Contacts of the helix formed by residues 101 - 112 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU* 3.4 31.5 + - - +
82B GLY* 6.1 0.9 - - - -
85B ILE* 3.3 29.0 - - + +
96B ASN 4.7 0.4 + - - -
97B LEU* 3.7 3.1 - - - -
98B ARG* 2.6 57.0 + - - +
100B GLY* 1.3 77.6 - - - +
102B ILE* 1.3 66.6 + - - +
103B MET 3.5 2.2 - - - -
104B ALA* 3.2 13.3 + - + +
105B VAL* 2.9 26.1 + - + +
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.8 27.6 - - + -
98B ARG 3.9 8.1 - - - +
99B GLU* 4.0 19.5 - - + +
100B GLY 5.3 0.2 - - - -
101B ASN* 1.3 80.3 + - - +
103B MET* 1.3 87.7 + - + +
105B VAL* 2.7 28.4 + - + +
106B MET* 3.0 44.4 + - + -
121B CYS* 3.8 13.9 - - + -
124B PHE* 4.7 15.3 - - + -
125B ILE* 4.4 5.2 - - + -
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Residues in contact with MET 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLY 5.4 1.7 + - - +
101B ASN 3.5 0.2 - - - -
102B ILE* 1.3 104.8 - - + +
104B ALA* 1.3 62.6 + - - +
106B MET* 3.3 12.1 + - - +
107B ALA* 3.0 24.8 + - - +
125B ILE* 3.1 40.4 - - + -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASN* 4.0 24.4 - - - +
82B GLY* 5.2 1.6 - - - -
100B GLY 5.3 1.9 + - - +
101B ASN* 3.2 19.6 + - + +
102B ILE 3.1 0.4 - - - -
103B MET* 1.3 78.8 - - - +
105B VAL* 1.3 52.4 + - + +
107B ALA* 3.3 8.3 + - - +
108B THR* 2.6 40.8 + - - -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B GLY* 4.5 9.4 - - - -
85B ILE* 4.3 23.8 - - + -
86B LEU* 4.1 23.7 - - + +
95B LEU* 4.3 10.5 - - + -
97B LEU* 4.0 27.4 - - + -
101B ASN* 2.9 27.7 + - + +
102B ILE* 2.7 18.6 + - + +
104B ALA* 1.3 68.7 - - - +
106B MET* 1.3 53.5 + - - +
108B THR* 3.1 8.6 + - - -
109B ALA* 2.8 33.1 + - - +
117B VAL* 5.1 1.8 - - + -
121B CYS* 4.8 6.5 - - - -
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Residues in contact with MET 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 3.0 36.1 + - + +
103B MET* 3.7 17.3 - - - +
105B VAL* 1.3 74.7 - - - +
107B ALA* 1.3 64.3 + - - +
109B ALA* 3.2 2.2 + - - -
110B MET* 2.9 29.4 + - + +
118B VAL* 3.2 46.4 - - + +
121B CYS* 3.5 11.4 - - + -
122B ARG* 3.2 30.7 - - + +
125B ILE* 3.8 15.5 - - + -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 5.8 0.6 - - - +
103B MET 3.0 13.5 + - - +
104B ALA* 3.3 12.8 - - - +
106B MET* 1.3 79.3 - - - +
108B THR* 1.3 61.6 + - - +
110B MET* 3.4 10.2 + - - +
111B TYR* 3.3 17.2 + - - +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 3.9 32.2 - - + +
79B ASN* 3.8 13.1 + - - +
82B GLY* 4.0 4.1 - - - -
83B PHE* 4.0 17.5 - - + +
86B LEU* 3.7 17.5 - - + -
104B ALA 2.6 27.3 + - - -
105B VAL* 3.1 8.0 + - - -
107B ALA* 1.3 71.0 - - - +
109B ALA* 1.3 65.6 + - - +
111B TYR* 3.0 10.9 + - + +
112B LEU* 3.0 25.9 + - + +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 3.5 23.9 - - + +
105B VAL 2.8 20.1 + - - +
106B MET* 4.4 1.1 - - - -
108B THR* 1.3 72.6 - - - +
110B MET* 1.3 52.3 + - - +
112B LEU* 3.0 4.0 + - - +
113B GLN 2.8 30.1 + - - -
114B MET* 2.9 28.8 + - + +
117B VAL* 4.3 7.0 - - + -
118B VAL* 3.7 19.5 - - + -
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Residues in contact with MET 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B MET 2.9 19.4 + - - +
107B ALA* 3.4 13.2 - - - +
108B THR 3.2 0.2 - - - -
109B ALA* 1.3 74.9 - - - +
111B TYR* 1.3 62.9 + - - +
113B GLN* 3.1 15.9 + - - +
114B MET 4.9 1.1 - - - +
115B GLU* 4.5 17.2 - - + +
118B VAL* 3.8 29.6 - - + +
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Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 3.6 41.8 - - + +
73B ASN 4.7 0.9 + - - -
74B LEU* 3.5 47.6 - - + +
75B ASP* 3.7 13.2 + - + -
78B ILE* 3.6 31.2 - - + -
107B ALA 3.3 7.5 + - - +
108B THR 3.0 10.0 + - - +
110B MET* 1.3 82.0 - - - +
112B LEU* 1.3 70.0 + - + +
113B GLN* 3.3 5.0 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B SER* 2.3 32.4 + - - +
56B LEU* 3.4 23.9 + - + -
57B PHE* 4.0 21.5 - - + -
74B LEU* 4.7 0.9 - - + -
83B PHE* 3.8 29.8 - - + -
86B LEU* 3.6 31.0 - - + -
90B MET* 4.5 6.3 - - + -
108B THR* 3.0 10.0 + - + +
109B ALA 3.0 6.7 + - - +
111B TYR* 1.3 88.2 - - + +
113B GLN* 1.3 71.6 + - - +
114B MET* 3.8 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