 88.1 - - + +
285B ASP* 1.3 65.6 + - - +
312B PRO* 4.3 23.6 - - + -
313B MET 3.3 18.2 - - - -
314B TYR* 3.5 40.7 - + + -
315B LYS* 4.3 1.3 - - - -
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Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ILE 3.3 5.8 - - - +
279B SER* 2.5 28.9 + - - -
280B MET* 4.8 2.0 - - - -
284B TRP* 1.3 78.9 - - - +
286B MET* 1.3 61.4 + - - +
312B PRO* 3.4 1.2 - - - +
313B MET* 2.6 43.4 + - + -
315B LYS* 3.1 30.3 + - - +
356B SER* 3.5 5.9 + - - -
357B ILE* 3.0 47.1 + - + +
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 3.1 4.2 - - - +
278B ILE* 2.9 51.3 + - + +
280B MET* 4.3 24.0 - - + -
285B ASP* 1.3 80.0 - - - +
287B MET* 1.3 75.1 + - - +
288B TYR* 4.4 18.8 - - + -
310B ILE* 4.3 27.1 - - + -
311B ARG 3.3 14.8 - - - +
312B PRO* 4.0 12.3 - - + -
357B ILE* 4.2 2.4 - - - +
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B HIS* 3.9 26.9 - - + -
114B MET* 3.9 18.6 - - + -
276B GLY 3.4 6.1 - - - +
277B ALA* 4.0 15.3 - - + -
286B MET* 1.3 78.1 - - - +
288B TYR* 1.3 65.1 + - - +
310B ILE* 3.4 0.9 - - - -
311B ARG* 2.7 55.0 + - + +
357B ILE* 4.0 27.8 - - + +
358B TRP* 3.5 50.3 - - + -
360B ARG* 5.1 0.4 - - - +
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Residues in contact with TYR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 5.2 0.9 - - - +
114B MET* 3.7 4.9 - - - +
227B PHE 3.8 5.2 + - - -
228B ASN* 2.6 31.0 + - - +
274B ASP* 3.5 20.0 - - - -
275B HIS* 3.3 7.0 - - - +
276B GLY* 3.1 56.3 + - - +
277B ALA 4.0 2.2 - - - -
278B ILE* 4.2 22.9 - - + +
286B MET* 4.4 20.2 - - + -
287B MET* 1.3 80.2 - - - +
289B VAL* 1.3 67.6 + - - +
309B GLY 3.3 11.2 - - - +
310B ILE* 4.0 13.9 - - + -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.9 22.4 - - + +
112B VAL* 3.4 27.8 - - + -
114B MET* 3.5 29.4 - - + -
115B ILE* 4.2 13.7 - - + -
273B LEU* 3.9 14.1 - - + -
274B ASP 3.5 4.5 - - - -
275B HIS* 3.7 10.3 - - + -
288B TYR* 1.3 75.8 - - - +
290B GLY* 1.3 63.1 + - - +
291B MET* 5.2 2.2 - - + +
307B THR* 5.4 1.8 - - - +
308B VAL* 3.2 5.0 - - - +
309B GLY 2.8 29.6 + - - +
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ILE 4.2 0.3 - - - +
273B LEU* 3.5 1.6 - - - +
274B ASP* 2.9 36.8 + - - +
289B VAL* 1.3 76.3 - - - +
291B MET* 1.3 61.8 + - - +
307B THR 3.2 8.7 - - - -
308B VAL* 3.7 11.7 - - - -
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Residues in contact with MET 291 (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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115B ILE* 4.6 7.6 - - + -
117B PHE* 3.7 36.8 - - + -
271B ARG* 3.8 21.1 - - + -
272B ILE 3.3 12.1 - - - +
273B LEU* 3.8 20.4 - - + -
289B VAL* 5.3 2.7 - - + -
290B GLY* 1.3 75.9 - - - +
292B TYR* 1.3 73.7 + - - +
293B GLN* 4.4 2.7 - - + +
305B TRP* 3.7 33.6 - - + +
306B TRP* 3.4 8.9 - - - +
307B THR* 2.8 49.6 + - - +
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Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 4.8 13.9 - - + -
271B ARG* 3.5 1.7 - - - -
272B ILE* 2.8 56.3 + - + +
291B MET* 1.3 75.6 - - - +
293B GLN* 1.3 64.6 + - - +
294B ASP* 3.7 23.9 + - + +
304B LYS* 3.4 45.8 + - + +
305B TRP 3.4 5.4 - - - -
306B TRP* 3.4 52.0 - + + +
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Residues in contact with GLN 293 (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* 3.4 24.7 - - - +
117B PHE* 3.9 7.3 - - - -
269B MET* 4.0 17.5 - - + -
270B LEU 3.4 5.2 - - - +
271B ARG* 2.7 46.9 + - + +
291B MET* 4.2 4.9 - - + +
292B TYR* 1.3 77.0 - - - +
294B ASP* 1.3 61.6 + - - +
295B ILE* 3.8 17.2 - - + +
303B THR* 3.9 3.9 + - - +
304B LYS* 3.4 1.9 - - - +
305B TRP* 2.7 71.9 + - + +
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Residues in contact with ASP 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B HIS* 3.8 13.8 + - - +
269B MET* 3.1 5.4 - - - +
270B LEU* 2.9 41.5 + - + +
292B TYR* 3.7 30.6 + - + +
293B GLN* 1.3 74.0 - - - +
295B ILE* 1.3 71.1 + - - +
296B ASN* 4.1 12.1 + - - +
303B THR 3.7 7.3 - - - +
304B LYS* 3.8 19.7 + - + +
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 3.9 14.4 - - - +
240B THR* 3.9 18.6 - - - +
241B SER 5.4 0.9 - - - +
268B HIS 3.7 4.9 - - - +
269B MET* 3.8 25.8 - - + -
293B GLN* 3.8 22.8 - - - +
294B ASP* 1.3 74.7 + - - +
296B ASN* 1.3 58.2 + - - +
297B TRP* 3.5 47.3 - - + +
302B GLY* 3.2 8.0 - - - -
303B THR* 2.6 48.5 + - - +
334B GLN* 3.7 2.3 - - - +
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Residues in contact with ASN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLY* 3.2 4.0 - - - -
268B HIS* 2.8 66.3 + - + +
294B ASP* 3.8 13.3 - - - +
295B ILE* 1.3 71.3 - - - +
297B TRP* 1.3 66.8 + - - +
298B ASP* 5.4 1.4 + - - +
334B GLN* 3.1 25.3 + - - +
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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
------------------------------------------------------------
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