Contacts of the helix formed by residues 80 - 91 (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 PRO 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B VAL* 3.3 33.7 - - + +
39B SER* 4.3 11.2 - - - +
41B GLU* 3.2 43.1 - - + +
43B PHE* 3.9 5.9 - - + -
78B ILE 3.4 4.6 - - - +
79B ASN* 1.3 83.8 - - + +
81B GLU* 1.3 60.3 + - - +
83B PHE* 3.6 3.7 - - + +
84B ASN* 2.7 33.2 + - - +
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Residues in contact with GLU 81 (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* 3.2 13.8 + - - +
80B PRO* 1.3 77.7 - - - +
82B GLY* 1.3 65.0 + - - +
84B ASN* 3.2 6.2 + - + +
85B ILE* 3.0 36.9 + - + +
98B ARG* 5.7 2.3 - - - -
101B ASN* 3.4 39.5 + - - +
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Residues in contact with GLY 82 (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* 3.1 22.8 + - - +
81B GLU* 1.3 81.0 + - - +
83B PHE* 1.3 60.7 + - - +
85B ILE* 3.6 5.5 + - - +
86B LEU* 3.4 25.1 + - - +
101B ASN* 6.1 0.7 - - - -
104B ALA* 5.3 1.3 - - - -
105B VAL* 4.5 19.6 - - - +
108B THR* 4.0 13.6 - - - -
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Residues in contact with PHE 83 (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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36B ILE* 3.8 24.7 - - + -
38B VAL* 4.1 9.4 - - + -
43B PHE* 3.7 40.8 - + + -
50B LEU* 5.5 1.1 - - + -
57B PHE* 4.2 12.8 - + - -
74B LEU* 4.0 20.9 - - + -
78B ILE* 4.6 3.1 - - + -
79B ASN 3.2 10.9 + - - +
80B PRO* 3.6 10.1 - - + +
81B GLU 3.2 0.4 - - - -
82B GLY* 1.3 75.6 - - - +
84B ASN* 1.3 61.1 + - - +
86B LEU* 3.1 5.9 + - - +
87B LEU* 2.8 44.4 + - + +
90B MET* 5.5 1.8 - - + -
108B THR* 4.0 14.3 - - + +
112B LEU* 3.8 33.2 - - + -
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Residues in contact with ASN 84 (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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26B ARG* 5.6 2.2 - - - +
43B PHE* 3.4 28.1 - - + -
80B PRO 2.7 22.2 + - - +
81B GLU* 3.7 6.5 - - + +
83B PHE* 1.3 75.9 - - - +
85B ILE* 1.3 60.7 + - - +
87B LEU* 3.3 12.1 + - - +
88B ASP* 2.9 43.5 + - - +
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Residues in contact with ILE 85 (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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81B GLU* 3.0 32.1 + - + +
82B GLY* 3.7 5.2 - - - +
84B ASN* 1.3 80.0 - - - +
86B LEU* 1.3 58.0 - - - +
88B ASP* 3.6 7.2 - - - +
89B PHE* 3.1 25.5 + - - +
94B ARG 4.6 1.6 - - - +
95B LEU* 3.5 21.3 - - + +
96B ASN* 3.3 35.3 + - + +
101B ASN* 3.3 32.8 - - - +
105B VAL* 4.3 18.2 - - + -
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Residues in contact with LEU 86 (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 3.4 7.4 + - - +
83B PHE* 3.1 7.0 + - - +
85B ILE* 1.3 74.9 - - - +
87B LEU* 1.3 61.6 + - - +
89B PHE* 3.4 8.7 - - + +
90B MET* 3.0 32.5 + - - +
95B LEU* 4.2 6.3 - - + -
105B VAL* 4.1 14.6 - - + +
108B THR* 3.7 17.0 - - + -
109B ALA* 3.5 42.8 - - + +
112B LEU* 3.6 28.9 - - + -
114B MET* 4.4 14.6 - - + -
117B VAL* 4.1 18.2 - - + -
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Residues in contact with LEU 87 (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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26B ARG* 3.5 22.7 - - - +
36B ILE* 6.5 0.2 - - + -
43B PHE* 3.9 39.3 - - + -
44B ARG 4.9 4.9 - - - +
45B ALA* 4.4 7.9 - - + -
50B LEU* 4.1 20.6 - - + -
83B PHE* 2.8 29.7 + - + +
84B ASN* 3.3 10.1 + - - +
86B LEU* 1.3 73.8 - - - +
88B ASP* 1.3 66.6 + - - +
90B MET* 3.2 24.8 - - - +
91B TYR* 3.3 28.8 + - + -
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Residues in contact with ASP 88 (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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23B ASN* 5.5 0.3 + - - -
26B ARG* 3.3 23.8 + - - +
84B ASN* 2.9 32.5 + - - +
85B ILE* 3.6 8.2 - - - +
87B LEU* 1.3 74.3 - - - +
89B PHE* 1.3 67.0 + - - +
91B TYR* 3.0 4.3 + - - -
92B THR* 3.0 36.8 + - + +
94B ARG 4.9 2.5 - - - +
96B ASN* 5.3 7.3 - - - +
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Residues in contact with PHE 89 (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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11A PHE* 3.4 42.0 - + - -
14A HIS* 3.4 36.8 + + - -
85B ILE 3.1 12.9 + - - +
86B LEU* 3.4 15.7 - - + +
88B ASP* 1.3 79.4 - - - +
90B MET* 1.3 69.7 + - + +
92B THR* 3.9 0.2 - - - -
93B SER* 2.7 35.2 + - - -
94B ARG 3.0 23.0 + - - +
95B LEU* 4.0 14.1 - - + -
114B MET* 3.6 27.4 - - + -
117B VAL* 3.7 19.7 - - + -
1424D SER* 4.1 9.2 - - - -
1425D ILE* 4.4 2.7 - - + -
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Residues in contact with MET 90 (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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14A HIS* 2.8 26.0 + - - -
18A VAL* 4.3 0.7 - - - +
19B LEU* 3.8 9.4 - - - +
49B VAL* 4.6 5.1 - - + +
50B LEU* 3.6 29.2 - - + -
53B CYS* 3.8 29.4 - - + -
54B SER* 4.1 17.3 - - - -
57B PHE* 4.4 15.3 - - + -
83B PHE* 5.5 2.0 - - + -
86B LEU 3.0 24.2 + - - +
87B LEU* 3.2 16.6 - - - +
88B ASP 3.1 0.2 - - - -
89B PHE* 1.3 78.5 - - - +
91B TYR* 1.3 64.5 + - + +
112B LEU* 4.5 7.6 - - + -
114B MET* 3.8 32.5 - - + -
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Residues in contact with TYR 91 (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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19B LEU* 3.3 30.1 - - + +
20B LEU* 4.9 1.2 - - - -
22B LEU* 3.6 21.8 - - + -
23B ASN* 3.3 41.5 - - - +
26B ARG* 3.6 34.8 - - + +
45B ALA* 4.4 3.4 - - + -
46B HIS* 2.7 45.9 + - - +
49B VAL* 3.5 35.0 - - + +
50B LEU* 5.0 1.6 - - + -
87B LEU* 3.3 27.5 + - + -
88B ASP 3.0 5.2 + - - +
90B MET* 1.3 80.9 - - + +
92B THR* 1.3 59.8 + - - +
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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