Contacts of the strand formed by residues 292 - 299 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ALA* 3.4 37.0 - - + +
284A ARG* 3.9 33.2 - - - +
289A ASP* 3.7 38.6 - - + +
290A ALA 3.3 2.2 - - - +
291A GLY* 1.3 75.1 - - - +
293A ILE* 1.3 57.8 + - - +
294A GLU* 4.3 1.8 - - + -
312A VAL 3.7 0.2 - - - +
313A ARG* 3.3 6.5 - - - +
314A LEU* 2.8 49.7 + - + +
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Residues in contact with ILE 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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291A GLY* 3.2 20.7 + - - +
292A VAL* 1.3 78.5 - - - +
294A GLU* 1.3 81.2 + - - +
311A LYS* 3.8 37.5 + - + +
312A VAL 3.2 11.0 - - - +
313A ARG* 4.1 11.4 - - + -
323A TYR* 3.7 24.2 - - + +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A MET* 3.6 28.2 - - + +
194A VAL* 5.4 1.9 - - - +
213A ASP* 5.7 0.9 - - - +
277A LYS* 4.4 16.1 + - - +
278A PHE* 3.9 22.4 - - + -
281A ALA* 3.8 29.5 - - + +
284A ARG* 4.4 8.0 + - - +
292A VAL* 4.3 1.1 + - + -
293A ILE* 1.3 90.0 - - - +
295A CYS* 1.3 58.8 + - - +
311A LYS* 4.3 5.6 - - - +
312A VAL* 2.7 41.6 + - + +
314A LEU* 4.7 5.3 - - + +
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Residues in contact with CYS 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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190A THR* 3.2 11.0 + - - +
191A MET* 4.2 13.6 + - - +
194A VAL* 3.9 20.6 - - + -
215A PRO* 4.1 5.8 - - - -
216A VAL* 3.6 39.0 - - + +
217A VAL* 5.7 0.7 - - - -
278A PHE* 3.9 9.9 - - - -
294A GLU* 1.3 76.6 + - - +
296A ALA* 1.3 63.0 + - - +
309A ALA 5.7 0.2 - - - -
310A SER 3.1 15.0 - - - +
311A LYS* 3.9 26.5 - - - -
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Residues in contact with ALA 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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187A LEU* 4.2 6.3 - - + -
188A GLY 3.6 7.6 - - - +
190A THR* 3.2 11.0 + - - +
278A PHE* 3.6 26.7 - - + -
294A GLU 3.9 1.0 + - - -
295A CYS* 1.3 76.3 - - - +
297A PHE* 1.3 62.7 + - - +
298A VAL* 3.4 22.0 + - + +
308A PHE 3.6 0.5 - - - +
309A ALA* 3.1 19.9 - - - +
310A SER 3.2 9.8 + - - +
312A VAL* 4.3 7.3 - - + +
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Residues in contact with PHE 297 (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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164A VAL* 3.8 22.9 - - + -
165A ASN* 3.8 24.5 - - - -
168A VAL* 3.6 33.1 - - + +
169A PRO* 4.3 0.9 - - + -
187A LEU* 3.8 1.0 - - - -
188A GLY* 2.8 41.1 + - - +
190A THR* 3.6 18.4 - - + +
218A GLY 3.4 26.0 - - - -
219A GLY* 4.2 2.5 - - - -
296A ALA* 1.3 68.9 - - - +
298A VAL* 1.3 60.0 + - - +
307A PHE* 3.6 40.4 - - + -
308A PHE 3.7 7.2 - - - -
309A ALA* 3.7 3.6 - - + +
343A LEU* 3.8 19.5 - - + -
347A ILE* 4.4 1.3 - - + -
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Residues in contact with VAL 298 (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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168A VAL* 5.3 0.9 - - - -
186A LEU 3.9 11.0 - - - +
187A LEU* 4.1 3.6 - - + -
296A ALA* 4.0 21.5 - - + +
297A PHE* 1.3 81.9 - - - +
299A SER* 1.3 72.4 + - - +
300A SER* 3.2 4.2 + - - -
307A PHE* 3.3 7.1 - - - -
308A PHE 2.9 37.9 + - - +
310A SER* 5.0 0.9 - - - +
312A VAL* 3.9 22.0 - - + -
319A ILE* 3.4 30.3 - - + -
322A VAL* 4.3 12.8 - - + -
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Residues in contact with SER 299 (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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168A VAL* 5.6 0.2 - - - +
181A TYR* 3.5 23.8 + - - -
183A PRO* 3.5 29.5 + - - +
186A LEU* 4.9 2.4 + - - -
298A VAL* 1.3 78.5 - - - +
300A SER* 1.3 62.2 + - - +
301A GLN* 4.3 10.0 + - - -
306A PRO 3.3 11.1 + - - -
307A PHE* 3.6 12.7 - - - -
319A ILE* 5.6 0.3 - - - +
322A VAL* 4.2 8.8 - - - +
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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