Contacts of the strand formed by residues 239 - 246 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PRO* 3.4 38.6 - - + -
59B THR* 4.4 5.2 - - + -
94B LEU* 5.7 2.0 - - + -
96B LEU* 3.5 24.1 - - + +
224B ALA* 3.9 32.3 - - + -
228B LEU* 4.0 25.3 - - + +
235B ASP 3.9 1.2 + - - -
236B VAL 3.1 17.4 + - - +
237B SER 4.6 2.4 - - - +
238B ARG* 1.3 76.7 - - - +
240B LYS* 1.3 60.4 + - - +
241B ALA* 4.3 4.5 - - - -
242B VAL* 2.8 40.6 - - + -
286B VAL* 3.8 20.9 - - + -
288B LEU* 4.2 7.0 - - + -
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Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B GLU* 3.4 5.8 - - + +
96B LEU 2.8 37.1 + - - +
237B SER 5.3 3.1 - - - +
238B ARG 3.2 8.3 + - - +
239B PHE* 1.3 76.9 - - - +
241B ALA* 1.3 61.9 + - + +
287B ASP* 3.0 25.7 + - + +
288B LEU 4.4 9.9 + - - +
289B ALA* 4.1 22.1 - - + +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B TYR* 3.9 15.3 - - + +
94B LEU 3.1 14.6 - - - +
95B GLU* 3.8 15.0 - - + -
96B LEU* 5.8 0.2 - - - -
239B PHE* 3.9 2.5 - - - -
240B LYS* 1.3 84.7 - - + +
242B VAL* 1.3 67.9 + - - +
285B TYR* 5.1 2.0 - - + -
286B VAL* 3.0 5.9 - - - +
287B ASP* 2.7 42.8 + - + +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B THR* 4.7 4.5 - - + -
93B TYR* 3.4 7.1 - - - -
94B LEU* 2.9 36.2 + - + +
220B PHE* 3.1 40.4 - - + -
224B ALA* 5.1 3.8 - - + -
239B PHE* 2.8 45.8 - - + -
241B ALA* 1.3 74.2 - - - +
243B LYS* 1.3 63.3 + - - +
269B PHE* 5.3 4.5 - - + -
285B TYR* 3.2 14.4 - - - +
286B VAL* 4.1 4.3 - - + -
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Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLU* 3.0 38.1 + - - +
92B GLN 3.3 17.7 + - - +
93B TYR* 4.1 15.5 - - + +
141B GLN* 5.1 4.9 + - - -
143B SER* 5.3 1.4 - - - -
162B LYS* 2.9 27.1 + - - +
163B VAL 3.6 14.8 - - - +
164B ALA* 3.6 26.9 - - - +
242B VAL* 1.3 75.8 - - - +
244B ALA* 1.3 69.0 + - - +
269B PHE* 4.4 0.5 - - - -
283B ASN 4.8 0.7 - - - +
284B ALA* 3.0 4.3 - - - +
285B TYR* 2.9 59.9 + - + +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLU* 3.5 6.1 - - - +
92B GLN* 3.2 31.4 + - - +
220B PHE* 3.6 32.5 - - + -
243B LYS* 1.3 83.4 - - - +
245B ARG* 1.3 61.9 + - - +
246B PHE* 5.0 4.0 - - + -
269B PHE* 4.4 2.2 - - + -
281B ILE* 3.8 12.1 - - + -
283B ASN 5.1 0.7 - - - -
284B ALA* 3.6 17.5 - - + +
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Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLY 3.9 8.3 - - - +
91B GLU* 3.0 29.1 + - + +
163B VAL* 5.7 2.4 - - - +
164B ALA* 3.4 26.4 + - + +
244B ALA* 1.3 75.7 - - - +
246B PHE* 1.3 74.5 + - - +
247B ALA* 6.0 0.2 - - + -
281B ILE* 3.3 6.5 - - - +
282B SER* 2.8 55.4 + - - +
283B ASN* 3.6 16.0 - - - +
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B HIS* 3.4 52.9 - + + +
90B GLY* 3.1 23.8 + - - +
91B GLU* 4.2 2.7 - - - -
92B GLN* 4.0 13.2 - - + -
216B GLY* 3.3 35.9 - - - -
217B LEU* 3.9 23.6 - - + -
220B PHE* 4.1 15.7 - + + -
244B ALA* 5.0 4.0 - - + -
245B ARG* 1.3 82.6 - - - +
247B ALA* 1.3 64.6 + - - +
280B VAL 3.7 3.1 - - - +
281B ILE* 4.2 18.4 - - + -
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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