Contacts of the strand formed by residues 267 - 280 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A THR* 3.6 2.9 + - - -
237A ASP* 2.8 32.1 + - - +
240A THR* 4.3 2.9 - - - -
265A ASN 3.3 1.4 + - - -
266A ASN* 1.3 75.6 - - - +
268A HIS* 1.3 66.5 + - - +
296A ASN 3.3 10.5 - - - -
297A TRP* 4.3 0.7 - - - -
298A ASP* 3.8 11.8 + - - -
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Residues in contact with HIS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A TYR* 3.6 36.6 + + + +
235A ALA 3.1 13.5 - - - +
236A THR* 4.7 2.0 - - - +
240A THR* 3.8 8.9 - - - +
267A GLY* 1.3 77.9 - - - +
269A MET* 1.3 69.5 + - - +
270A LEU* 4.3 6.3 - - + +
294A ASP* 4.4 10.1 + - - -
295A ILE* 3.7 1.9 - - - +
296A ASN* 2.9 63.0 + - + +
297A TRP* 4.9 0.6 - - - -
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Residues in contact with MET 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 6.0 0.4 - - - -
214A LEU* 4.6 7.2 - - + -
233A GLN* 4.0 2.4 - - + +
234A TYR* 3.3 8.5 - - - -
235A ALA* 2.7 53.4 + - + +
239A MET 4.9 0.2 - - - +
240A THR* 3.8 14.5 - - + +
243A GLY* 3.6 31.9 - - - +
268A HIS* 1.3 78.5 - - - +
270A LEU* 1.3 70.8 + - - +
271A ARG* 3.6 33.0 - - + +
293A GLN* 3.9 15.9 - - + +
294A ASP 3.1 11.7 - - - +
295A ILE* 3.8 20.4 - - + -
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A VAL* 4.5 10.5 - - + -
233A GLN 3.6 12.8 - - - +
234A TYR* 4.5 16.4 - - + -
268A HIS* 4.3 8.4 - - + +
269A MET* 1.3 76.2 - - - +
271A ARG* 1.3 62.5 + - - +
272A ILE* 4.2 30.7 - - + -
292A TYR* 3.9 14.0 - - + +
293A GLN* 3.5 2.1 - - - -
294A ASP* 2.8 41.8 + - + +
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN* 4.3 5.1 - - - +
117A PHE* 3.8 20.2 - - - -
119A TYR* 3.2 22.6 + - - +
231A VAL* 3.9 1.4 - - + +
232A VAL* 3.3 4.5 - - - +
233A GLN* 2.8 75.5 + - + +
243A GLY* 2.9 32.9 + - - -
244A LYS* 5.1 1.6 - - - +
269A MET* 3.6 22.9 - - + +
270A LEU* 1.3 73.9 - - - +
272A ILE* 1.3 66.7 - - - +
273A LEU* 4.6 6.7 - - + -
291A MET* 3.8 26.9 - - + -
292A TYR 3.5 3.6 - - - +
293A GLN* 2.7 33.3 + - + +
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PHE* 4.0 27.6 - - + -
231A VAL 3.5 4.7 - - - +
232A VAL* 4.6 10.1 - - + -
270A LEU* 4.2 30.3 - - + -
271A ARG* 1.3 76.8 - - - +
273A LEU* 1.3 63.4 + - - +
290A GLY 4.8 0.2 - - - -
291A MET* 3.3 3.0 - - - +
292A TYR* 2.9 53.0 + - + +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 4.0 5.8 - - + -
117A PHE* 5.6 0.2 - - + -
119A TYR* 3.6 47.6 - - + -
229A LYS 3.9 0.3 - - - +
230A PHE* 3.5 4.2 - - - -
231A VAL* 2.6 56.1 + - + +
271A ARG* 4.6 5.2 - - + -
272A ILE* 1.3 77.2 - - - +
274A ASP* 1.3 82.5 + - - +
275A HIS* 3.9 13.2 - - + -
289A VAL* 3.9 17.0 - - + -
290A GLY 3.6 11.4 - - - +
291A MET* 3.9 23.8 - - + +
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Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASN* 2.6 41.5 + - - +
229A LYS 3.2 10.9 - - - +
230A PHE* 3.3 23.0 - - + +
273A LEU* 1.3 77.0 - - - +
275A HIS* 1.3 63.3 + - - +
288A TYR* 3.6 10.0 - - - -
289A VAL* 3.5 0.9 - - - -
290A GLY* 2.9 36.4 + - - +
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Residues in contact with HIS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASP 3.5 21.5 - - - -
112A VAL* 3.9 23.8 - - + +
113A HIS 5.5 0.6 + - - -
119A TYR* 3.1 24.2 + - - -
227A PHE* 4.4 10.3 - + - -
228A ASN* 3.5 0.7 + - - -
229A LYS* 2.6 72.6 + - + +
231A VAL* 4.8 0.9 - - + -
273A LEU* 3.9 14.6 - - + -
274A ASP* 1.3 78.0 + - - +
276A GLY* 1.3 56.5 + - - +
288A TYR* 3.3 22.4 - - - +
289A VAL* 3.8 14.8 - - + -
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A PHE* 3.1 27.6 - - - -
275A HIS* 1.3 80.1 + - - +
277A ALA* 1.3 65.2 + - - +
287A MET* 3.4 4.3 - - - +
288A TYR* 3.2 40.6 + - - +
358A TRP* 5.6 0.6 - - - -
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLY* 3.2 6.5 - - - -
227A PHE* 2.9 34.2 + - + -
276A GLY* 1.3 76.1 - - - +
278A ILE* 1.3 60.6 + - - +
286A MET 3.1 11.2 - - - +
287A MET* 4.0 9.4 - - + -
288A TYR* 3.9 1.2 - - - -
357A ILE* 4.7 5.4 - - + -
358A TRP* 3.5 39.5 - - + +
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A VAL* 4.0 22.0 - - + +
224A LEU* 3.9 33.0 - - + -
226A GLY* 4.6 1.3 - - - -
227A PHE 4.2 9.6 - - - +
277A ALA* 1.3 80.2 - - - +
279A SER* 1.3 61.6 + - - +
280A MET* 4.4 19.6 - - + +
285A ASP* 3.4 4.6 - - - +
286A MET* 2.8 53.6 + - + +
288A TYR* 4.3 19.3 - - + +
357A ILE* 5.8 0.2 - - - +
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 2.9 38.7 + - - +
225A LYS* 3.9 31.6 + - - +
226A GLY 4.9 0.4 - - - +
278A ILE* 1.3 74.2 - - - +
280A MET* 1.3 64.3 + - - +
281A GLY 3.8 4.4 + - - -
284A TRP 3.4 4.9 - - - -
285A ASP* 2.5 24.6 + - - -
315A LYS* 4.7 2.4 + - - -
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Residues in contact with MET 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 5.4 5.6 - - + -
278A ILE* 4.4 19.3 - - + +
279A SER* 1.3 76.8 - - - +
281A GLY* 1.3 61.6 + - - +
282A ASP 3.9 0.2 + - - -
283A ASN 4.4 0.2 + - - -
284A TRP* 2.9 62.5 + - + +
285A ASP 5.7 0.2 - - - -
286A MET* 4.4 33.7 - - + -
312A PRO* 6.3 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