Contacts of the strand formed by residues 284 - 296 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279C SER* 3.4 0.9 - - - -
280C MET* 2.8 69.5 + - + +
281C GLY 4.9 1.0 - - - +
282C ASP 3.7 0.8 - - - -
283C ASN* 1.3 87.3 - - + +
285C ASP* 1.3 69.7 + - - +
312C PRO* 4.3 22.7 - - + -
313C MET 3.3 18.8 - - - -
314C TYR* 3.5 40.4 - + + -
315C LYS* 4.3 1.5 + - - +
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Residues in contact with ASP 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ILE 3.4 7.2 - - - +
279C SER* 2.5 29.5 + - - -
280C MET* 4.8 2.2 - - - +
284C TRP* 1.3 78.4 - - - +
286C MET* 1.3 58.9 + - - +
312C PRO* 3.4 2.8 - - - +
313C MET* 2.6 42.0 + - + -
315C LYS* 3.1 30.5 + - - +
356C SER* 3.5 6.2 + - - -
357C ILE* 3.0 47.0 + - + +
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Residues in contact with MET 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C ALA* 3.2 4.5 - - - +
278C ILE* 2.9 51.1 + - + +
280C MET* 4.3 23.8 - - + -
285C ASP* 1.3 77.4 - - - +
287C MET* 1.3 75.5 + - - +
288C TYR* 4.4 18.6 - - + -
310C ILE* 4.2 26.9 - - + -
311C ARG 3.3 9.2 - - - +
312C PRO* 3.9 17.7 - - + -
357C ILE* 4.2 2.9 - - - -
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Residues in contact with MET 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C HIS* 3.9 27.4 - - + -
114C MET* 3.8 18.4 - - + -
276C GLY 3.4 6.7 - - - +
277C ALA* 4.0 15.5 - - + -
286C MET* 1.3 78.1 - - - +
288C TYR* 1.3 63.7 + - - +
310C ILE* 3.4 0.9 - - - -
311C ARG* 2.7 55.3 + - + +
357C ILE* 4.0 29.3 - - + +
358C TRP* 3.6 48.5 - - + -
360C ARG* 5.1 0.7 - - - +
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Residues in contact with TYR 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C VAL* 5.2 0.7 - - - +
114C MET* 3.7 4.4 - - - +
227C PHE 3.8 2.1 + - - -
228C ASN* 2.7 31.6 + - - +
274C ASP* 3.6 20.2 - - - -
275C HIS* 3.3 7.8 - - - +
276C GLY* 3.1 50.1 + - - +
277C ALA 3.9 2.7 - - - -
278C ILE* 4.3 23.8 - - + +
286C MET* 4.4 20.4 - - + -
287C MET* 1.3 79.3 - - - +
289C VAL* 1.3 65.5 - - - +
309C GLY 3.4 12.8 - - - +
310C ILE* 4.0 12.8 - - + -
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 3.9 24.9 - - + +
112C VAL* 3.4 27.6 - - + -
114C MET* 3.6 29.4 - - + -
115C ILE* 4.3 13.0 - - + -
273C LEU* 3.8 15.3 - - + -
274C ASP 3.5 4.0 - - - -
275C HIS* 3.7 10.1 - - + -
288C TYR* 1.3 76.5 - - - +
290C GLY* 1.3 62.9 + - - +
291C MET* 5.2 1.6 - - + +
307C THR* 5.3 1.6 - - - +
308C VAL* 3.2 5.4 - - - +
309C GLY 2.9 28.0 + - - +
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C ILE 4.7 0.2 - - - -
273C LEU* 3.5 2.4 - - - +
274C ASP* 2.9 36.6 + - - +
289C VAL* 1.3 76.1 - - - +
291C MET* 1.3 62.8 + - - +
307C THR 3.3 7.9 - - - -
308C VAL* 3.7 12.1 - - - -
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Residues in contact with MET 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ILE* 4.7 7.6 - - + -
117C PHE* 3.7 27.6 - - + -
271C ARG* 3.7 25.1 - - + -
272C ILE 3.3 12.8 - - - +
273C LEU* 3.9 19.1 - - + -
289C VAL* 5.3 2.9 - - + -
290C GLY* 1.3 75.5 - - - +
292C TYR* 1.3 73.5 + - - +
293C GLN* 4.2 2.7 - - - +
305C TRP* 3.7 40.3 - - + +
306C TRP* 3.4 8.7 - - - +
307C THR* 2.8 49.3 + - - +
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Residues in contact with TYR 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 4.7 13.9 - - + -
271C ARG* 3.5 1.4 - - - -
272C ILE* 2.8 56.5 + - + +
291C MET* 1.3 76.3 - - - +
293C GLN* 1.3 62.1 + - - +
294C ASP* 3.6 29.3 + - + +
304C LYS* 3.4 36.8 + - + +
305C TRP 3.4 4.9 - - - -
306C TRP* 3.3 56.5 - + + -
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Residues in contact with GLN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLN* 3.5 24.9 - - - +
117C PHE* 3.9 8.0 - - - -
269C MET* 4.0 18.2 - - + -
270C LEU 3.4 4.9 - - - +
271C ARG* 2.7 42.7 + - + +
291C MET* 4.2 8.4 - - + +
292C TYR* 1.3 77.8 - - - +
294C ASP* 1.3 61.3 + - - +
295C ILE* 3.8 16.2 - - + +
303C THR* 3.9 3.9 + - - +
304C LYS* 3.5 1.6 - - - -
305C TRP* 2.7 70.3 + - + +
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Residues in contact with ASP 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C HIS* 3.9 13.3 + - - +
269C MET* 3.1 4.9 - - - +
270C LEU* 2.9 44.9 + - + +
292C TYR* 3.6 31.0 + - + +
293C GLN* 1.3 72.3 - - - +
295C ILE* 1.3 71.7 + - - +
296C ASN* 3.9 12.0 + - - +
303C THR 3.7 8.1 - - - +
304C LYS* 3.7 20.9 + - + +
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Residues in contact with ILE 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLN* 4.0 14.1 - - - +
240C THR* 3.9 19.5 - - - +
241C SER 5.4 0.7 - - - +
268C HIS 3.7 4.9 - - - +
269C MET* 3.8 25.1 - - + -
293C GLN* 3.8 22.6 - - - +
294C ASP* 1.3 73.8 - - - +
296C ASN* 1.3 59.3 + - - +
297C TRP* 3.5 45.1 - - + +
302C GLY* 3.2 9.0 - - - -
303C THR* 2.7 48.0 + - - +
334C GLN* 3.7 2.1 - - - +
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Residues in contact with ASN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C GLY* 3.1 3.8 - - - -
268C HIS* 2.9 66.9 + - + +
294C ASP* 3.8 13.5 - - - +
295C ILE* 1.3 71.6 - - - +
297C TRP* 1.3 67.8 + - - +
298C ASP* 5.4 1.8 + - - +
334C GLN* 3.0 24.6 + - - +
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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