Contacts of the helix formed by residues 115 - 122 (chain A) in PDB entry 2BY4
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A GLU 3.8 2.4 + - - -
114A ASN* 1.3 73.5 - - - +
116A ILE* 1.3 58.7 + - + +
118A ALA* 2.9 24.6 + - - +
119A LEU* 3.5 6.6 + - - +
239A MET* 3.6 26.0 - - + -
712A LYS* 4.6 16.7 - - + +
726A VAL* 4.5 3.9 - - - +
729A THR* 3.2 36.7 + - - +
730A ALA* 4.2 4.5 - - + -
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Residues in contact with ILE 116 (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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114A ASN* 3.0 10.7 - - + +
115A ALA* 1.3 74.9 - - + +
117A GLU* 1.3 57.1 + - - +
118A ALA 2.8 5.2 - - - -
119A LEU* 2.8 35.4 + - + +
120A LYS* 3.5 27.7 + - + +
236A ARG* 3.5 53.2 - - + +
239A MET* 4.3 12.3 - - + -
240A ALA* 3.6 24.9 - - + +
712A LYS* 6.1 1.3 - - - +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLU* 4.3 24.1 - - - +
113A GLU* 3.0 34.9 - - - +
114A ASN* 3.0 23.7 + - + +
116A ILE* 1.3 77.9 - - - +
118A ALA* 1.3 57.5 + - - +
120A LYS* 4.0 25.8 + - + +
121A GLU* 3.6 18.9 - - - +
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Residues in contact with ALA 118 (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 GLU* 6.2 1.1 - - + -
114A ASN 3.3 3.9 + - - +
115A ALA 2.9 16.1 + - - +
116A ILE 2.8 0.2 - - - -
117A GLU* 1.3 79.1 - - - +
119A LEU* 1.3 57.8 + - - +
120A LYS 3.5 0.2 - - - -
121A GLU* 3.0 29.7 - - + +
122A TYR* 4.1 1.0 - - - -
725A ALA* 5.2 2.2 - - + -
726A VAL* 3.6 25.5 - - + +
729A THR* 3.7 23.6 - - + +
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Residues in contact with LEU 119 (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* 4.4 13.0 - - + -
115A ALA 4.1 7.6 - - - +
116A ILE* 2.8 18.4 + - + +
118A ALA* 1.3 73.9 - - - +
120A LYS* 1.3 51.8 + - - +
121A GLU 2.4 17.1 + - - -
122A TYR* 2.5 31.9 + - + +
123A GLU* 4.1 2.4 + - - +
232A ILE* 4.1 11.9 - - + -
235A ILE* 5.2 0.2 - - + -
236A ARG* 3.7 40.2 - - + +
239A MET* 3.7 18.4 - - - -
705A VAL* 4.1 24.9 - - + -
726A VAL* 3.9 24.9 - - + -
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Residues in contact with LYS 120 (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* 4.1 15.3 - - + +
42A PRO 3.3 27.0 + - - -
43A ALA* 3.9 3.8 - - - +
44A GLU* 3.8 31.5 + - - +
116A ILE* 3.5 28.4 + - - +
117A GLU* 4.2 20.2 - - + +
118A ALA 3.5 0.4 - - - -
119A LEU* 1.3 72.4 - - - +
121A GLU* 1.3 60.6 + - - +
122A TYR 3.0 3.7 + - - -
123A GLU* 3.4 46.1 + - - +
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Residues in contact with GLU 121 (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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117A GLU* 3.6 14.9 - - - +
118A ALA* 3.0 31.0 - - + +
119A LEU 2.4 6.9 + - - -
120A LYS* 1.3 78.6 - - - +
122A TYR* 1.3 63.2 + - + -
123A GLU 3.5 2.6 - - - +
158A LYS* 4.7 7.3 - - - -
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Residues in contact with TYR 122 (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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118A ALA 4.1 3.1 - - - -
119A LEU* 2.5 36.2 + - + +
121A GLU* 1.3 78.5 - - + +
123A GLU* 1.3 59.4 - - + +
124A PRO* 3.6 0.9 - - - +
158A LYS* 3.0 28.9 - - - +
179A ILE* 3.9 37.0 - - + +
210A SER* 5.5 0.3 + - - -
211A GLY* 3.5 30.4 - - - -
232A ILE* 4.4 12.1 - - + -
705A VAL* 3.8 18.7 - - + +
724A THR* 4.1 19.2 - - - +
725A ALA* 5.1 4.3 + - - +
726A VAL* 3.2 33.6 + - + +
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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