Contacts of the strand formed by residues 293 - 299 (chain F) 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 ILE 293 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284F ARG* 5.7 0.4 - - - +
291F GLY* 3.0 20.6 + - - +
292F VAL* 1.3 79.2 - - - +
294F GLU* 1.3 79.5 + - - +
311F LYS* 3.9 36.8 - - + -
312F VAL 3.5 6.5 - - - +
313F ARG* 4.2 7.0 - - + -
323F TYR* 3.6 34.8 - - + +
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Residues in contact with GLU 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F MET* 4.1 23.0 - - + +
194F VAL* 5.8 1.2 - - - +
213F ASP* 5.7 0.9 - - - +
277F LYS* 4.7 9.9 - - - +
278F PHE* 3.9 22.4 - - + -
281F ALA* 3.7 32.1 - - + +
284F ARG* 4.7 8.6 + - - +
292F VAL* 4.9 0.7 - - + -
293F ILE* 1.3 90.9 - - - +
295F CYS* 1.3 64.0 + - - +
311F LYS* 4.1 4.0 - - - -
312F VAL* 2.8 36.6 + - + +
314F LEU* 4.6 6.9 - - + +
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Residues in contact with CYS 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F THR* 3.7 10.7 + - - +
191F MET* 3.9 17.8 + - - +
194F VAL* 3.9 18.8 - - + -
215F PRO* 4.0 8.3 - - - -
216F VAL 3.5 40.8 - - - +
217F VAL* 5.4 0.4 - - - -
278F PHE* 4.0 6.4 - - - -
294F GLU* 1.3 75.3 + - - +
296F ALA* 1.3 60.8 - - - +
309F ALA* 5.7 0.2 - - + -
310F SER 3.4 8.1 - - - +
311F LYS* 3.7 28.9 - - - -
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Residues in contact with ALA 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F LEU* 4.4 2.7 - - + -
188F GLY 3.8 7.6 - - - +
190F THR* 3.5 6.5 - - - +
278F PHE* 3.7 26.9 - - + -
295F CYS* 1.3 76.4 - - - +
297F PHE* 1.3 60.0 + - - +
298F VAL* 3.3 25.0 + - + +
308F PHE 3.7 0.5 - - - +
309F ALA* 3.0 20.3 - - - +
310F SER 3.2 12.2 + - - +
312F VAL* 4.2 10.8 - - + -
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Residues in contact with PHE 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F VAL* 3.7 34.1 - - + -
165F ASN* 3.7 32.1 - - - -
168F VAL* 3.8 21.5 - - + +
169F PRO* 4.3 0.4 - - + -
187F LEU* 3.9 0.7 - - - -
188F GLY 2.9 32.5 + - - +
190F THR* 3.6 20.6 + - + -
218F GLY 3.3 27.4 - - - -
219F GLY* 4.2 1.6 - - - -
296F ALA* 1.3 68.5 - - - +
298F VAL* 1.3 59.7 + - - +
307F PHE* 3.7 24.7 - - + -
308F PHE* 3.8 12.1 - - - -
309F ALA* 3.5 9.2 - - + +
343F LEU* 4.0 15.3 - - + -
347F ILE* 4.8 1.1 - - + -
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Residues in contact with VAL 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F VAL* 5.4 0.9 - - - -
186F LEU 3.9 12.6 - - - +
187F LEU* 4.0 5.2 - - + -
296F ALA* 3.3 22.4 + - + +
297F PHE* 1.3 79.0 - - - +
299F SER* 1.3 73.6 + - - +
300F SER* 3.6 0.4 + - - -
307F PHE* 3.2 9.0 - - - -
308F PHE 2.8 38.0 + - - +
310F SER* 5.3 0.4 - - - +
312F VAL* 3.9 22.9 - - + -
319F ILE* 3.5 28.0 - - + -
322F VAL* 4.1 14.1 - - + -
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Residues in contact with SER 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F TYR* 3.4 26.4 + - - -
183F PRO* 3.7 25.5 + - - +
186F LEU 4.8 1.6 + - - -
298F VAL* 1.3 83.0 - - - +
300F SER* 1.3 63.1 + - - +
301F GLN* 4.5 8.3 + - - -
306F PRO 3.2 13.4 + - - -
307F PHE* 3.5 12.3 - - - -
319F ILE* 5.7 0.2 - - - +
322F VAL* 4.1 7.6 - - - +
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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