Contacts of the strand formed by residues 286 - 294 (chain A) in PDB entry 4J15
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 PHE 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A PRO* 3.4 5.4 - - - +
271A VAL* 2.8 63.0 + - + -
272A PHE 4.8 5.4 - - - -
284A THR* 4.9 14.6 - - + +
285A GLU* 1.3 78.8 - - - +
287A VAL* 1.3 86.6 + - - +
288A GLY* 4.2 7.2 - - - -
471A ILE 4.6 1.3 - - - -
472A GLY* 3.8 23.6 - - - -
474A GLU* 3.6 19.1 - - - +
603A GOL 4.7 1.8 - - - -
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Residues in contact with VAL 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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268A ILE* 4.2 4.3 - - + -
269A GLY 3.6 13.2 - - - +
270A PRO* 5.1 3.4 - - + -
285A GLU* 6.1 0.7 - - + +
286A PHE* 1.3 82.5 - - - +
288A GLY* 1.3 59.5 + - - +
289A LEU* 4.1 19.1 - - + -
472A GLY* 3.2 4.2 - - - -
473A LEU* 2.7 42.4 + - + +
474A GLU* 3.1 17.6 + - - +
603A GOL 4.2 7.6 - - - +
219B GLN* 3.0 50.3 - - + +
220B THR 6.2 0.2 - - - +
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Residues in contact with GLY 288 (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 SER* 3.5 2.6 + - - +
268A ILE* 3.3 5.9 - - - -
269A GLY 3.1 31.8 + - - +
271A VAL* 4.0 15.7 - - - +
286A PHE* 4.0 7.2 + - - -
287A VAL* 1.3 71.7 - - - +
289A LEU* 1.3 64.0 + - - +
290A ASP* 3.9 10.2 - - - +
471A ILE 3.1 9.4 - - - -
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Residues in contact with LEU 289 (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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202A ILE* 4.7 2.9 - - + -
203A CYS* 4.3 16.8 - - - -
206A PHE* 3.5 54.5 - - + -
267A SER 3.5 3.4 - - - -
268A ILE* 3.2 38.8 - - + -
287A VAL* 4.1 10.5 - - + -
288A GLY* 1.3 74.9 - - - +
290A ASP* 1.3 58.3 + - - +
291A ILE* 4.3 0.9 + - - +
469A GLY 4.5 0.2 - - - +
470A GLY* 3.3 2.6 - - - -
471A ILE* 2.8 50.4 + - + +
473A LEU* 4.6 16.4 - - + -
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Residues in contact with ASP 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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206A PHE* 4.0 0.6 - - - -
250A PRO* 3.8 22.4 - - - +
251A GLN* 5.6 0.9 - - - +
254A LYS* 3.2 32.7 + - + +
266A PHE* 2.9 30.3 - - - +
267A SER* 2.9 29.2 + - - +
271A VAL* 4.8 2.6 - - - +
288A GLY* 4.3 12.6 - - - -
289A LEU* 1.3 74.9 - - - +
291A ILE* 1.3 61.3 + - - +
469A GLY* 3.9 1.7 - - - -
470A GLY* 3.7 15.7 + - - -
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Residues in contact with ILE 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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206A PHE* 3.9 22.7 - - + -
210A LEU* 3.8 27.1 - - + -
215A PHE* 3.8 26.0 - - + -
254A LYS* 3.1 8.1 + - - -
265A VAL 3.6 2.9 - - - -
266A PHE* 4.6 0.4 - - + -
289A LEU 5.0 0.9 - - - +
290A ASP* 1.3 79.2 - - - +
292A GLU* 1.3 66.8 + - - +
293A MET* 4.8 4.9 - - + -
302A VAL* 5.3 0.7 - - + -
305A GLU* 5.9 0.9 - - + -
306A ILE* 4.0 41.7 - - + -
309A THR* 4.8 5.8 - - + -
426A LEU* 6.1 0.7 - - + -
468A GLY* 3.1 1.2 - - - -
469A GLY 2.9 39.8 + - - +
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Residues in contact with GLU 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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215A PHE* 4.0 0.9 - - - -
251A GLN* 3.7 7.0 + - - -
254A LYS* 3.0 41.8 + - + +
255A GLN* 4.4 2.0 - - + -
258A ILE* 3.7 21.4 - - + +
265A VAL* 3.0 41.6 + - + +
291A ILE* 1.3 73.2 - - - +
293A MET* 1.3 63.5 + - - +
431A ARG* 2.9 44.9 + - - -
466A HIS* 3.4 16.0 - - + -
467A ALA 3.1 17.9 - - - +
468A GLY* 4.1 0.2 - - - -
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Residues in contact with MET 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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215A PHE* 3.8 25.6 - - + -
258A ILE* 3.9 0.6 - - - +
263A GLU 3.4 4.7 - - - +
264A LYS* 3.9 29.2 - - + +
291A ILE* 4.8 2.2 - - + -
292A GLU* 1.3 78.2 - - - +
294A ALA* 1.3 76.2 + - - +
295A PHE* 5.3 1.3 - - + -
301A GLU* 4.4 11.9 - - + +
302A VAL* 3.4 29.4 - - + +
305A GLU* 4.0 32.8 - - + +
466A HIS* 3.3 4.4 - - - -
467A ALA 2.7 36.5 + - - +
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Residues in contact with ALA 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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258A ILE* 3.7 5.8 - - + +
263A GLU* 3.0 29.6 + - + +
264A LYS* 5.4 1.4 - - - +
293A MET* 1.3 92.9 - - - +
295A PHE* 1.3 59.4 + - - +
464A PRO* 4.0 25.4 - - + -
465A PRO 3.3 12.6 - - - +
466A HIS* 3.7 3.4 - - + -
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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