Contacts of the strand formed by residues 235 - 241 (chain F) in PDB entry 6S1M
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 LEU 235 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144F PHE* 5.9 0.7 - - + -
160F ILE* 4.2 9.2 - - + -
205F LEU* 5.9 0.2 - - - -
207F PHE* 3.1 41.8 - - + -
212F LEU* 3.8 29.4 - - + -
227F LEU* 4.2 12.3 - - + -
228F SER 3.7 9.0 - - - +
229F MET* 3.7 29.8 - - + +
233F VAL 3.5 3.0 + - - -
234F PRO* 1.3 72.9 - - - +
236F VAL* 1.3 76.9 + - - +
237F VAL* 3.8 13.2 - - + -
249F TYR 3.5 1.0 - - - +
250F TYR* 3.3 5.9 - - - -
251F LEU* 2.9 33.7 + - + +
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Residues in contact with VAL 236 (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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133F TYR* 3.1 41.1 - - + +
226F THR 3.6 1.4 - - - +
227F LEU* 3.3 6.9 - - - -
228F SER* 2.8 44.4 + - - +
234F PRO 3.9 1.8 - - - +
235F LEU* 1.3 78.5 - - - +
237F VAL* 1.3 67.8 + - - +
238F GLU* 4.0 6.5 - - + +
248F LYS* 4.6 17.3 - - + -
249F TYR 3.5 4.9 - - - +
250F TYR* 3.6 30.5 - - + +
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Residues in contact with VAL 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F PHE* 4.1 11.0 - - + -
212F LEU* 4.5 4.0 - - + -
215F PHE* 3.8 25.8 - - + -
225F VAL* 3.9 12.6 - - + -
226F THR 3.8 2.5 - - - -
227F LEU* 3.9 15.0 - - + -
235F LEU* 3.8 22.9 - - + -
236F VAL* 1.3 76.7 - - - +
238F GLU* 1.3 60.5 + - - +
239F TYR* 3.8 24.0 - - + +
248F LYS* 3.5 0.9 - - - -
249F TYR* 2.7 52.0 + - + +
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Residues in contact with GLU 238 (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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224F THR 4.5 0.2 - - - +
225F VAL* 3.3 6.5 - - - +
226F THR* 3.2 48.8 + - + +
236F VAL* 4.0 7.6 - - + +
237F VAL* 1.3 76.6 - - - +
239F TYR* 1.3 72.7 + - - +
240F LYS* 3.4 33.9 + - + +
246F HIS* 3.6 7.4 - - + -
247F LEU 3.5 4.0 - - - +
248F LYS* 3.1 43.3 - - + -
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Residues in contact with TYR 239 (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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141F SER* 4.0 16.3 + - - -
144F PHE* 3.9 19.4 - - - -
215F PHE 3.5 19.9 + - - -
216F THR* 3.5 21.7 - - - +
218F ALA* 3.6 27.6 - - + +
219F THR* 4.0 13.4 + - - -
221F LEU* 4.8 5.8 - - + -
222F SER* 4.4 9.2 - - - -
224F THR 4.2 8.7 - - - -
225F VAL* 3.7 26.0 - - + -
237F VAL* 3.8 17.5 - - + -
238F GLU* 1.3 77.3 - - - +
240F LYS* 1.3 64.9 + - - +
241F ILE* 4.1 1.4 - - - +
246F HIS* 3.4 1.0 - - - +
247F LEU* 3.0 39.1 + - + +
249F TYR* 3.9 13.7 - + - -
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Residues in contact with LYS 240 (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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53F ARG* 4.7 10.5 - - - +
221F LEU 3.4 6.8 - - - +
222F SER* 3.3 29.6 + - - +
224F THR 4.7 1.2 + - - -
226F THR* 6.2 4.0 - - + -
238F GLU* 3.4 27.5 + - + +
239F TYR* 1.3 73.2 - - - +
241F ILE* 1.3 61.6 + - - +
242F ALA* 3.6 6.4 + - - +
245F GLY 4.0 4.5 - - - +
246F HIS* 3.9 22.4 + - + -
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Residues in contact with ILE 241 (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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11F ILE* 4.0 26.9 - - + -
15F VAL* 4.3 5.4 - - + -
50F LEU* 3.8 17.5 - - + -
52F LEU* 4.0 10.8 - - + -
221F LEU* 4.3 35.9 - - + +
239F TYR 4.1 2.9 - - - +
240F LYS* 1.3 76.5 - - - +
242F ALA* 1.3 68.4 + - - +
244F MET* 2.7 31.4 + - + +
245F GLY 2.8 20.2 + - - +
246F HIS* 3.6 28.5 - - - +
247F LEU* 4.2 1.1 - - + +
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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