Contacts of the helix formed by residues 100 - 114 (chain A) in PDB entry 1BY7
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A TYR* 4.4 9.0 + - - +
51A GLU* 5.9 2.7 - - - +
99A ALA* 1.3 72.6 - - - +
101A ASP* 1.3 59.3 + - + +
102A LYS 3.0 5.2 + - - -
103A ILE* 3.4 27.0 + - - +
104A HIS* 4.5 10.4 + - - -
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Residues in contact with ASP 101 (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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99A ALA 3.1 1.8 + - - +
100A ALA* 1.3 77.9 - - - +
102A LYS* 1.3 79.5 + - - +
104A HIS* 5.3 1.7 + - - -
105A SER* 4.6 5.2 + - - -
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Residues in contact with LYS 102 (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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99A ALA* 2.7 38.2 + - + +
101A ASP* 1.3 88.1 - - - +
103A ILE* 1.3 63.2 + - - +
104A HIS 3.4 2.5 - - - -
105A SER* 3.2 9.8 + - - +
106A SER* 2.9 34.1 + - - +
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Residues in contact with ILE 103 (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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4A LEU* 4.0 10.5 - - + +
40A ALA* 4.6 0.4 - - + -
43A TYR* 3.5 26.7 - - + +
60A PHE* 3.7 38.1 - - + -
99A ALA* 3.4 13.4 + - + +
100A ALA* 3.4 23.2 + - - +
102A LYS* 1.3 77.6 - - - +
104A HIS* 1.4 77.3 + - + +
106A SER* 3.2 6.0 + - - -
107A PHE* 2.9 52.7 + - + -
149A TYR* 4.5 0.2 - - - +
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Residues in contact with HIS 104 (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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40A ALA 3.4 9.4 + - - -
43A TYR* 3.8 22.3 - + - -
44A MET* 3.3 42.5 - - + +
100A ALA 4.5 9.6 + - - -
101A ASP 5.3 1.0 - - - -
102A LYS 3.4 0.4 - - - +
103A ILE* 1.4 79.2 - - + +
105A SER* 1.4 67.8 + - - +
107A PHE* 3.3 3.8 + - - +
108A ARG* 3.0 18.2 + - - +
148A TYR* 3.5 36.9 - - + +
149A TYR* 2.7 38.6 - + - +
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Residues in contact with SER 105 (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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101A ASP 4.6 3.5 + - - -
102A LYS* 3.2 18.7 + - - +
104A HIS* 1.4 80.5 - - - +
106A SER* 1.3 63.7 + - - +
108A ARG* 3.2 3.7 + - - +
109A SER* 3.0 25.1 + - - -
148A TYR* 3.6 27.1 - - - -
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Residues in contact with SER 106 (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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4A LEU* 3.3 25.6 - - - -
102A LYS* 2.9 29.6 + - - +
103A ILE* 3.2 1.5 + - - -
105A SER* 1.3 73.9 + - - +
107A PHE* 1.4 61.0 + - - +
109A SER* 3.2 7.3 + - - +
110A LEU* 2.9 35.0 + - - +
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Residues in contact with PHE 107 (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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4A LEU* 3.3 25.2 - - + +
8A ASN* 6.5 0.4 - - + -
33A TRP* 5.0 8.3 - + - -
36A SER* 3.8 16.6 - - - -
37A SER* 3.6 30.7 - - - +
40A ALA* 3.2 24.5 - - + -
60A PHE* 3.7 17.7 - + - -
103A ILE* 2.9 38.5 + - + -
104A HIS 3.3 4.2 + - - +
106A SER* 1.4 77.2 - - - +
108A ARG* 1.3 62.7 + - - +
110A LEU* 3.8 6.1 - - + +
111A SER* 3.1 25.5 + - - -
148A TYR 4.6 0.7 - - - -
149A TYR* 3.4 34.5 - + + -
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Residues in contact with ARG 108 (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 HIS 3.0 12.4 + - - +
105A SER* 3.2 6.7 + - - +
107A PHE* 1.3 75.9 - - - +
109A SER* 1.3 63.2 + - - +
111A SER* 3.4 5.9 + - - -
112A SER* 3.2 23.6 + - - +
147A LYS* 2.9 46.2 + - - +
148A TYR* 3.4 29.8 + - + +
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Residues in contact with SER 109 (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 SER* 3.0 14.2 + - - -
106A SER* 3.2 9.5 + - - -
108A ARG* 1.3 77.4 - - - +
110A LEU* 1.3 62.2 + - - +
112A SER* 3.0 20.2 + - - -
113A ALA* 3.0 12.6 + - - +
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Residues in contact with LEU 110 (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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3A ASP* 5.0 2.5 - - - +
4A LEU* 3.3 44.0 - - + +
5A CYS* 3.8 29.4 - - - +
33A TRP* 5.9 1.1 - - + +
106A SER* 2.9 16.3 + - - +
107A PHE* 3.8 9.2 - - + +
109A SER* 1.3 70.9 - - - +
111A SER* 1.3 57.7 + - - +
113A ALA* 3.1 4.4 + - + +
114A ILE* 2.8 53.2 + - + +
403A THR* 3.8 16.8 - - + -
405A CYS* 4.9 1.6 - - - -
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Residues in contact with SER 111 (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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33A TRP* 5.4 8.9 - - - +
107A PHE 3.1 16.3 + - - -
108A ARG* 3.7 6.7 - - - -
109A SER 3.2 0.2 - - - -
110A LEU* 1.3 76.0 - - - +
112A SER* 1.4 57.9 + - - +
114A ILE* 4.6 4.3 - - - -
115A ASN* 2.7 59.0 + - - +
148A TYR 6.1 0.2 - - - -
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Residues in contact with SER 112 (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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108A ARG* 3.2 16.5 + - - +
109A SER* 3.0 12.0 + - - -
111A SER* 1.4 78.8 - - - +
113A ALA* 1.3 61.2 + - - +
115A ASN* 3.9 12.4 + - - -
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Residues in contact with ALA 113 (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 SER 3.0 11.7 + - - +
110A LEU* 3.1 8.5 + - + +
112A SER* 1.3 75.7 - - - +
114A ILE* 1.3 67.7 + - - +
115A ASN 4.2 2.6 - - - -
400A HIS* 3.8 12.4 + - + -
402A ILE* 6.1 2.5 - - + -
403A THR* 4.1 18.6 - - + -
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Residues in contact with ILE 114 (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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33A TRP* 3.5 49.8 - - + +
110A LEU* 2.8 41.5 + - + +
111A SER* 4.1 2.9 - - - +
113A ALA* 1.3 74.6 - - - +
115A ASN* 1.3 63.8 + - - +
123A LEU* 4.2 14.7 - - + +
400A HIS* 3.7 25.3 + - + +
403A THR* 3.9 16.4 - - + +
405A CYS* 4.0 17.3 - - + -
407A LEU* 4.0 16.2 - - + -
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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