Contacts of the strand formed by residues 239 - 246 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PRO* 3.4 36.3 - - + -
59C THR* 4.6 3.6 - - + -
94C LEU* 5.9 1.6 - - + -
96C LEU* 3.5 23.0 - - + +
224C ALA* 3.9 33.4 - - + -
228C LEU* 4.0 26.0 - - + +
235C ASP 3.9 1.0 + - - -
236C VAL 3.2 17.6 + - - +
237C SER 3.3 2.3 - - - +
238C ARG* 1.3 74.8 - - - +
240C LYS* 1.3 60.8 + - - +
241C ALA* 4.3 4.9 - - - -
242C VAL* 2.9 39.3 - - + -
286C VAL* 3.7 21.5 - - + -
288C LEU* 4.2 8.0 - - + +
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Residues in contact with LYS 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU* 3.4 4.7 - - + +
96C LEU* 2.7 40.6 + - - +
237C SER 5.4 2.7 - - - +
238C ARG 3.2 8.5 + - - +
239C PHE* 1.3 76.7 - - - +
241C ALA* 1.3 59.2 + - + +
287C ASP* 3.0 25.7 + - + +
288C LEU 4.5 4.4 + - - +
289C ALA* 3.9 29.0 - - + +
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C TYR* 3.9 15.5 - - + +
94C LEU 3.1 13.7 - - - +
95C GLU* 3.8 16.2 - - + -
96C LEU* 5.8 0.2 - - - -
239C PHE* 3.8 2.5 - - - -
240C LYS* 1.3 84.8 - - + +
242C VAL* 1.3 66.9 + - - +
285C TYR* 5.1 2.9 - - + -
286C VAL* 2.9 5.5 - - - +
287C ASP* 2.7 43.5 + - + +
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 4.8 5.2 - - + -
93C TYR* 3.3 7.3 - - - -
94C LEU* 2.8 37.3 + - + +
220C PHE* 3.1 39.9 - - + -
224C ALA* 5.1 3.4 - - + -
239C PHE* 2.9 45.5 - - + -
241C ALA* 1.3 73.0 - - - +
243C LYS* 1.3 60.9 + - - +
269C PHE* 5.3 4.9 - - + -
285C TYR* 3.2 13.0 - - - +
286C VAL* 4.1 4.5 - - + -
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Residues in contact with LYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLU* 3.1 41.0 + - - +
92C GLN* 3.3 18.6 + - - +
93C TYR* 3.9 17.9 - - + +
141C GLN* 4.9 5.7 + - - -
143C SER* 5.1 2.2 - - - -
161C VAL* 5.3 0.6 - - - +
162C LYS* 2.9 27.7 + - - +
163C VAL 3.6 15.0 - - - +
164C ALA* 3.7 25.8 - - + +
242C VAL* 1.3 75.8 - - - +
244C ALA* 1.3 64.2 + - - +
269C PHE* 4.4 0.2 - - - -
283C ASN 4.8 0.7 - - - +
284C ALA* 3.0 5.8 - - - +
285C TYR* 2.9 56.7 + - + +
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Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLU* 3.3 5.8 - - - +
92C GLN 2.9 32.6 + - - +
220C PHE* 3.6 31.6 - - + -
243C LYS* 1.3 82.1 - - - +
245C ARG* 1.3 61.2 + - - +
246C PHE* 5.1 4.0 - - + -
269C PHE* 4.4 3.1 - - + -
281C ILE* 3.9 12.3 - - + -
283C ASN 5.3 0.9 - - - -
284C ALA* 3.6 17.5 - - + +
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Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLY 3.7 10.3 - - - +
91C GLU* 2.6 31.8 + - + +
163C VAL* 5.7 2.6 - - - +
164C ALA* 3.4 25.9 - - + +
244C ALA* 1.3 74.0 - - - +
246C PHE* 1.3 73.3 + - - +
281C ILE* 3.3 4.6 - - - -
282C SER* 2.8 58.8 + - - +
283C ASN* 3.7 16.2 - - - +
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Residues in contact with PHE 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C HIS* 3.2 55.9 - + + +
90C GLY* 2.8 29.0 + - - +
91C GLU* 4.1 1.8 - - - -
92C GLN* 4.0 14.8 - - + -
216C GLY* 3.3 34.1 - - - -
217C LEU* 3.9 22.7 - - + -
220C PHE* 4.0 16.6 - + + -
244C ALA* 5.1 3.8 - - + -
245C ARG* 1.3 80.9 - - - +
247C ALA* 1.3 63.4 + - - +
280C VAL 3.7 3.4 - - - +
281C ILE* 4.2 17.3 - - + -
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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