Contacts of the strand formed by residues 280 - 287 (chain B) in PDB entry 4EGA
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 VAL 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B VAL* 3.7 5.3 - - - +
242B PHE* 3.2 13.0 - - + +
244B VAL* 4.7 3.4 - - + -
270B GLY* 3.9 18.8 - - - +
273B HIS* 3.7 15.0 - - + -
274B ARG* 3.3 62.4 + - + +
278B GLU 3.6 7.3 + - - +
279B ARG* 1.3 82.2 - - - +
281B PHE* 1.3 72.4 + - - +
282B ALA 4.3 1.3 - - - +
327B ASP* 3.8 11.4 - - - +
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Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B VAL* 4.1 7.9 - - + -
242B PHE 2.7 10.9 + - - +
243B PHE* 3.1 32.5 - + + -
244B VAL 3.1 22.4 + - - -
280B VAL* 1.3 76.9 - - - +
282B ALA* 1.3 59.3 + - - +
283B LEU* 4.0 15.7 - - + -
327B ASP* 3.4 19.3 - - + -
328B TYR* 3.7 22.0 - + + -
484B GLY 3.6 19.1 - - - -
489B VAL* 4.2 16.2 - - + -
507B ARG* 3.3 56.1 - - + +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 3.2 22.9 - - + +
266B THR* 4.2 11.9 - - + +
267B ASP* 5.5 0.4 - - - -
270B GLY* 4.9 4.5 - - - -
274B ARG* 4.6 4.9 - - - +
280B VAL* 4.8 1.6 - - + -
281B PHE* 1.3 75.0 - - - +
283B LEU* 1.3 59.5 + - - +
325B SER 4.4 4.7 - - - +
326B ILE* 3.1 17.3 - - + +
327B ASP* 2.6 44.4 + - - +
328B TYR 3.2 5.7 + - - -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B PHE* 3.9 29.8 - - + -
244B VAL 3.1 6.4 + - - +
245B THR* 3.5 7.0 - - + -
246B SER* 2.9 28.3 + - - +
266B THR* 4.2 2.1 - - - +
281B PHE* 4.0 14.4 - - + -
282B ALA* 1.3 73.6 - - - +
284B THR* 1.3 62.7 + - - +
326B ILE* 3.9 2.7 - - - -
328B TYR* 3.5 44.0 - - + +
330B ILE* 3.8 17.0 - - + -
480B ASN* 3.8 31.6 - - - +
481B TYR* 4.3 4.0 - - + -
484B GLY* 4.0 8.5 - - - -
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B SER* 2.7 30.3 + - - -
248B ILE* 4.3 3.1 - - - -
249B TYR* 3.4 14.2 - - - -
263B THR* 3.6 5.5 + - - -
283B LEU* 1.3 73.2 - - - +
285B GLY* 1.3 63.6 + - - +
319B PHE* 3.6 16.0 - - + -
326B ILE* 3.5 28.5 - - + -
328B TYR 3.1 6.1 + - - +
329B PHE* 3.9 20.2 - - + -
330B ILE* 2.9 31.7 + - - +
809B DMS 6.2 0.7 - - + -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B SER* 4.3 0.6 + - - -
248B ILE* 3.0 12.1 - - - +
249B TYR* 2.8 36.4 + - - -
284B THR* 1.3 86.6 + - - +
286B THR* 1.3 57.7 + - - +
329B PHE* 3.5 17.9 - - - -
330B ILE 3.2 10.8 - - - -
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ILE* 3.8 5.7 - - - +
249B TYR 3.3 5.6 - - - +
251B VAL* 3.5 28.3 - - + -
285B GLY* 1.3 78.5 - - - +
287B ASP* 1.3 60.0 + - - +
288B GLU* 2.6 24.4 + - - +
312B ALA* 3.9 5.5 - - - +
315B PHE* 4.1 20.0 - - + -
329B PHE* 3.6 19.6 - - + -
330B ILE 3.1 5.3 + - - +
331B ARG* 3.5 12.1 - - - +
332B THR* 3.3 28.2 + - - +
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Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 3.5 27.8 - - + +
249B TYR 2.8 17.6 + - - +
250B TYR* 3.0 22.9 - - + +
251B VAL* 3.5 11.3 + - - +
286B THR* 1.3 69.3 - - - +
288B GLU* 1.3 60.2 + - - +
289B HIS 4.0 0.7 + - - -
332B THR* 3.8 5.5 + - - +
473B VAL* 4.1 4.9 - - - +
476B ASP* 4.9 1.2 - - - +
477B ALA* 4.1 9.9 - - - +
813B 0P8 2.6 64.0 + - - +
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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