Contacts of the helix formed by residues 79 - 90 (chain B) in PDB entry 4H7Y
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 ALA 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B ALA 4.4 1.3 - - - +
71B LYS* 3.9 4.0 - - + -
72B ALA* 3.6 37.9 - - + +
75B GLU 3.4 5.0 + - - +
76B PRO 3.3 12.4 + - - +
78B ASP* 1.3 75.6 - - - +
80B ARG* 1.3 65.2 + - - +
81B ASP 3.2 3.1 - - - -
82B TYR* 3.0 24.9 + - - +
83B PHE* 3.4 16.2 + - + -
103B PHE* 3.9 9.2 - - + -
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Residues in contact with ARG 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 PRO 4.5 0.6 + - - +
77B ASP 5.4 7.4 + - - +
78B ASP 3.4 2.7 - - - -
79B ALA* 1.3 78.0 - - - +
81B ASP* 1.3 66.2 + - - +
83B PHE* 3.1 7.3 + - - +
84B GLN* 3.0 43.4 + - - +
100B PHE* 4.3 8.1 - - + -
103B PHE* 3.9 26.4 - - + -
104B GLU* 2.5 43.1 + - - +
107B GLN* 4.7 4.0 - - - +
109B ASN* 3.4 13.5 - - - +
112B LYS* 6.5 0.2 - - - +
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Residues in contact with ASP 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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78B ASP 4.3 8.2 + - - +
79B ALA 3.2 0.8 - - - -
80B ARG* 1.3 79.6 - - - +
82B TYR* 1.3 64.0 + - + +
84B GLN* 3.4 23.9 + - - +
85B MET* 3.0 25.6 + - - +
84C GLN* 3.9 17.3 + - - +
87C ARG* 2.7 33.9 + - - +
112C LYS* 4.0 21.8 + - - -
116C LEU* 5.1 0.2 - - - +
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 3.5 24.9 - + + -
68B ALA* 3.7 22.6 - - + +
71B LYS* 3.7 35.0 - - + -
78B ASP* 3.7 19.5 - - + -
79B ALA* 3.0 13.8 + - - +
81B ASP* 1.3 81.2 - - + +
83B PHE* 1.3 60.6 + - - +
85B MET* 3.4 19.4 + - + +
86B ALA* 3.0 27.7 + - - +
84C GLN* 4.0 26.4 + - - -
85C MET* 4.4 4.0 - - + -
87C ARG* 4.6 11.5 + - - +
88C ALA* 3.2 31.0 + - + +
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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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65B VAL* 5.0 2.2 - - + -
68B ALA* 3.5 41.1 - - + -
69B GLU* 3.9 7.6 - - + -
72B ALA* 3.9 10.3 - - + -
79B ALA* 3.4 21.5 - - + -
80B ARG* 3.1 5.2 + - - +
82B TYR* 1.3 76.4 - - - +
84B GLN* 1.3 58.5 + - - +
86B ALA* 3.8 5.5 - - + +
87B ARG* 3.0 30.5 + - - +
96B VAL* 5.2 1.6 - - - +
99B SER* 3.4 31.6 - - - -
100B PHE* 3.5 46.3 - + + +
103B PHE* 3.5 39.9 - + + -
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Residues in contact with GLN 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 ARG* 3.0 39.9 + - - +
81B ASP* 3.4 26.1 + - - +
82B TYR 3.3 0.2 - - - -
83B PHE* 1.3 76.7 - - - +
85B MET* 1.3 57.8 + - - +
87B ARG* 3.4 11.4 + - - +
88B ALA* 3.0 31.0 + - - +
100B PHE* 3.7 22.4 - - + -
112C LYS* 5.2 3.5 + - - -
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Residues in contact with MET 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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46B ILE* 4.2 21.5 - - + -
64B GLN* 3.9 18.8 - - - +
67B PHE* 4.4 5.4 - - + -
81B ASP 3.0 17.1 + - - +
82B TYR* 3.5 24.5 - - + +
84B GLN* 1.3 73.8 - - - +
86B ALA* 1.3 65.4 + - - +
88B ALA* 3.2 6.0 + - - +
89B ASN* 3.0 33.0 + - - +
80C ARG* 6.4 0.2 - - + -
81C ASP* 3.4 34.1 - - - +
84C GLN* 4.0 25.3 - - - +
85C MET* 4.1 21.3 - - + -
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Residues in contact with ALA 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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64B GLN* 3.5 41.0 + - + +
65B VAL* 4.3 7.0 - - + +
68B ALA* 5.1 0.7 - - + -
82B TYR 3.0 17.4 + - - +
83B PHE* 3.9 7.6 - - + +
84B GLN 3.4 0.2 - - - -
85B MET* 1.3 77.7 - - + +
87B ARG* 1.3 57.6 + - - +
90B CYS* 2.9 35.0 + - - +
96B VAL* 3.6 14.8 - - + +
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Residues in contact with ARG 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 PHE 3.0 18.0 + - - +
84B GLN* 3.9 10.3 + - - +
86B ALA* 1.3 76.7 - - - +
88B ALA* 1.3 63.5 + - - +
91B LYS* 3.2 25.6 + - + +
96B VAL* 3.7 13.8 - - + +
97B HIS* 3.5 40.4 + - + +
100B PHE* 3.9 25.8 - - + -
112B LYS* 5.6 3.6 - - - +
115B GLN* 4.7 7.5 - - - +
116B LEU* 3.3 27.8 - - - +
119B LYS* 5.1 8.9 - - - +
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Residues in contact with ALA 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 GLN 3.0 19.0 + - - +
85B MET* 3.6 6.1 - - - +
87B ARG* 1.3 78.7 - - - +
89B ASN* 1.3 67.5 + - - +
91B LYS* 3.9 22.1 + - - +
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Residues in contact with ASN 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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51B PRO* 3.6 23.5 - - + +
55B GLY* 3.4 25.6 - - - +
60B PHE* 4.1 8.0 - - + -
64B GLN* 2.9 27.5 + - - +
85B MET* 3.0 18.6 + - - +
88B ALA* 1.3 83.8 - - - +
90B CYS* 1.3 64.4 + - - +
91B LYS 3.7 1.3 + - - -
81C ASP* 3.0 31.7 + - - +
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Residues in contact with CYS 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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55B GLY 3.9 11.0 - - - +
57B ASN 5.5 0.2 - - - -
60B PHE* 3.8 20.9 - - - -
61B ALA* 3.6 39.3 - - + -
64B GLN* 4.1 10.1 - - - -
86B ALA* 2.9 17.5 + - - +
87B ARG 3.9 1.3 - - - -
89B ASN* 1.3 88.9 - - - +
91B LYS* 1.3 63.3 + - - +
92B LYS 3.0 5.0 + - - -
93B PHE* 3.3 13.4 + - + -
96B VAL* 3.7 16.6 - - + +
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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