Contacts of the strand formed by residues 239 - 246 (chain F) in PDB entry 1S9C
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 PHE 239 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F PRO* 3.4 37.7 - - + -
59F THR* 4.6 4.7 - - + -
94F LEU* 5.7 2.7 - - + -
96F LEU* 3.6 22.9 - - + +
224F ALA* 3.9 32.8 - - + -
228F LEU* 4.0 25.5 - - + +
235F ASP 3.9 1.0 + - - -
236F VAL 3.1 18.3 + - - +
237F SER 3.3 2.8 - - - +
238F ARG* 1.3 75.0 - - - +
240F LYS* 1.3 61.2 + - - +
241F ALA* 4.3 5.2 - - - -
242F VAL* 2.9 39.9 - - + -
286F VAL* 3.8 20.6 - - + -
288F LEU* 4.2 7.9 - - + -
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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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95F GLU* 3.5 4.9 - - + +
96F LEU* 2.8 37.4 + - - +
237F SER 5.3 2.5 - - - +
238F ARG 3.3 1.3 + - - +
239F PHE* 1.3 76.6 - - - +
241F ALA* 1.3 62.4 + - + +
287F ASP* 3.0 25.9 + - + +
288F LEU 4.5 4.0 + - - +
289F ALA* 3.3 40.4 - - + +
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Residues in contact with ALA 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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93F TYR* 4.0 15.7 - - + +
94F LEU 3.1 14.4 - - - +
95F GLU* 3.9 14.8 - - + -
96F LEU* 5.9 0.4 - - - -
239F PHE* 3.9 2.6 - - - -
240F LYS* 1.3 83.6 - - + +
242F VAL* 1.3 67.0 + - - +
285F TYR* 5.1 2.7 - - + +
286F VAL* 3.0 5.6 - - - +
287F ASP* 2.7 43.3 + - + +
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Residues in contact with VAL 242 (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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59F THR* 4.8 4.5 - - + -
93F TYR* 3.3 7.2 - - - -
94F LEU* 2.9 36.3 + - + +
220F PHE* 3.0 40.2 - - + -
224F ALA* 4.9 4.0 - - + -
239F PHE* 2.9 45.1 - - + -
241F ALA* 1.3 72.7 - - - +
243F LYS* 1.3 61.3 + - - +
269F PHE* 5.3 4.0 - - + -
285F TYR* 3.2 13.5 - - - +
286F VAL* 4.0 5.8 - - + +
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Residues in contact with LYS 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F GLU* 3.0 40.1 + - - +
92F GLN 3.2 18.8 + - - +
93F TYR* 4.0 15.5 - - + +
141F GLN* 4.9 5.5 + - - -
143F SER* 5.0 2.6 - - - -
161F VAL* 5.5 0.4 - - - +
162F LYS* 2.8 28.3 + - - +
163F VAL 3.5 15.0 - - - +
164F ALA* 3.5 27.4 - - - +
242F VAL* 1.3 75.2 - - - +
244F ALA* 1.3 64.1 + - - +
269F PHE* 4.3 0.5 - - - -
283F ASN 4.8 0.7 - - - +
284F ALA* 3.0 5.6 - - - +
285F TYR* 2.9 59.7 + - + +
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Residues in contact with ALA 244 (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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91F GLU* 3.3 6.6 - - - +
92F GLN 3.0 31.4 + - - +
164F ALA* 5.4 0.2 - - - -
220F PHE* 3.6 33.0 - - + -
243F LYS* 1.3 82.6 - - - +
245F ARG* 1.3 61.7 + - - +
246F PHE* 5.0 4.9 - - + -
269F PHE* 4.4 1.8 - - + -
281F ILE* 3.9 11.0 - - + -
283F ASN 5.2 0.4 - - - -
284F ALA* 3.6 19.1 - - + +
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Residues in contact with ARG 245 (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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90F GLY 3.7 10.3 - - - +
91F GLU* 2.7 31.0 + - + +
163F VAL* 5.8 2.2 - - - +
164F ALA* 3.5 24.8 - - + +
244F ALA* 1.3 74.3 - - - +
246F PHE* 1.3 71.8 + - - +
247F ALA* 6.1 0.2 - - + -
281F ILE* 3.3 6.1 - - - +
282F SER* 2.8 57.2 + - - +
283F ASN* 3.8 15.1 - - - +
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Residues in contact with PHE 246 (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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89F HIS* 3.6 47.6 - + - +
90F GLY* 2.9 31.3 + - - +
91F GLU* 4.1 2.2 - - - -
92F GLN* 4.0 14.6 - - + -
216F GLY* 3.3 37.2 - - - -
217F LEU* 3.8 23.8 - - + -
219F THR* 6.1 0.2 - - - -
220F PHE* 4.1 15.0 - + + -
244F ALA* 5.0 3.6 - - + -
245F ARG* 1.3 82.7 - - - +
247F ALA* 1.3 63.3 + - - +
280F VAL 3.8 3.1 - - - +
281F ILE* 4.3 17.5 - - + -
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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
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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