Contacts of the strand formed by residues 296 - 302 (chain A) in PDB entry 2BBV
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 THR 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A LEU* 3.9 28.3 - - + -
115A ILE 3.2 18.4 - - - +
116A ALA* 3.5 27.3 - - + +
117A PRO* 4.1 3.6 - - - +
192A LYS* 3.3 3.5 - - - -
193A CYS* 2.7 36.1 + - - -
195A VAL* 3.4 33.8 + - + +
220A LEU* 6.0 0.4 - - + -
291A TRP* 4.0 3.2 - - + -
294A MET 3.7 0.6 + - - -
295A ASP* 1.3 72.2 - - - +
297A ILE* 1.3 65.2 - - - +
298A VAL* 3.7 4.0 + - + +
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Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE 3.9 0.3 - - - +
114A LEU* 3.4 3.6 - - - -
115A ILE* 2.7 59.1 + - + +
171A MET 4.1 5.6 - - - +
173A VAL* 4.2 14.8 - - + +
190A VAL* 3.4 31.9 - - + -
191A TRP 4.0 1.6 - - - -
192A LYS* 4.2 12.3 - - + -
241A SER* 3.9 13.7 - - - +
242A GLN* 3.5 40.8 - - - +
243A SER* 3.6 20.9 - - - +
295A ASP 4.2 0.4 - - - +
296A THR* 1.3 73.3 - - - +
298A VAL* 1.3 59.8 + - - +
299A ILE* 4.0 3.1 - - + -
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.4 7.6 - - + -
113A ILE 3.5 4.3 - - - +
114A LEU* 4.1 23.1 - - + -
189A THR 3.5 1.4 - - - +
190A VAL* 3.3 7.6 - - - +
191A TRP* 2.8 71.9 + - + +
193A CYS* 3.7 27.8 - - + -
223A VAL* 4.2 16.4 - - + -
296A THR* 4.2 7.9 - - + +
297A ILE* 1.3 74.7 - - - +
299A ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR 3.7 0.5 - - - +
112A PHE* 3.3 5.0 - - - +
113A ILE* 2.6 45.8 + - + +
115A ILE* 3.9 14.8 - - + -
173A VAL* 3.6 43.1 - - + -
175A ILE* 4.5 24.5 - - + -
188A ILE* 3.7 28.0 - - + -
189A THR 3.4 2.0 - - - -
190A VAL* 3.9 12.6 - - + -
239A VAL* 4.6 3.4 - - + -
297A ILE* 4.6 4.7 - - + +
298A VAL* 1.3 80.3 - - - +
300A ARG* 1.3 61.6 + - - +
301A VAL* 4.0 9.2 - - + -
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 3.8 23.6 + - + -
111A THR 3.2 7.6 - - - +
112A PHE* 3.5 39.0 - - + -
131A GLY* 5.8 2.8 - - - -
132A THR 5.7 0.6 + - - -
133A PHE* 3.7 24.2 - - - -
187A SER* 3.7 6.2 + - - +
188A ILE 4.0 0.2 - - - -
189A THR* 3.1 47.0 + - - +
191A TRP* 4.0 11.9 - - + -
226A VAL* 3.6 23.2 - - - +
232A SER* 5.2 1.0 + - - -
299A ILE* 1.3 73.4 - - - +
301A VAL* 1.3 69.9 + - - +
302A SER* 4.7 7.4 - - - -
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.1 53.2 - - + -
109A ARG 4.3 0.2 - - - +
110A ASP* 3.5 2.1 - - - -
111A THR* 2.8 32.9 + - - +
113A ILE* 4.2 12.8 - - + -
175A ILE* 4.3 10.5 - - + -
187A SER 3.5 4.9 - - - +
188A ILE* 4.8 5.6 - - + +
235A PHE* 3.5 36.3 - - + -
299A ILE* 4.5 6.5 - - + -
300A ARG* 1.3 75.6 - - - +
302A SER* 1.3 65.4 + - - +
303A ALA 4.2 0.4 - - - -
309A ASN* 4.9 3.6 - - - +
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ARG 4.0 0.9 - - - -
110A ASP* 2.6 31.7 + - - -
130A ALA* 5.2 1.0 - - - +
186A GLY* 3.1 27.0 - - - -
187A SER* 3.1 22.8 + - - -
300A ARG* 4.7 12.1 - - - -
301A VAL* 1.3 80.3 - - - +
303A ALA* 1.3 59.9 + - - +
304A PRO* 3.4 3.5 - - - +
309A ASN* 4.5 2.0 - - - -
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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