Contacts of the strand formed by residues 292 - 299 (chain G) in PDB entry 1SMK
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 292 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281G ALA* 3.3 33.7 - - + +
284G ARG* 3.8 30.5 - - + +
289G ASP* 3.5 36.3 + - + +
290G ALA 2.9 8.8 + - - +
291G GLY* 1.3 68.6 - - - +
293G ILE* 1.3 58.5 + - - +
294G GLU* 5.0 0.9 - - + -
313G ARG* 3.3 5.9 - - - +
314G LEU* 2.6 60.5 + - + +
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Residues in contact with ILE 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291G GLY* 3.0 23.7 + - - +
292G VAL* 1.3 75.8 - - - +
294G GLU* 1.3 83.3 + - - +
311G LYS* 4.3 26.9 - - + +
312G VAL 3.3 18.6 - - - +
313G ARG* 4.3 9.9 - - + -
323G TYR* 4.1 26.5 - - + +
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Residues in contact with GLU 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G MET* 3.2 27.4 - - - +
194G VAL* 5.8 0.7 - - - +
277G LYS 5.4 0.7 - - - -
278G PHE* 3.9 24.9 - - + -
281G ALA* 3.5 32.3 - - + +
284G ARG* 4.3 9.4 + - - -
292G VAL* 4.3 0.8 + - + +
293G ILE* 1.3 86.8 + - - +
295G CYS* 1.3 63.1 + - - +
311G LYS* 3.6 1.5 - - - -
312G VAL* 2.9 36.7 + - - +
314G LEU* 4.3 6.7 - - + +
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Residues in contact with CYS 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G THR* 3.8 9.8 + - - +
191G MET* 3.9 13.2 + - - +
194G VAL* 3.8 22.2 - - + -
214G VAL 4.8 0.7 - - - -
215G PRO* 4.1 9.4 - - - -
216G VAL 3.5 41.7 - - - +
217G VAL* 5.5 0.7 - - - -
278G PHE* 3.8 9.5 - - - -
294G GLU* 1.3 77.7 + - - +
296G ALA* 1.3 65.5 + - - +
310G SER 4.0 5.8 - - - +
311G LYS* 4.3 20.9 - - - -
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Residues in contact with ALA 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G LEU* 4.0 5.6 - - + -
188G GLY 3.9 6.5 - - - +
190G THR* 3.7 8.9 + - - +
278G PHE* 3.7 27.6 - - + -
294G GLU 4.0 0.4 + - - -
295G CYS* 1.3 78.0 - - - +
297G PHE* 1.3 59.8 + - - +
298G VAL* 3.3 24.5 + - + +
308G PHE 3.9 0.3 - - - +
309G ALA* 3.1 19.6 - - - +
310G SER 3.2 14.7 + - - +
312G VAL* 4.5 5.8 - - + -
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Residues in contact with PHE 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G VAL* 3.8 20.6 - - + -
165G ASN* 3.9 18.6 - - - -
168G VAL* 3.6 31.9 - - + +
169G PRO* 4.3 2.2 - - + -
187G LEU* 3.8 0.7 - - - -
188G GLY* 2.8 40.8 + - - +
190G THR* 3.6 21.0 - - + +
218G GLY 3.5 12.1 - - - -
219G GLY* 4.4 2.7 - - - -
296G ALA* 1.3 69.1 - - - +
298G VAL* 1.3 59.5 + - - +
307G PHE* 3.5 26.2 - - + -
308G PHE* 3.5 23.1 - - - -
309G ALA* 3.2 18.2 - - + +
343G LEU* 4.0 24.0 - - + -
347G ILE* 4.5 3.1 - - + -
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Residues in contact with VAL 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G VAL* 5.3 0.9 - - - -
183G PRO 5.0 0.2 - - - +
186G LEU 4.0 13.2 - - - +
187G LEU* 4.0 4.9 - - + -
296G ALA* 3.3 22.5 + - + +
297G PHE* 1.3 78.6 - - - +
299G SER* 1.3 73.2 + - - +
300G SER* 4.5 3.4 - - - -
307G PHE* 3.0 15.5 - - - +
308G PHE 3.0 34.3 + - - +
310G SER* 5.2 0.7 - - - +
312G VAL* 4.2 16.6 - - + -
319G ILE* 3.3 35.7 - - + -
322G VAL* 4.4 9.4 - - + -
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Residues in contact with SER 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G TYR* 3.3 26.5 + - - -
183G PRO* 4.0 23.9 + - - +
186G LEU 5.1 0.8 + - - -
298G VAL* 1.3 82.8 - - - +
300G SER* 1.3 58.5 + - - +
301G GLN* 4.3 10.4 + - - +
306G PRO* 3.2 13.8 + - - +
307G PHE* 3.6 13.3 - - - -
319G ILE* 5.9 0.2 - - - +
322G VAL* 4.5 7.4 - - - +
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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