Contacts of the strand formed by residues 223 - 229 (chain C) in PDB entry 1SMV
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* 3.8 21.5 + - - -
89C GLU 3.3 12.8 - - - +
90C LEU* 4.1 13.9 - - + -
91C VAL* 4.0 0.7 - - - -
135C PHE* 3.4 8.5 - - - -
136C GLN* 2.7 68.7 + - + +
138C ASP 4.5 2.4 + - - -
139C MET* 3.3 52.2 + - + +
141C ASP 3.0 25.5 + - - -
143C VAL* 3.7 21.0 - - - +
222C ALA* 1.3 78.3 - - - +
224C LEU* 1.3 60.4 + - - +
225C VAL* 4.2 3.9 - - + +
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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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75C THR* 5.9 0.4 - - + -
88C SER* 3.0 6.6 - - - -
89C GLU* 2.7 43.2 + - + +
91C VAL* 4.3 2.0 - - - +
117C TYR* 3.6 46.4 - - + -
133C MET* 4.1 19.5 - - + -
134C GLY 3.6 16.6 - - - +
135C PHE* 4.1 26.7 - - + -
185C THR* 4.4 5.4 - - + -
223C ARG* 1.3 71.6 - - - +
225C VAL* 1.3 65.1 + - - +
226C ILE* 3.9 28.1 + - + +
242C ILE* 5.2 1.3 - - + -
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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* 3.5 27.8 - - + -
87C SER 3.3 4.3 - - - +
88C SER* 4.5 4.0 - - - -
132C HIS 4.5 0.4 - - - -
133C MET* 3.4 7.1 - - - +
134C GLY 2.8 35.2 + - - +
136C GLN* 3.6 35.0 - - + +
143C VAL* 4.3 1.6 - - + -
144C PRO* 3.9 18.6 - - + -
150C LEU* 4.5 10.6 - - + +
153C LEU* 4.6 4.7 - - + -
223C ARG* 4.2 12.8 - - - +
224C LEU* 1.3 78.2 - - - +
226C ILE* 1.3 66.3 + - - +
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Residues in contact with ILE 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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75C THR* 6.3 0.7 - - + -
76C ALA* 5.1 9.0 - - + -
78C ILE* 4.3 14.1 - - + -
85C VAL 3.7 1.0 - - - +
86C VAL* 3.2 3.0 - - - +
87C SER* 2.6 58.0 + - - +
88C SER 5.8 0.4 - - - +
89C GLU* 5.3 8.5 - - + -
131C ILE* 4.4 9.0 - - + -
132C HIS 3.4 7.4 - - - +
133C MET* 4.2 9.6 - - + -
224C LEU* 3.9 25.1 - - + +
225C VAL* 1.3 81.0 - - - +
227C ALA* 1.3 61.8 + - - +
228C LEU* 4.3 20.4 - - + -
242C ILE* 3.7 22.7 - - + -
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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 11.0 - - + -
85C VAL 3.3 4.7 - - - +
86C VAL* 3.8 17.5 - - + -
131C ILE* 3.6 1.2 - - - +
132C HIS* 2.9 41.8 + - + +
147C VAL* 6.0 0.2 - - - -
150C LEU* 3.3 30.7 - - + +
226C ILE* 1.3 75.1 - - - +
228C LEU* 1.3 66.5 + - - +
229C LEU* 5.2 1.1 - - + -
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Residues in contact with LEU 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 ILE* 3.3 49.6 - - + -
79C GLY 3.9 16.4 - - - +
80C VAL* 3.7 24.9 - - + -
81C THR* 4.5 1.8 + - - +
83C SER 3.5 2.9 - - - +
84C ILE* 3.5 0.9 - - - -
85C VAL* 3.0 39.7 + - + +
87C SER* 6.4 1.3 - - - -
130C SER 3.5 9.0 - - - +
131C ILE* 4.1 9.2 - - + -
161C VAL* 3.9 15.7 - - + -
226C ILE* 4.3 9.2 - - + -
227C ALA* 1.3 80.5 - - - +
229C LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 229 (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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80C VAL* 3.5 2.8 - - - +
81C THR 3.7 11.0 - - - -
82C ASP 5.0 0.9 - - - +
83C SER 4.0 1.8 - - - -
84C ILE* 3.6 36.6 - - + +
129C GLY* 3.4 1.7 - - - -
130C SER* 3.0 21.6 + - - +
132C HIS* 3.6 33.4 - - + +
147C VAL* 3.9 26.7 - - + -
227C ALA* 4.8 0.7 - - + -
228C LEU* 1.3 80.4 - - - +
230C ASP* 1.3 85.8 + - - +
231C GLY 3.1 6.8 + - - -
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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