Contacts of the helix formed by residues 101 - 112 (chain A) in PDB entry 1R2B
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 ASN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ASN* 6.0 0.4 - - - +
81A GLU* 2.9 34.4 + - - +
82A GLY 6.0 0.4 - - - +
85A ILE* 4.0 14.5 - - + +
96A ASN 5.0 0.2 + - - -
97A LEU* 3.7 8.8 - - - +
98A ARG* 3.0 49.3 + - - +
100A GLY* 1.3 78.4 - - - +
102A ILE* 1.3 61.7 + - - +
103A MET 3.2 3.1 - - - -
104A ALA* 3.2 14.0 + - + +
105A VAL* 2.8 36.5 + - + +
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Residues in contact with ILE 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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97A LEU* 4.2 18.2 - - + -
98A ARG 3.2 7.8 + - - +
99A GLU* 3.3 24.9 - - - +
101A ASN* 1.3 84.5 + - - +
103A MET* 1.3 74.6 + - + +
105A VAL* 3.2 6.6 + - - +
106A MET* 2.8 28.4 + - + +
121A CYS* 4.3 18.6 - - + +
124A PHE* 3.6 30.7 - - + -
125A ILE* 3.5 30.7 - - + -
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Residues in contact with MET 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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99A GLU 5.7 0.7 - - - +
100A GLY 5.4 1.5 - - - +
101A ASN* 3.2 1.0 - - - +
102A ILE* 1.3 85.1 - - + +
104A ALA* 1.3 61.7 + - - +
106A MET* 3.3 22.8 + - + +
107A ALA* 2.8 32.2 + - - +
125A ILE* 3.5 33.7 - - + -
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Residues in contact with ALA 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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79A ASN* 3.9 27.8 - - - +
82A GLY* 4.8 2.5 - - - -
100A GLY 5.7 0.9 - - - +
101A ASN* 3.2 15.9 + - + +
103A MET* 1.3 79.2 - - - +
105A VAL* 1.3 53.5 + - - +
107A ALA* 3.5 6.6 + - - +
108A THR* 2.5 38.8 + - - -
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Residues in contact with VAL 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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82A GLY* 4.1 10.5 - - - -
85A ILE* 3.7 31.9 - - + -
86A LEU* 3.7 11.9 - - + +
95A LEU* 4.3 22.9 - - + -
97A LEU* 3.8 27.1 - - + -
101A ASN* 2.8 21.9 + - - +
102A ILE 3.4 5.2 - - - +
104A ALA* 1.3 75.8 - - - +
106A MET* 1.3 61.7 + - - +
108A THR* 3.2 6.9 + - - -
109A ALA* 2.9 28.6 + - - +
117A VAL* 5.4 1.1 - - + -
121A CYS* 4.6 4.7 - - - -
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 2.8 21.8 + - + +
103A MET* 3.7 24.2 - - + +
105A VAL* 1.3 73.4 - - - +
107A ALA* 1.3 70.8 + - + +
109A ALA* 3.5 3.1 + - - -
110A MET* 3.2 32.8 + - + +
118A VAL* 3.6 30.4 - - + +
121A CYS* 4.3 27.8 - - + -
122A ARG 5.7 0.7 - - - +
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Residues in contact with ALA 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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78A ILE* 5.1 3.8 - - + +
103A MET 2.8 17.7 + - - +
104A ALA* 3.8 7.6 - - - +
106A MET* 1.3 86.4 - - + +
108A THR* 1.3 61.3 + - - +
110A MET* 3.3 9.1 + - - +
111A TYR* 3.1 20.4 + - - +
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Residues in contact with THR 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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78A ILE* 4.2 26.7 - - + +
79A ASN* 3.7 14.0 + - - -
82A GLY 4.1 5.5 - - - -
83A PHE* 4.0 17.9 - - + +
86A LEU* 3.4 21.8 - - + -
104A ALA 2.5 24.6 + - - -
105A VAL 3.6 1.1 - - - -
107A ALA* 1.3 74.9 - - - +
109A ALA* 1.3 60.7 + - - +
111A TYR* 3.2 8.8 + - + +
112A LEU* 2.9 37.4 + - + +
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Residues in contact with ALA 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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86A LEU* 3.4 24.4 - - + +
105A VAL 2.9 16.5 + - - +
106A MET* 3.9 6.1 - - - +
107A ALA 3.3 0.2 - - - -
108A THR* 1.3 73.4 - - - +
110A MET* 1.3 59.9 + - - +
112A LEU* 3.0 4.7 + - - +
113A GLN 2.9 10.0 + - - -
114A MET* 2.9 45.9 + - + +
117A VAL* 4.0 12.8 - - + -
118A VAL* 3.9 5.8 - - + -
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Residues in contact with MET 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 MET* 3.2 22.4 + - + +
107A ALA* 3.5 11.2 - - - +
108A THR 3.3 0.2 - - - -
109A ALA* 1.3 78.7 - - - +
111A TYR* 1.3 61.0 + - - +
113A GLN* 3.1 15.6 + - - +
114A MET 4.8 1.6 - - - +
115A GLU* 4.1 16.4 - - - +
118A VAL* 3.5 32.0 - - + +
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Residues in contact with TYR 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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56A LEU* 3.5 31.6 - - + +
74A LEU* 3.5 22.5 - - + +
75A ASP* 2.9 38.3 + - + +
78A ILE* 4.0 27.1 - - + -
107A ALA 3.1 12.8 + - - +
108A THR* 3.2 12.6 - - + +
110A MET* 1.3 78.5 - - - +
112A LEU* 1.3 73.4 + - + +
113A GLN* 3.1 10.3 + - - +
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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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54A SER* 2.5 29.1 + - - +
56A LEU* 3.4 9.9 + - + -
57A PHE* 3.9 27.4 - - + -
74A LEU* 5.1 1.6 - - + -
83A PHE* 4.0 22.0 - - + -
86A LEU* 3.8 25.4 - - + -
90A MET* 4.5 4.9 - - + -
108A THR* 2.9 27.4 + - + +
109A ALA 3.0 5.1 + - - +
111A TYR* 1.3 94.0 - - + +
113A GLN* 1.3 70.9 + - - +
114A MET* 3.6 19.7 + - - -
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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