Contacts of the strand formed by residues 223 - 228 (chain C) in PDB entry 4SBV
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 ARG 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C SER* 3.6 26.4 + - - -
89C GLU 3.2 15.7 - - - +
90C LEU* 4.1 12.5 - - + +
135C PHE* 3.7 5.8 - - - -
136C GLN* 2.9 60.5 + - + +
138C ASP 4.1 12.3 + - - -
139C MET* 3.7 42.0 + - + +
141C ASP 2.6 32.7 + - - +
143C LEU* 3.2 13.7 - - - +
222C ALA* 1.3 74.8 - - - +
224C LEU* 1.3 60.9 - - - +
225C VAL* 4.2 2.4 - - + +
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Residues in contact with LEU 224 (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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88C SER* 3.3 6.2 - - - -
89C GLU* 2.7 49.0 + - + +
91C VAL* 3.9 6.3 - - + +
117C TYR* 3.4 42.0 - - + -
133C MET* 3.9 35.7 - - + -
134C GLY 3.8 2.9 - - - +
135C PHE* 3.9 16.4 - - + -
185C ILE* 4.0 22.0 - - + -
223C ARG* 1.3 72.2 - - - +
225C VAL* 1.3 66.3 + - - +
226C THR* 4.1 10.9 + - - +
242C LEU* 5.1 5.2 - - + -
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Residues in contact with VAL 225 (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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86C VAL* 4.0 21.1 - - + -
87C THR 4.0 2.7 - - - +
88C SER* 4.4 1.6 - - - -
132C HIS 3.6 0.3 - - - +
133C MET* 2.9 28.8 - - - +
134C GLY 2.7 20.5 + - - +
136C GLN* 4.0 34.5 - - + +
143C LEU* 4.3 5.4 - - + -
144C PRO* 4.1 5.4 - - + -
150C LEU* 3.6 27.5 - - + +
153C LEU* 4.4 2.2 - - + -
223C ARG* 4.2 11.9 - - - +
224C LEU* 1.3 78.4 - - - +
226C THR* 1.3 67.6 - - - +
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Residues in contact with THR 226 (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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78C LEU* 3.8 16.6 - - + -
86C VAL* 3.1 9.4 - - - +
87C THR* 3.1 56.0 + - + +
88C SER* 5.2 0.9 - - - -
89C GLU* 5.7 1.4 + - - +
131C ILE* 4.7 4.0 - - + -
132C HIS 3.5 4.9 - - - +
133C MET* 4.5 6.9 - - - -
224C LEU* 4.1 18.5 + - - +
225C VAL* 1.3 81.2 + - - +
227C ALA* 1.3 63.4 + - - +
228C MET* 3.8 26.0 - - + -
242C LEU* 5.5 1.8 - - + +
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Residues in contact with ALA 227 (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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84C ILE* 4.2 22.2 - - + -
85C VAL 3.4 4.3 - - - +
86C VAL* 4.4 7.4 - - + -
131C ILE* 3.5 5.7 - - - +
132C HIS* 2.8 54.4 + - + +
147C VAL* 5.4 0.9 - - + -
150C LEU* 4.7 11.2 - - + -
226C THR* 1.3 76.2 - - - +
228C MET* 1.3 67.9 - - - +
229C GLU 4.1 0.7 - - - -
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Residues in contact with MET 228 (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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78C LEU* 3.1 40.8 - - + -
79C ALA 4.0 19.1 - - - +
80C VAL* 3.7 22.7 - - + -
81C THR* 4.1 2.5 - - + +
83C THR 3.1 8.7 - - - +
84C ILE* 4.8 0.2 - - - -
85C VAL* 3.0 40.0 + - + +
87C THR* 5.1 4.0 - - + -
119C TYR* 5.1 1.1 - - + -
130C ALA 3.8 4.5 - - - +
131C ILE* 3.0 47.8 - - + -
161C VAL* 4.9 6.3 - - - -
226C THR* 3.8 8.5 - - + -
227C ALA* 1.3 74.5 - - - +
229C GLU* 1.3 62.7 + - - +
239C THR* 5.5 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