Contacts of the strand formed by residues 292 - 299 (chain B) in PDB entry 1SHY
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 MET 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ILE* 3.5 1.0 - - - -
280B ARG* 3.1 46.0 + - + +
290B SER* 3.5 15.7 - - - +
291B TYR* 1.3 86.6 - - - +
293B GLU* 1.3 62.3 + - - +
374B PHE* 3.5 45.6 - - + +
383B VAL* 6.0 1.1 - - + -
400B ARG* 6.4 0.2 - - - +
418B THR* 3.1 29.8 - - + +
420B PHE* 3.6 26.2 - - + -
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ILE* 5.3 0.3 - - - +
247B ILE* 5.8 1.0 - - - +
265B GLN* 3.2 9.7 + - - -
277B ARG* 2.6 41.3 + - - +
278B ILE 3.0 10.8 - - - +
279B ILE* 3.4 16.1 - - + +
291B TYR* 2.5 40.2 + - + -
292B MET* 1.3 74.4 - - - +
294B MET* 1.3 60.3 + - - +
295B PRO* 3.9 3.0 - - - +
374B PHE* 4.3 0.4 - - - -
386B LEU* 3.9 9.4 - - + -
388B HIS* 3.1 27.3 + - - -
418B THR 3.1 4.9 + - - +
419B GLU* 3.7 4.5 - - + +
420B PHE* 3.2 23.9 + - - +
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Residues in contact with MET 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ARG* 3.9 1.6 - - - -
278B ILE* 2.8 41.2 + - + +
293B GLU* 1.3 74.6 - - - +
295B PRO* 1.3 72.7 - - + +
296B LEU* 3.9 10.1 - - + +
370B VAL* 3.8 19.5 - - + -
373B PHE* 3.7 30.5 - - + -
374B PHE* 3.5 39.0 - - + -
420B PHE* 3.9 14.6 - - + -
422B THR 4.7 0.7 - - - +
424B LEU* 3.4 41.5 - - + -
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Residues in contact with PRO 295 (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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275B HIS* 3.2 32.3 - - + +
276B THR 3.5 7.6 - - - +
277B ARG* 3.7 12.5 - - + +
293B GLU 3.9 3.4 - - - +
294B MET* 1.3 90.7 - - + +
296B LEU* 1.3 62.3 + - - +
419B GLU* 5.8 0.4 - - + -
420B PHE* 3.5 26.2 - - + +
421B THR 4.7 1.6 - - - +
422B THR* 3.6 24.5 - - - +
423B ALA* 3.2 11.6 - - + +
424B LEU 3.2 19.4 + - - -
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Residues in contact with LEU 296 (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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262B LEU* 4.5 5.4 - - + -
275B HIS* 5.0 3.6 + - - -
276B THR* 2.8 37.0 + - + +
277B ARG 4.6 0.9 - - - -
278B ILE* 3.6 42.2 - - + +
294B MET* 3.9 19.3 - - + +
295B PRO* 1.3 85.7 - - - +
297B GLU* 1.3 65.2 + - - +
298B CYS 4.4 0.2 + - - -
314B PHE 5.3 1.9 - - - +
315B ASN* 5.4 2.9 - - - -
342B LEU* 4.4 6.5 - - + -
346B PHE* 4.7 10.6 - - + -
365B PHE* 3.8 37.0 - - + -
370B VAL* 5.7 0.4 - - + -
423B ALA* 4.1 0.2 - - - -
424B LEU* 3.8 14.6 - - + +
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Residues in contact with GLU 297 (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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275B HIS* 6.3 2.2 - - + -
296B LEU* 1.3 75.1 - - - +
298B CYS* 1.3 59.6 + - - +
299B ILE* 4.6 2.8 - - + +
311B LYS* 4.3 14.3 + - - +
313B VAL* 3.7 28.8 - - + +
314B PHE 5.3 0.4 - - - -
346B PHE* 5.6 0.4 - - - -
365B PHE* 4.1 7.7 - - - -
423B ALA* 3.7 21.3 - - + +
424B LEU 3.2 7.8 + - - +
425B GLN* 3.4 34.0 + - + +
426B ARG 3.2 24.9 + - - +
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Residues in contact with CYS 298 (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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297B GLU* 1.3 74.1 - - - +
299B ILE* 1.3 61.7 + - - +
313B VAL* 3.2 4.6 - - - +
314B PHE* 2.6 46.0 + - + +
346B PHE* 3.9 27.8 - - + -
361B ALA* 4.3 14.6 - - - -
362B MET 4.2 4.5 - - - -
363B CYS* 2.0 49.8 - - - -
426B ARG 3.6 2.0 - - - -
428B ASP 4.3 7.0 - - - -
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Residues in contact with ILE 299 (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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297B GLU* 4.6 7.4 - - + +
298B CYS* 1.3 80.8 - - - +
300B LEU* 1.3 62.0 + - - +
301B THR* 4.6 11.9 - - - +
311B LYS* 4.3 20.2 - - + -
312B GLU 3.1 14.4 - - - +
313B VAL* 3.7 25.4 - - + -
314B PHE* 4.4 5.6 - - - -
425B GLN* 3.4 29.2 - - + +
426B ARG 3.3 17.5 + - - +
427B VAL* 3.5 22.0 - - + -
428B ASP* 2.9 27.5 + - - +
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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
------------------------------------------------------------
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