Contacts of the strand formed by residues 284 - 296 (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 TRP 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A SER* 3.4 0.9 - - - -
280A MET* 2.9 70.1 + - + +
281A GLY 4.9 1.0 - - - +
282A ASP 3.7 0.8 - - - -
283A ASN* 1.3 88.2 - - + +
285A ASP* 1.3 68.5 + - - +
312A PRO* 4.3 23.1 - - + -
313A MET 3.3 18.4 - - - -
314A TYR* 3.5 40.9 - + + -
315A LYS* 4.3 0.7 - - - -
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ILE 3.4 6.5 - - - +
279A SER* 2.5 30.1 + - - -
280A MET* 4.9 1.5 - - - +
284A TRP* 1.3 80.1 - - - +
286A MET* 1.3 60.5 + - - +
312A PRO* 3.4 1.4 - - - +
313A MET* 2.6 43.1 + - + +
315A LYS* 3.1 31.0 + - - +
356A SER* 3.5 5.5 + - - -
357A ILE* 3.0 47.6 + - + +
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Residues in contact with MET 286 (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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277A ALA* 3.1 3.7 - - - +
278A ILE* 2.8 51.0 + - + +
280A MET* 4.4 24.0 - - + -
285A ASP* 1.3 77.4 - - - +
287A MET* 1.3 76.6 + - - +
288A TYR* 4.4 18.8 - - + -
310A ILE* 4.2 27.8 - - + -
311A ARG 3.3 14.6 - - - +
312A PRO* 4.0 13.0 - - + -
357A ILE* 4.2 3.1 - - - +
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Residues in contact with MET 287 (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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113A HIS* 4.0 26.7 - - + +
114A MET* 3.9 20.4 - - + -
276A GLY 3.4 6.7 - - - +
277A ALA* 4.0 15.0 - - + -
286A MET* 1.3 81.3 - - - +
288A TYR* 1.3 60.0 + - - +
311A ARG* 2.7 55.3 + - + +
357A ILE* 3.9 29.8 - - + +
358A TRP* 3.6 47.3 - - + -
360A ARG* 5.1 0.7 - - - +
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Residues in contact with TYR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 5.1 0.9 - - - +
114A MET* 3.7 4.6 - - - +
227A PHE 3.8 1.9 + - - -
228A ASN* 2.6 31.6 + - - +
274A ASP* 3.6 20.0 - - - -
275A HIS* 3.3 7.7 - - - +
276A GLY* 3.2 60.0 + - - +
277A ALA 3.9 2.7 - - - -
278A ILE* 4.3 22.3 - - + +
286A MET* 4.4 22.0 - - + -
287A MET* 1.3 79.7 - - - +
289A VAL* 1.3 65.9 + - - +
309A GLY 3.3 12.1 - - - +
310A ILE* 4.0 13.2 - - + -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.8 24.9 - - + +
112A VAL* 3.4 27.8 - - + -
114A MET* 3.5 30.1 - - + -
115A ILE* 4.3 13.0 - - + -
273A LEU* 3.9 13.7 - - + -
274A ASP 3.5 5.2 - - - -
275A HIS* 3.8 9.6 - - + -
288A TYR* 1.3 76.0 - - - +
290A GLY* 1.3 62.8 - - - +
291A MET* 5.2 2.5 - - + +
307A THR* 5.3 2.0 - - - +
308A VAL* 3.2 4.8 - - - +
309A GLY 2.9 27.2 + - - +
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Residues in contact with GLY 290 (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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273A LEU* 3.6 2.0 - - - +
274A ASP* 2.9 35.8 + - - +
289A VAL* 1.3 77.4 - - - +
291A MET* 1.3 61.1 + - - +
307A THR 3.3 9.0 - - - -
308A VAL* 3.7 11.7 - - - -
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Residues in contact with MET 291 (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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115A ILE* 4.7 7.6 - - + -
117A PHE* 3.7 29.8 - - + -
271A ARG* 3.8 20.9 - - + -
272A ILE 3.3 13.0 - - - +
273A LEU* 3.9 21.3 - - + -
289A VAL* 5.3 2.9 - - + -
290A GLY* 1.3 75.2 - - - +
292A TYR* 1.3 72.8 + - - +
293A GLN* 4.2 2.7 - - + +
305A TRP* 3.6 41.8 - - + +
306A TRP* 3.4 8.8 - - - +
307A THR* 2.8 46.4 + - - +
308A VAL* 4.9 0.2 - - - +
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Residues in contact with TYR 292 (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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270A LEU* 4.8 13.9 - - + -
271A ARG* 3.5 1.4 - - - -
272A ILE* 2.9 55.6 + - + +
291A MET* 1.3 76.7 - - - +
293A GLN* 1.3 62.6 + - - +
294A ASP* 3.7 29.1 + - + +
304A LYS* 3.4 37.0 + - + +
305A TRP 3.4 4.7 - - - -
306A TRP* 3.3 57.4 - + + +
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Residues in contact with GLN 293 (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* 3.5 24.5 - - - +
117A PHE* 3.9 7.4 - - - -
269A MET* 3.9 17.9 - - + -
270A LEU 3.5 5.4 - - - +
271A ARG* 2.7 42.6 + - + +
291A MET* 4.2 9.1 - - + +
292A TYR* 1.3 78.5 - - - +
294A ASP* 1.3 61.4 + - - +
295A ILE* 3.8 16.5 - - + +
303A THR* 3.9 4.5 + - - +
304A LYS* 3.5 1.9 - - - -
305A TRP* 2.7 69.6 + - + +
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Residues in contact with ASP 294 (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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268A HIS* 3.8 14.0 + - - +
269A MET* 3.1 5.0 - - - +
270A LEU* 2.8 44.2 + - + +
292A TYR* 3.7 30.7 + - + +
293A GLN* 1.3 73.6 - - - +
295A ILE* 1.3 71.7 + - - +
296A ASN* 4.1 11.7 + - - +
303A THR 3.7 7.1 - - - +
304A LYS* 3.9 19.5 + - + +
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Residues in contact with ILE 295 (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* 3.9 14.1 - - - +
240A THR* 3.9 18.8 - - - +
241A SER 5.4 0.9 - - - +
268A HIS 3.7 5.2 - - - +
269A MET* 3.8 25.6 - - + -
293A GLN* 3.8 23.5 - - + +
294A ASP* 1.3 74.4 + - - +
296A ASN* 1.3 61.1 + - - +
297A TRP* 3.5 45.8 - - + +
302A GLY* 3.2 8.5 - - - -
303A THR* 2.7 48.4 + - - +
334A GLN* 3.7 2.3 - - - +
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Residues in contact with ASN 296 (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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267A GLY* 3.3 4.0 - - - -
268A HIS* 2.9 67.2 + - + +
294A ASP* 3.8 14.1 - - - +
295A ILE* 1.3 71.5 - - - +
297A TRP* 1.3 68.5 + - - +
298A ASP* 5.5 1.2 + - - -
334A GLN* 3.0 24.9 + - - +
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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