Contacts of the strand formed by residues 235 - 239 (chain C) in PDB entry 3R2W
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 TYR 235 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LYS 3.7 5.0 + - - +
97C LEU* 3.4 17.8 - - + +
98C VAL* 3.4 23.9 + - - +
233C LYS* 5.1 0.5 - - - +
234C GLU* 1.3 93.3 - - + +
236C ILE* 1.3 66.3 + - - +
253C LEU* 6.0 2.2 - - + -
256C LEU* 3.5 50.1 - - + +
265C CYS 3.1 40.3 + - - -
322C TRP* 5.0 7.9 - - + -
323C ILE 3.3 20.4 - - - -
324C SER* 4.1 13.5 - - - -
325C LEU* 3.7 4.0 - - - +
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Residues in contact with ILE 236 (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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98C VAL* 3.5 9.2 - - + +
100C VAL* 3.4 33.7 - - + -
219C PHE* 4.6 20.4 - - + -
228C PHE* 6.4 0.2 - - + -
235C TYR* 1.3 77.8 - - - +
237C PHE* 1.3 58.7 + - - +
238C VAL* 3.3 19.0 + - + -
322C TRP* 3.6 2.4 - - - -
323C ILE* 2.8 53.9 + - + +
325C LEU* 3.4 40.8 - - + +
328C VAL* 4.8 9.4 - - + -
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Residues in contact with PHE 237 (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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97C LEU* 3.8 12.8 - - + +
98C VAL 3.2 10.3 + - - +
99C VAL* 3.5 24.9 - - + -
100C VAL 2.9 27.2 + - - +
101C LYS* 4.9 0.7 - - - -
236C ILE* 1.3 68.8 - - - +
238C VAL* 1.3 64.4 + - - +
239C SER* 3.7 27.8 - - - -
246C ALA* 4.1 15.3 - - + -
247C THR 3.7 25.6 - - - -
248C VAL* 4.6 9.0 - - + -
270C GLU* 3.9 11.0 - - - -
320C ASN* 4.6 1.3 - - + -
321C LEU 3.2 17.3 - - - -
322C TRP* 3.1 51.1 - + + +
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Residues in contact with VAL 238 (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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100C VAL* 3.7 22.4 - - + -
102C LEU* 4.7 15.7 - - + +
215C ILE* 5.2 12.3 - - + -
236C ILE* 3.3 26.3 + - + -
237C PHE* 1.3 72.5 - - - +
239C SER* 1.3 72.3 + - - +
319C ASN 3.6 4.0 - - - +
320C ASN* 3.8 0.2 - - - -
321C LEU* 2.9 46.0 + - + +
323C ILE* 3.8 24.2 - - + -
361C VAL* 5.3 6.5 - - + -
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Residues in contact with SER 239 (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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100C VAL 3.3 7.2 + - - -
101C LYS* 3.0 30.1 + - - +
102C LEU* 3.2 25.2 + - - +
237C PHE* 3.7 16.8 - - - -
238C VAL* 1.3 81.1 - - - +
240C ASN* 1.3 60.2 + - - +
246C ALA* 3.7 13.7 - - - -
319C ASN* 4.0 8.5 - - - -
320C ASN* 3.6 21.1 - - - +
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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