Contacts of the helix formed by residues 74 - 86 (chain B) in PDB entry 2HDH
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 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B LYS* 6.0 3.4 - - - +
70B PHE* 3.3 8.7 - - + +
71B ALA 3.8 10.3 - - - +
72B GLU 4.2 0.9 - - - -
73B ASN* 1.3 85.8 - - - +
75B LYS* 1.3 66.9 + - + +
77B GLY* 3.3 3.0 + - - +
78B ASP* 3.1 31.8 + - - +
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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 ASN* 3.2 13.0 - - - +
74B PRO* 1.3 84.7 - - + +
76B ALA* 1.3 66.1 + - - +
78B ASP* 3.1 6.7 + - - +
79B GLU* 3.1 50.2 + - + +
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Residues in contact with ALA 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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70B PHE* 3.3 23.9 - - + -
73B ASN* 3.3 25.6 + - + +
75B LYS* 1.3 78.9 - - - +
77B GLY* 1.3 66.7 + - - +
79B GLU* 3.0 18.0 + - - +
80B PHE* 2.8 24.8 + - - +
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Residues in contact with GLY 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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66B ALA* 3.9 10.9 - - - +
70B PHE* 3.0 36.9 - - - -
73B ASN 3.4 1.8 + - - -
74B PRO* 3.3 6.2 + - - -
75B LYS 3.2 1.2 - - - -
76B ALA* 1.3 75.8 - - - +
78B ASP* 1.3 62.3 + - - +
80B PHE* 3.3 4.8 + - - +
81B VAL* 3.1 25.9 + - - +
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Residues in contact with ASP 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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63B ARG* 3.1 27.5 + - - +
67B LYS* 5.5 8.5 + - - -
74B PRO* 3.1 20.0 + - - +
75B LYS* 3.1 8.8 + - - +
77B GLY* 1.3 72.8 - - - +
79B GLU* 1.3 61.9 + - + +
81B VAL* 3.8 5.7 - - - +
82B ALA* 2.9 31.4 + - - +
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Residues in contact with GLU 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 42.2 + - + +
76B ALA* 3.0 19.9 + - - +
78B ASP* 1.3 75.8 - - + +
80B PHE* 1.3 54.8 + - - +
82B ALA* 3.3 5.4 + - - +
83B LYS* 2.8 38.0 + - - +
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Residues in contact with PHE 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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36B ALA* 5.1 18.2 - - + -
62B LEU* 4.8 21.3 - - + -
65B VAL* 5.7 7.9 - - + -
66B ALA* 4.6 6.7 - - + -
70B PHE* 4.2 29.4 - + + -
76B ALA 2.8 12.3 + - - +
77B GLY 3.4 11.0 - - - +
79B GLU* 1.3 76.8 - - - +
81B VAL* 1.3 69.5 + - + +
83B LYS* 3.6 10.2 - - + +
84B THR* 3.0 45.8 + - - -
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Residues in contact with VAL 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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59B GLU* 4.3 10.5 - - + -
62B LEU* 3.8 42.5 - - + +
63B ARG* 3.9 43.3 - - + +
66B ALA* 3.8 11.0 - - + -
77B GLY 3.1 13.5 + - - +
78B ASP 3.8 5.8 - - - +
79B GLU 3.3 0.2 - - - -
80B PHE* 1.3 80.2 - - + +
82B ALA* 1.3 59.3 + - - +
84B THR* 4.0 3.7 - - - -
85B LEU* 2.9 37.8 + - + +
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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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63B ARG* 5.5 2.7 - - - +
78B ASP 2.9 18.8 + - - +
79B GLU* 3.7 6.1 - - - +
81B VAL* 1.3 78.5 - - - +
83B LYS* 1.3 57.6 - - - +
85B LEU* 3.5 6.0 + - - +
86B SER* 2.8 31.9 + - - -
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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 GLU 2.8 22.6 + - - +
80B PHE* 3.6 11.4 - - + +
82B ALA* 1.3 72.8 - - - +
84B THR* 1.3 66.3 + - - +
86B SER* 2.6 23.9 + - - +
87B THR* 3.3 20.8 + - + +
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Residues in contact with THR 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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32B GLN* 4.4 2.2 - - + +
35B ALA* 3.6 13.7 + - + +
36B ALA* 3.6 35.5 + - + +
62B LEU* 3.8 29.4 - - + -
80B PHE* 3.0 35.3 + - - -
81B VAL* 4.0 3.1 - - - -
83B LYS* 1.3 80.1 - - - +
85B LEU* 1.3 60.6 + - - +
87B THR* 3.0 22.7 + - - -
88B ILE* 3.7 4.5 - - + +
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Residues in contact with LEU 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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55B LYS* 3.6 55.4 + - + +
58B ILE* 4.3 17.0 - - + -
59B GLU* 3.6 42.4 - - + +
62B LEU* 4.4 3.4 - - + -
63B ARG* 5.9 0.7 - - - +
81B VAL* 2.9 22.5 + - + +
82B ALA* 3.9 5.6 - - - +
84B THR* 1.3 79.3 - - - +
86B SER* 1.3 60.6 + - - +
87B THR 3.4 0.3 + - - -
88B ILE* 3.5 13.7 + - + +
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Residues in contact with SER 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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55B LYS* 5.6 1.1 - - - +
82B ALA 2.8 15.8 + - - -
83B LYS* 2.6 23.2 + - - +
85B LEU* 1.3 77.9 - - - +
87B THR* 1.3 61.3 + - - +
88B ILE 3.2 7.6 + - - +
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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