Contacts of the strand formed by residues 131 - 136 (chain A) in PDB entry 3BYH
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 ALA 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A PRO* 3.3 13.5 - - + +
103A VAL 3.1 20.5 + - - -
124A PHE* 4.0 4.7 - - - -
129A THR* 3.1 9.9 - - - +
130A PRO* 1.4 83.6 - - + +
132A MET* 1.3 69.0 + - - +
353A GLN* 4.9 3.8 - - - +
356A TRP* 3.8 24.7 - - + -
357A ILE 3.2 15.0 - - - +
358A SER* 4.2 4.5 - - - -
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Residues in contact with MET 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.3 19.1 - - + +
105A LEU* 3.5 35.7 - - + -
119A MET 3.9 5.8 - - - +
120A THR* 4.1 20.9 - - - -
123A MET* 3.8 21.8 - - + -
124A PHE* 3.6 26.2 - - + -
129A THR* 4.8 2.0 - - + -
131A ALA* 1.3 80.4 - - - +
133A TYR* 1.3 62.0 + - - +
134A VAL* 4.0 23.8 - - + -
356A TRP* 3.4 5.1 - - - -
357A ILE* 2.9 43.6 + - + +
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Residues in contact with TYR 133 (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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103A VAL 3.1 4.7 + - - +
104A LEU* 3.4 9.6 - - + -
105A LEU* 2.8 32.2 + - - +
132A MET* 1.3 77.3 - - - +
134A VAL* 1.3 85.2 + - - +
135A ALA* 3.9 13.5 - - + -
346A LEU* 5.1 2.0 - - + -
352A PHE* 3.5 23.8 - + + -
355A MET* 3.1 44.1 - - + +
356A TRP* 3.4 21.7 - - + -
357A ILE* 5.1 0.4 - - + -
373A LYS 3.7 18.3 + - - -
374A CYS* 3.7 31.5 - - - -
375A PHE* 4.5 12.8 + - - -
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Residues in contact with VAL 134 (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 LEU* 3.4 11.7 - - + +
106A THR 4.4 0.2 - - - -
107A GLU* 3.4 40.7 - - + +
116A ARG* 4.4 9.6 + - + +
119A MET* 3.9 24.9 - - + -
132A MET* 4.0 21.3 - - + -
133A TYR* 1.3 85.0 + - - +
135A ALA* 1.3 57.0 + - - +
136A ILE 4.3 0.2 + - - -
370A VAL* 3.8 23.8 - - + -
374A CYS* 3.7 23.1 - - - +
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Residues in contact with ALA 135 (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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104A LEU* 4.4 16.1 - - + +
105A LEU 3.4 5.5 + - - -
106A THR* 3.2 6.6 - - - -
107A GLU* 2.7 33.5 + - - -
133A TYR* 3.9 19.2 - - + -
134A VAL* 1.3 74.2 - - - +
136A ILE* 1.3 58.2 + - - +
139A VAL* 6.1 2.2 - - + -
140A LEU* 3.4 26.2 - - + -
346A LEU* 5.3 3.1 - - + -
375A PHE* 6.6 0.4 - - - -
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Residues in contact with ILE 136 (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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107A GLU* 3.3 27.3 + - + +
108A ALA 4.4 6.7 - - - +
109A PRO* 3.8 33.2 - - + -
110A LEU 5.3 2.9 - - - +
135A ALA* 1.3 71.6 - - - +
137A GLN* 1.3 64.1 + - - +
138A ALA* 3.9 10.3 - - + +
139A VAL* 3.5 23.5 + - + +
140A LEU* 2.9 20.0 - - - +
163A VAL* 5.8 6.5 - - + -
170A ALA* 5.5 3.8 - - + -
175A ILE* 5.6 7.9 - - + -
374A CYS 6.1 0.9 - - - +
375A PHE* 4.2 31.7 - - + -
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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