Contacts of the helix formed by residues 74 - 90 (chain B) in PDB entry 2IHB
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 ASP 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B MET* 3.8 3.6 - - + +
73B GLN* 1.3 80.2 - - + +
75B LYS* 1.3 54.9 + - - +
76B THR* 2.9 18.7 + - - -
77B GLN* 2.9 39.4 + - + +
78B MET* 2.8 35.7 + - - +
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Residues in contact with LYS 75 (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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73B GLN 3.3 8.0 + - - +
74B ASP* 1.3 73.0 + - - +
76B THR* 1.3 58.6 + - - +
78B MET* 3.7 16.6 - - + +
79B GLN* 3.1 45.0 + - - +
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Residues in contact with THR 76 (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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74B ASP* 2.9 9.8 + - - -
75B LYS* 1.3 76.6 - - - +
77B GLN* 1.3 64.6 + - - +
78B MET 3.2 0.4 - - - -
79B GLN* 3.6 9.8 + - + +
80B GLU* 3.4 30.7 + - + +
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Residues in contact with GLN 77 (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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72B MET* 3.7 15.5 - - + +
74B ASP* 2.9 26.8 + - + +
76B THR* 1.3 76.0 - - - +
78B MET* 1.3 60.6 + - - +
80B GLU* 4.3 4.0 - - - +
81B LYS* 3.4 22.9 + - - +
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Residues in contact with MET 78 (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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69B PHE* 3.2 30.7 - - + +
72B MET* 4.2 28.7 - - + +
73B GLN* 4.0 20.6 - - - +
74B ASP 2.8 11.4 + - - +
75B LYS* 3.7 18.4 - - + +
77B GLN* 1.3 77.0 - - - +
79B GLN* 1.3 59.8 + - - +
81B LYS 3.4 0.2 + - - -
82B ALA* 2.9 27.3 + - - +
114B PRO* 4.6 6.7 - - + -
115B HIS* 3.8 37.2 - - - -
116B PRO* 4.0 11.4 - - + -
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Residues in contact with GLN 79 (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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75B LYS* 3.1 33.0 + - - +
76B THR* 3.6 10.4 + - + +
77B GLN 3.6 0.2 - - - -
78B MET* 1.3 77.0 - - + +
80B GLU* 1.3 61.4 + - + +
82B ALA* 3.7 5.9 - - - +
83B LYS* 3.2 26.6 + - - +
114B PRO* 4.1 30.1 - - + +
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Residues in contact with GLU 80 (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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76B THR* 3.4 21.9 + - + +
77B GLN* 4.4 4.3 - - - +
78B MET 3.3 0.6 - - - -
79B GLN* 1.3 77.6 - - + +
81B LYS* 1.3 58.0 + - - +
83B LYS* 3.4 8.6 + - - +
84B GLU* 2.9 32.8 + - - +
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Residues in contact with LYS 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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65B ALA* 4.2 30.8 - - - +
68B ASP* 4.6 13.9 + - - +
69B PHE* 3.7 20.6 - - + +
72B MET* 4.2 16.6 - - + -
77B GLN 3.4 17.7 + - - +
78B MET 3.4 3.9 + - - +
80B GLU* 1.3 75.3 - - - +
82B ALA* 1.3 60.7 + - - +
84B GLU* 3.4 25.9 + - + +
85B ILE* 2.8 41.2 + - + +
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Residues in contact with ALA 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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69B PHE* 3.5 23.3 - - + -
78B MET 2.9 18.0 + - - +
79B GLN* 3.7 7.4 - - - +
81B LYS* 1.3 73.7 - - - +
83B LYS* 1.3 65.1 + - - +
85B ILE* 3.4 2.9 + - - +
86B TYR* 3.1 22.2 + - - +
114B PRO* 5.1 6.5 - - + -
118B MET* 3.6 22.1 - - + +
119B PHE* 4.0 10.5 - - - -
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Residues in contact with LYS 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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79B GLN 3.2 13.0 + - - +
80B GLU* 3.4 10.5 - - - +
82B ALA* 1.3 77.4 - - - +
84B GLU* 1.3 57.2 + - - +
86B TYR* 3.0 8.8 + - - +
87B MET* 3.0 38.4 + - + +
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Residues in contact with GLU 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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80B GLU* 2.9 21.4 + - - +
81B LYS* 3.2 30.1 + - + +
83B LYS* 1.3 74.2 - - - +
85B ILE* 1.3 64.0 + - + +
87B MET* 4.0 5.8 - - - +
88B THR* 2.8 37.0 + - - +
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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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62B PHE* 3.8 31.9 - - + -
65B ALA* 3.9 39.3 - - + +
66B CYS* 4.5 1.3 - - - +
69B PHE* 4.0 13.9 - - + -
81B LYS* 2.8 33.1 + - - +
82B ALA 3.8 4.3 - - - +
84B GLU* 1.3 71.4 - - - +
86B TYR* 1.3 64.8 + - - +
89B PHE* 3.1 32.2 + - + +
90B LEU* 3.8 2.4 + - + +
119B PHE* 3.7 35.0 - - + -
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Residues in contact with TYR 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 ALA 3.1 13.1 + - - +
83B LYS* 3.0 12.6 + - - +
85B ILE* 1.3 78.9 - - - +
87B MET* 1.3 71.6 + - + +
90B LEU* 3.1 40.8 + - + -
91B SER* 2.9 49.3 + - - -
119B PHE* 5.6 2.7 - + + -
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Residues in contact with MET 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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83B LYS* 3.0 24.9 + - + +
84B GLU* 3.5 5.6 + - - +
86B TYR* 1.3 90.5 - - + +
88B THR* 1.3 59.0 + - - +
91B SER* 4.3 9.3 - - - -
94B ALA* 3.1 23.2 - - - +
95B SER 4.9 0.3 + - - -
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Residues in contact with THR 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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84B GLU* 2.8 29.6 + - - +
87B MET* 1.3 79.2 - - - +
89B PHE* 1.3 91.1 + - + +
94B ALA* 3.5 3.6 - - - +
95B SER 4.4 1.0 + - - +
96B SER* 3.3 34.7 + - - +
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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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58B GLU* 3.7 7.2 - - - -
61B LEU* 3.9 18.8 - - + -
62B PHE* 3.6 65.7 - + + -
65B ALA* 4.2 13.2 - - + -
85B ILE* 3.1 25.2 + - + +
88B THR* 1.3 102.0 - - + +
90B LEU* 1.3 58.9 + - + +
91B SER 3.8 0.7 - - - -
94B ALA* 4.4 0.4 - - - -
96B SER* 3.4 24.9 - - - -
97B GLN* 3.2 8.2 - - - +
98B VAL* 2.8 36.7 + - + +
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Residues in contact with LEU 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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62B PHE* 4.3 11.4 - - + -
85B ILE* 4.3 8.5 - - + +
86B TYR* 3.1 41.5 + - + +
89B PHE* 1.3 84.1 - - + +
91B SER* 1.3 68.5 + - - +
92B SER 3.7 0.9 + - - -
97B GLN* 4.1 9.7 + - - -
98B VAL* 4.0 16.8 - - + -
100B VAL* 4.9 10.8 - - + -
119B PHE* 4.0 22.4 - - + -
122B LEU* 3.9 33.7 - - + -
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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