Contacts of the strand formed by residues 125 - 129 (chain A) in PDB entry 1BO6
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 MET 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.3 0.4 - - - -
42A VAL* 3.2 23.1 - - + +
44A ALA* 6.1 0.4 - - + +
114A LEU* 4.0 5.4 - - + -
118A PHE* 3.9 32.3 - - + +
119A TRP* 3.4 42.8 - - + -
122A ASN 5.6 0.4 - - - -
123A CYS 3.2 14.8 - - - +
124A LYS* 1.3 81.6 - - - +
126A ILE* 1.3 64.7 + - - +
127A TYR 4.2 0.2 - - - -
179A TRP* 3.8 24.9 - - + -
187A ARG 2.7 9.2 + - - +
188A VAL* 3.3 16.2 - - + -
189A LEU 2.8 25.0 + - - -
210A PHE* 3.5 5.2 - - - -
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Residues in contact with ILE 126 (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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41A LEU* 3.9 30.3 - - + -
42A VAL 2.7 11.4 + - - +
43A ILE* 3.5 12.0 - - + +
44A ALA* 2.9 25.3 + - - +
54A ILE* 3.8 28.7 - - + -
58A VAL* 4.0 12.3 - - + -
125A MET* 1.3 81.0 - - - +
127A TYR* 1.3 66.6 + - - +
128A LEU* 5.4 0.8 - - + +
189A LEU* 3.4 10.5 - - + +
191A MET* 4.6 5.8 - - + -
207A LEU* 3.8 24.2 - - + -
210A PHE* 3.6 20.9 - - + -
211A LEU* 4.3 3.4 - - + -
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Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.2 27.6 - - + +
45A THR* 4.1 4.0 - - - -
46A TYR* 4.3 6.5 + - - +
125A MET 4.2 0.4 - - - -
126A ILE* 1.3 74.8 - - - +
128A LEU* 1.3 66.3 + - - +
129A CYS* 3.9 14.8 - - + +
175A HIS* 2.9 29.3 + + - -
176A VAL* 3.6 22.0 - - - +
179A TRP* 3.2 57.7 - + + -
188A VAL* 5.0 4.0 - - + +
189A LEU 2.7 14.4 + - - +
190A PHE* 3.3 44.6 - + + -
191A MET* 2.8 29.1 + - - +
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Residues in contact with LEU 128 (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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43A ILE* 6.2 0.2 - - + -
44A ALA 3.1 7.3 + - - -
45A THR* 3.6 31.2 - - + -
46A TYR 4.2 0.7 + - - -
49A SER* 3.3 28.9 - - - +
50A GLY* 3.5 26.0 - - - +
51A THR 4.2 0.9 - - - +
54A ILE* 3.9 24.7 - - + -
126A ILE* 4.0 1.1 + - + +
127A TYR* 1.3 81.7 - - - +
129A CYS* 1.3 61.1 + - - +
191A MET* 3.5 29.8 - - + +
192A PHE 3.7 16.6 - - - +
193A TYR* 3.7 2.9 - - + +
196A MET* 4.0 18.2 - - - -
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Residues in contact with CYS 129 (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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46A TYR* 6.2 1.1 - - + -
49A SER* 4.2 7.4 - - - -
127A TYR* 3.9 14.6 - - + +
128A LEU* 1.3 75.8 - - - +
130A ARG* 1.3 60.1 + - - +
172A TRP* 5.3 0.9 - - - +
176A VAL* 4.3 15.5 - - + -
190A PHE* 3.4 31.9 - - - -
191A MET 3.0 8.4 + - - -
192A PHE* 3.4 28.2 - - - -
193A TYR* 2.8 27.7 + - - +
291A PHE* 3.7 14.4 - - + -
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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