Contacts of the strand formed by residues 130 - 138 (chain B) in PDB entry 1SBB
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 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 3.7 34.1 - - + +
128B LYS 3.4 5.6 + - - -
129B TYR* 1.3 74.0 - - - +
131B SER* 1.3 62.6 + - - +
132B ILE* 3.9 8.7 - - + -
149B GLN* 3.0 6.6 - - - +
150B THR* 2.5 46.2 + - + +
151B ASN* 4.6 0.2 - - - +
153B LYS* 4.6 6.1 - - - +
224B ASP* 4.9 1.8 + - - -
225B SER* 3.1 46.5 + - - +
226B LYS* 4.1 25.1 - - - +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR 3.7 3.1 + - - -
130B ARG* 1.3 80.6 - - - +
132B ILE* 1.3 61.1 + - - +
133B THR* 4.1 4.2 + - - -
147B ASP* 3.1 32.4 + - - +
148B VAL 3.6 3.4 - - - -
149B GLN* 4.3 14.3 + - - +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 3.9 11.2 - - + -
131B SER* 1.3 77.4 - - - +
133B THR* 1.3 79.2 + - - +
147B ASP* 2.9 8.0 - - - +
148B VAL* 2.6 53.9 + - + +
150B THR* 3.4 28.9 - - + -
160B LEU* 4.7 10.3 - - + -
225B SER* 3.9 8.5 - - - +
228B VAL* 3.3 49.8 - - + +
230B ILE* 4.2 17.0 - - + -
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Residues in contact with THR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B SER 4.5 2.8 + - - -
132B ILE* 1.3 81.4 - - - +
134B VAL* 1.3 74.2 + - - +
135B ARG* 4.9 11.1 - - + +
145B SER* 5.0 6.1 - - - -
146B PHE 3.8 5.6 - - - +
147B ASP* 2.9 23.6 + - - +
228B VAL 5.0 0.6 + - - -
229B LYS* 4.7 1.7 - - - -
230B ILE* 3.4 24.8 + - - +
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Residues in contact with VAL 134 (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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133B THR* 1.3 77.7 - - - +
135B ARG* 1.3 67.8 + - - +
136B VAL* 4.3 2.7 - - + +
145B SER* 3.0 29.3 - - - -
146B PHE* 2.6 47.5 + - + +
148B VAL* 3.4 33.2 - - + -
164B THR* 3.8 24.0 - - + +
230B ILE* 3.4 13.0 - - + -
232B VAL* 4.0 16.4 - - + -
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Residues in contact with ARG 135 (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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133B THR* 4.9 11.4 - - + +
134B VAL* 1.3 75.8 - - - +
136B VAL* 1.3 58.4 + - - +
137B PHE* 3.1 39.9 - - + -
142B ASN* 3.7 17.7 - - - +
144B LEU 3.9 0.2 - - - -
145B SER* 3.9 10.7 + - - +
229B LYS* 5.6 6.3 - - - +
230B ILE 2.9 13.7 + - - +
231B GLU* 3.3 28.4 + - + -
232B VAL 2.8 22.7 + - - -
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Residues in contact with VAL 136 (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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134B VAL* 4.4 2.2 - - + -
135B ARG* 1.3 71.5 - - - +
137B PHE* 1.3 61.8 + - - +
138B GLU* 4.2 17.4 + - + +
142B ASN* 3.7 3.8 - - - +
143B LEU 3.7 6.1 + - - -
144B LEU* 2.9 72.7 + - + +
145B SER* 4.0 1.3 - - - +
146B PHE* 4.0 16.8 - - + -
168B LEU* 4.3 7.4 - - + -
172B LYS* 4.8 0.9 - - + +
232B VAL* 3.3 17.0 - - + +
234B LEU* 4.0 25.8 - - + -
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Residues in contact with PHE 137 (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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135B ARG* 3.1 53.4 - - + -
136B VAL* 1.3 72.3 - - - +
138B GLU* 1.3 59.8 + - - +
139B ASP 3.5 1.6 + - - -
140B GLY 3.2 30.6 + - - +
141B LYS 3.6 3.4 - - - -
142B ASN* 3.1 37.2 - - + -
231B GLU* 4.0 5.8 - - + -
232B VAL 2.7 15.9 + - - +
233B TYR* 3.5 46.1 - + + -
234B LEU 2.8 32.4 + - - +
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Residues in contact with GLU 138 (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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136B VAL* 4.2 16.2 - - + +
137B PHE* 1.3 72.5 - - - +
139B ASP* 1.3 72.5 + - - +
140B GLY 3.5 0.2 - - - -
141B LYS* 3.1 27.7 + - - +
143B LEU* 3.4 34.9 + - + +
144B LEU 4.2 1.6 + - - -
172B LYS* 2.9 33.4 + - - +
182B TYR* 3.5 20.7 + - + -
234B LEU* 3.3 19.3 - - + +
236B THR* 4.4 14.8 - - + +
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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