Contacts of the strand formed by residues 267 - 280 (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 GLY 267 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236C THR* 3.7 2.8 + - - -
237C ASP* 2.8 30.8 + - - +
240C THR* 4.3 3.6 - - - -
265C ASN 3.4 1.0 + - - -
266C ASN* 1.3 76.0 - - - +
268C HIS* 1.3 66.1 + - - +
296C ASN* 3.1 11.9 - - - -
297C TRP* 4.2 0.7 - - - -
298C ASP* 3.8 12.8 + - - -
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Residues in contact with HIS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C TYR* 3.6 36.1 + + + +
235C ALA 3.1 13.0 - - - +
236C THR* 4.7 2.5 - - - +
240C THR* 3.7 7.0 - - - +
267C GLY* 1.3 78.1 - - - +
269C MET* 1.3 69.0 + - - +
270C LEU* 4.3 6.2 - - + +
294C ASP* 4.4 10.3 + - - -
295C ILE* 3.7 1.6 - - - +
296C ASN* 2.9 63.7 + - + +
297C TRP* 4.9 0.4 - - - -
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Residues in contact with MET 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLN* 5.9 0.2 - - - -
214C LEU* 4.6 7.9 - - + -
233C GLN* 3.9 2.8 - - + +
234C TYR* 3.3 7.6 - - - -
235C ALA* 2.7 54.2 + - + +
239C MET 5.0 0.2 - - - +
240C THR* 4.1 14.6 - - + +
243C GLY* 3.7 22.2 - - - +
268C HIS* 1.3 78.6 - - - +
270C LEU* 1.3 70.3 + - - +
271C ARG* 3.6 43.7 - - + +
293C GLN* 4.0 14.6 - - + +
294C ASP 3.1 11.4 - - - +
295C ILE* 3.8 21.3 - - + -
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Residues in contact with LEU 270 (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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232C VAL* 4.5 10.5 - - + -
233C GLN 3.6 13.0 - - - +
234C TYR* 4.5 15.9 - - + -
268C HIS* 4.3 7.5 - - + +
269C MET* 1.3 74.4 - - - +
271C ARG* 1.3 61.4 + - - +
272C ILE* 4.1 32.8 - - + -
292C TYR* 3.8 15.2 - - + +
293C GLN* 3.4 2.6 - - - -
294C ASP* 2.9 41.4 + - + +
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Residues in contact with ARG 271 (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* 4.2 4.9 - - - +
117C PHE* 3.8 20.7 - - - -
119C TYR* 3.2 21.0 + - - +
214C LEU* 5.6 0.2 - - - +
231C VAL* 3.9 1.9 - - + +
232C VAL* 3.4 4.2 - - - +
233C GLN* 2.8 81.0 + - + +
242C GLN 5.2 0.2 + - - -
243C GLY* 2.9 33.3 + - - -
244C LYS* 5.2 1.2 - - - +
269C MET* 3.6 22.7 - - + +
270C LEU* 1.3 76.2 - - - +
272C ILE* 1.3 67.3 + - - +
273C LEU* 4.7 7.2 - - + -
291C MET* 3.7 26.7 - - + -
292C TYR 3.5 3.6 - - - +
293C GLN* 2.7 33.4 + - + +
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Residues in contact with ILE 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 4.0 28.3 - - + -
231C VAL 3.5 3.6 - - - +
232C VAL* 4.6 10.1 - - + -
270C LEU* 4.1 29.8 - - + -
271C ARG* 1.3 78.7 - - - +
273C LEU* 1.3 63.3 + - - +
290C GLY 4.2 0.2 - - - +
291C MET* 3.3 4.0 - - - +
292C TYR* 2.8 52.4 + - + +
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Residues in contact with LEU 273 (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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112C VAL* 3.9 6.1 - - + -
119C TYR* 3.6 48.2 - - + -
229C LYS 4.0 0.4 - - - +
230C PHE* 3.5 5.3 - - - -
231C VAL* 2.6 55.3 + - + +
271C ARG* 4.7 5.4 - - + -
272C ILE* 1.3 76.9 - - - +
274C ASP* 1.3 80.0 + - - +
275C HIS* 3.9 12.6 - - + -
289C VAL* 3.8 19.3 - - + -
290C GLY 3.5 12.1 - - - +
291C MET* 3.9 24.5 - - + +
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Residues in contact with ASP 274 (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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228C ASN* 2.5 41.1 + - - +
229C LYS 3.2 10.7 - - - +
230C PHE* 3.3 23.1 - - + +
273C LEU* 1.3 76.4 - - - +
275C HIS* 1.3 62.5 + - - +
288C TYR* 3.6 9.7 - - - -
289C VAL* 3.5 0.9 - - - -
290C GLY* 2.9 36.8 + - - +
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Residues in contact with HIS 275 (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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111C ASP 3.5 22.7 - - - -
112C VAL* 4.0 16.0 - - + +
113C HIS 5.4 0.6 + - - -
119C TYR* 3.1 22.6 + - - -
227C PHE* 4.4 9.4 - + - -
228C ASN* 3.5 0.9 + - - -
229C LYS* 2.6 72.3 + - + +
231C VAL* 4.8 1.3 - - + -
273C LEU* 3.9 22.7 - - + -
274C ASP* 1.3 76.4 + - - +
276C GLY* 1.3 57.6 + - - +
288C TYR* 3.3 22.7 - - - +
289C VAL* 3.7 15.0 - - + -
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PHE* 3.1 28.5 - - - -
275C HIS* 1.3 79.5 + - - +
277C ALA* 1.3 63.7 + - - +
287C MET* 3.4 5.0 - - - +
288C TYR* 3.1 40.1 + - - +
358C TRP* 5.6 0.4 - - - -
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Residues in contact with ALA 277 (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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226C GLY* 3.2 6.1 - - - -
227C PHE* 2.9 35.4 + - + -
276C GLY* 1.3 75.8 - - - +
278C ILE* 1.3 61.0 + - - +
286C MET 3.2 11.0 - - - +
287C MET* 4.0 9.0 - - + -
288C TYR* 3.9 0.8 - - - -
357C ILE* 4.7 4.7 - - + -
358C TRP* 3.4 41.1 - - + +
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Residues in contact with ILE 278 (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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223C VAL* 4.0 21.5 - - + +
224C LEU* 3.9 31.4 - - + -
226C GLY* 4.6 1.3 - - - -
227C PHE 4.2 9.2 - - - +
277C ALA* 1.3 80.4 - - - +
279C SER* 1.3 60.5 + - - +
280C MET* 4.4 20.3 - - + +
285C ASP* 3.4 4.4 - - - +
286C MET* 2.9 53.4 + - + +
288C TYR* 4.3 20.6 - - + +
357C ILE* 5.8 0.5 - - - +
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Residues in contact with SER 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 3.0 39.2 + - - +
225C LYS* 3.9 32.6 + - - +
226C GLY 5.0 0.2 - - - +
278C ILE* 1.3 72.9 - - - +
280C MET* 1.3 65.8 + - - +
281C GLY 3.8 4.9 + - - -
284C TRP 3.4 5.4 - - - -
285C ASP* 2.5 24.1 + - - -
315C LYS* 4.7 2.2 + - - -
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Residues in contact with MET 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 5.4 5.2 - - + -
278C ILE* 4.4 19.5 - - + +
279C SER* 1.3 78.1 - - - +
281C GLY* 1.3 60.2 + - - +
282C ASP 3.9 0.2 + - - -
283C ASN 4.4 0.2 + - - -
284C TRP* 2.8 62.2 + - + +
285C ASP 5.7 0.2 - - - -
286C MET* 4.3 35.7 - - + -
312C PRO* 6.2 0.4 - - + -
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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