Contacts of the helix formed by residues 101 - 112 (chain A) in PDB entry 2BBM
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 SER 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A PHE* 5.5 1.0 - - - -
100A ILE* 1.3 78.3 + - - +
102A ALA* 1.3 67.9 + - - +
103A ALA* 3.3 4.0 - - - -
104A GLU* 3.4 33.6 + - - +
105A LEU* 3.3 21.7 + - - +
125A ILE* 3.9 5.6 - - - +
135A GLN* 4.4 15.9 + - - +
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Residues in contact with ALA 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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101A SER* 1.3 73.8 - - - +
103A ALA* 1.3 64.7 + - - +
105A LEU* 4.3 0.9 - - - +
106A ARG* 3.2 23.9 + - - +
118A ASP* 4.3 21.5 - - - +
121A VAL* 4.4 9.5 - - + +
122A ASP* 5.1 12.3 - - + +
125A ILE* 4.1 15.0 - - + +
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Residues in contact with ALA 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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101A SER* 3.3 3.9 - - - -
102A ALA* 1.3 79.1 - - - +
104A GLU* 1.3 71.6 + - - +
106A ARG* 3.1 12.0 + - - +
107A HIS* 3.1 20.5 + - + +
118A ASP* 5.3 1.1 - - - -
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Residues in contact with GLU 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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92A PHE 5.2 5.2 - - - +
93A ASP* 2.6 16.7 - - - +
94A LYS* 4.2 4.2 + - + +
95A ASP* 2.4 26.7 - - - +
97A ASN* 3.6 2.3 - - - +
99A PHE 3.7 6.2 - - - +
100A ILE* 4.7 3.6 - - + +
101A SER* 3.4 33.5 + - - +
103A ALA* 1.3 80.6 - - - +
105A LEU* 1.3 67.5 + - - +
107A HIS* 2.8 19.2 + - - +
108A VAL* 3.3 8.1 + - - +
183A CA 2.0 31.3 - - - -
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Residues in contact with LEU 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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92A PHE* 3.9 23.1 + - + +
100A ILE* 3.9 13.3 - - + +
101A SER 3.3 14.4 + - - +
102A ALA 4.3 1.3 - - - +
104A GLU* 1.3 78.1 - - - +
106A ARG* 1.3 53.9 + - - +
107A HIS 2.5 1.7 + - - -
108A VAL* 2.4 37.1 + - + +
109A MET* 2.7 47.0 + - + +
121A VAL* 3.6 26.2 - - + -
124A MET* 5.6 0.9 - - + -
4B TRP* 3.4 42.8 - - + -
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Residues in contact with ARG 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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102A ALA 3.2 17.8 + - - +
103A ALA* 3.1 9.6 + - - +
105A LEU* 1.3 79.5 - - - +
107A HIS* 1.3 61.3 + - - +
109A MET* 4.6 6.1 - - - -
110A THR* 2.6 50.6 + - - +
116A LEU 4.4 15.8 + - - +
117A THR* 4.9 3.6 - - - +
118A ASP* 3.1 29.2 - - - +
121A VAL* 5.0 8.7 - - + +
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Residues in contact with HIS 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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94A LYS* 5.9 10.2 + - + +
103A ALA 3.1 9.6 + - - +
104A GLU* 2.8 13.1 + - - +
105A LEU 2.5 5.3 + - - -
106A ARG* 1.3 80.3 - - - +
108A VAL* 1.3 64.5 + - + +
110A THR* 4.0 2.6 - - - -
111A ASN* 3.1 36.4 + - - +
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Residues in contact with VAL 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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39A LEU* 6.5 1.1 - - + -
91A VAL* 4.0 15.0 - - + +
92A PHE* 3.8 48.0 - - + +
94A LYS* 5.1 16.4 - - + +
104A GLU 3.3 6.0 + - - +
105A LEU* 2.4 25.7 + - + +
107A HIS* 1.3 78.2 - - + +
109A MET* 1.3 63.9 + - + +
111A ASN* 3.5 6.0 + - - +
112A LEU* 3.4 31.3 + - + +
7B ASN* 5.7 1.6 - - - +
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Residues in contact with MET 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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92A PHE* 5.7 1.6 - - + -
105A LEU* 2.7 52.6 + - + +
106A ARG* 4.4 4.7 - - - +
108A VAL* 1.3 76.2 - - + +
110A THR* 1.3 64.8 + - - +
112A LEU* 3.3 20.9 + - + +
113A GLY 4.2 1.6 + - - -
114A GLU* 4.4 4.5 + - - +
116A LEU* 3.7 34.9 - - + +
121A VAL* 3.9 14.4 - - + -
124A MET* 4.1 25.6 - - + +
3B ARG 6.0 0.2 - - - +
4B TRP* 5.2 8.7 - - + -
7B ASN* 2.9 38.6 - - + +
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Residues in contact with THR 110 (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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106A ARG* 2.6 43.2 + - - +
107A HIS* 4.0 4.5 - - - -
109A MET* 1.3 79.5 - - - +
111A ASN* 1.3 66.3 + - - +
112A LEU 3.4 0.3 + - - -
113A GLY* 3.5 8.8 + - - -
114A GLU 3.8 18.1 + - - +
115A LYS* 6.1 0.4 - - - -
116A LEU* 4.6 11.2 + - - +
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Residues in contact with ASN 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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38A SER* 4.3 27.2 + - - +
107A HIS* 3.1 32.4 + - - +
108A VAL* 3.8 7.2 - - - +
109A MET 3.2 0.4 - - - -
110A THR* 1.3 77.3 - - - +
112A LEU* 1.3 66.3 + - - +
113A GLY* 3.0 4.6 + - - -
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Residues in contact with LEU 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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18A LEU* 3.9 36.5 - - + +
21A LYS* 3.3 26.3 + - - -
35A VAL* 6.5 1.3 - - + -
39A LEU* 5.5 9.9 - - + -
108A VAL* 3.4 27.6 + - + +
109A MET* 3.3 14.9 + - + +
110A THR 3.2 1.0 - - - -
111A ASN* 1.3 78.6 - - - +
113A GLY* 1.3 58.5 + - - +
114A GLU* 3.7 4.0 - - + +
7B ASN* 3.6 28.7 - - - +
10B ALA* 5.7 4.7 - - + -
11B VAL* 5.4 11.0 - - + -
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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