Contacts of the strand formed by residues 223 - 229 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B SER* 3.5 20.5 + - - +
89B GLU 3.9 8.1 - - - +
90B LEU* 4.2 14.3 - - + +
91B VAL* 4.2 1.3 - - - -
135B PHE* 3.5 4.2 - - - +
136B GLN* 2.7 67.9 + - + +
138B ASP 4.1 3.8 + - - -
139B MET* 3.3 55.4 + - + +
141B ASP* 3.3 24.5 + - - +
143B LEU* 3.5 17.1 - - - +
222B ALA* 1.3 73.4 - - - +
224B LEU* 1.3 67.5 - - - +
225B VAL* 3.8 7.8 + - + -
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Residues in contact with LEU 224 (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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76B THR* 6.4 0.2 - - + -
88B SER* 3.3 4.0 - - - -
89B GLU* 3.1 40.9 + - + +
91B VAL* 3.9 6.3 - - + +
117B TYR* 3.5 40.6 - - + -
133B MET* 3.8 24.7 - - + -
134B GLY 3.4 15.7 - - - +
135B PHE* 3.9 23.1 - - + -
185B ILE* 4.2 9.9 - - + -
223B ARG* 1.3 73.6 - - - +
225B VAL* 1.3 65.4 - - - +
226B THR* 4.2 8.0 + - + -
242B LEU* 4.2 14.8 - - + -
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Residues in contact with VAL 225 (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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86B VAL* 4.4 7.6 - - + -
87B THR 3.6 10.1 - - - +
88B SER* 4.5 1.3 - - - -
132B HIS 3.5 1.2 - - - +
133B MET* 3.1 24.1 - - - -
134B GLY 2.6 21.9 + - - +
136B GLN* 4.0 18.8 - - + -
143B LEU* 4.2 11.4 - - + -
144B PRO* 3.6 32.3 - - + -
150B LEU* 3.7 14.7 - - + +
153B LEU* 5.2 2.7 - - + -
223B ARG* 3.8 21.3 - - + +
224B LEU* 1.3 78.3 - - - +
226B THR* 1.3 61.9 + - - +
227B ALA 4.0 0.2 + - - -
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Residues in contact with THR 226 (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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76B THR* 5.7 4.0 - - + -
78B LEU* 3.9 23.1 - - + +
85B VAL 3.8 0.3 - - - +
86B VAL* 3.4 1.9 - - - -
87B THR* 2.8 61.8 + - + +
88B SER* 4.9 1.6 - - - +
89B GLU* 5.3 8.1 - - + -
131B ILE* 4.5 2.6 - - - +
132B HIS 3.3 6.5 + - - -
133B MET* 4.3 15.6 - - - +
150B LEU* 4.9 0.7 - - - -
224B LEU* 4.7 17.0 - - + +
225B VAL* 1.3 77.0 - - - +
227B ALA* 1.3 60.7 + - - +
228B MET* 4.1 6.6 - - - +
242B LEU* 5.0 7.9 - - + -
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Residues in contact with ALA 227 (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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84B ILE* 5.5 3.1 - - + -
85B VAL 3.4 6.1 - - - +
86B VAL* 4.3 12.1 - - + +
131B ILE* 3.6 3.3 - - - +
132B HIS* 2.8 45.6 + - + +
147B VAL* 4.5 9.4 - - + -
150B LEU* 3.6 26.0 - - + -
225B VAL 4.0 0.4 + - - -
226B THR* 1.3 71.2 + - - +
228B MET* 1.3 66.8 + - - +
229B GLU* 3.9 2.2 - - + +
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Residues in contact with MET 228 (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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78B LEU* 3.2 48.0 - - + -
79B ALA 3.4 31.2 - - - +
80B VAL* 3.8 16.2 - - + +
81B THR 4.5 2.8 + - - -
83B THR 3.4 14.4 - - - +
84B ILE* 5.5 0.4 - - - +
85B VAL* 2.6 34.0 + - + +
87B THR* 5.5 3.8 - - - +
119B TYR* 4.9 1.8 - - + -
130B ALA 3.7 11.0 - - - +
131B ILE* 3.9 19.5 - - - -
161B VAL* 4.7 2.0 - - + -
226B THR* 4.1 7.6 - - - +
227B ALA* 1.3 75.7 - - - +
229B GLU* 1.3 58.3 + - - +
239B THR* 3.8 17.9 - - - +
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Residues in contact with GLU 229 (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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80B VAL* 4.0 4.4 - - - +
81B THR 4.6 1.3 - - - -
83B THR 4.1 8.7 - - - -
84B ILE* 4.0 25.7 - - + +
129B GLY* 4.0 0.3 - - - -
130B ALA* 3.0 27.7 + - + +
132B HIS* 2.6 38.2 + - + +
147B VAL* 4.3 10.7 - - + +
227B ALA* 3.9 2.3 + - + -
228B MET* 1.3 73.9 - - - +
230B GLY* 1.3 64.4 + - - +
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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