Contacts of the helix formed by residues 73 - 89 (chain B) in PDB entry 6DXW
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 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B ARG 3.8 4.7 - - - +
72B VAL* 1.3 89.3 - - + +
74B LYS* 1.3 66.7 + - - +
75B TRP* 3.5 31.4 - - + +
76B VAL* 3.0 18.2 + - + +
77B HIS* 3.1 9.9 + - - +
202B TRP* 3.4 36.3 - - + +
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Residues in contact with LYS 74 (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 VAL 3.4 3.1 + - - -
73B PRO* 1.3 72.6 - - - +
75B TRP* 1.3 58.8 + - - +
77B HIS* 3.1 10.8 + - + +
78B VAL* 2.9 40.6 + - + +
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Residues in contact with TRP 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 PRO* 3.5 24.0 - - + +
74B LYS* 1.3 78.8 - - - +
76B VAL* 1.3 76.6 + - + +
78B VAL* 3.8 7.0 - - - +
79B LEU* 2.8 48.4 + - + +
202B TRP* 4.0 6.3 - - + -
203B GLU* 3.9 44.2 + - + -
206B ILE* 3.9 25.4 - - + -
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Residues in contact with VAL 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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72B VAL* 3.8 6.5 - - + -
73B PRO* 3.0 12.8 + - + +
75B TRP* 1.3 115.4 - - + +
77B HIS* 1.3 60.9 + - - +
79B LEU* 4.4 2.2 - - - -
80B ILE* 2.8 40.2 + - + +
115B LEU* 3.6 22.0 - - + -
202B TRP* 3.6 41.7 - - + -
206B ILE* 4.1 4.0 - - + -
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Residues in contact with HIS 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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68B ILE* 3.8 23.0 + - + +
69B GLY* 5.9 1.8 - - - -
72B VAL* 4.3 5.8 - - + +
73B PRO 3.1 9.5 + - - +
74B LYS* 3.1 15.4 + - + +
76B VAL* 1.3 77.7 - - - +
78B VAL* 1.3 62.3 + - + +
81B GLY* 3.1 22.3 + - - -
111B ALA* 5.8 0.7 - - + -
112B ASP* 2.9 32.4 + - - -
115B LEU* 3.5 22.0 - - + -
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS* 2.9 34.9 + - + +
75B TRP* 3.8 6.7 - - - +
77B HIS* 1.3 78.0 - - + +
79B LEU* 1.3 67.7 + - - +
81B GLY* 3.4 1.4 + - - -
82B LYS* 3.3 38.2 + - + +
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Residues in contact with LEU 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 TRP* 2.8 46.8 + - + +
76B VAL 3.8 2.0 - - - +
78B VAL* 1.3 75.3 - - - +
80B ILE* 1.3 58.9 - - + +
82B LYS* 2.9 23.1 + - + +
83B VAL* 3.0 39.2 + - + +
206B ILE* 4.2 26.0 - - + -
210B PHE* 6.4 0.2 - - + -
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Residues in contact with ILE 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 VAL* 2.8 37.7 + - + +
79B LEU* 1.3 76.6 - - + +
81B GLY* 1.3 64.1 + - - +
83B VAL* 4.1 12.8 - - + -
84B VAL* 2.9 41.5 + - + +
87B LEU* 4.2 19.5 - - + -
111B ALA* 4.2 17.5 - - + +
114B LEU* 4.6 12.3 - - + -
115B LEU* 4.0 21.1 - - + -
118B LEU* 6.3 1.3 - - + -
202B TRP* 5.8 0.7 - - + -
206B ILE* 4.3 27.6 - - + -
209B LEU* 6.4 0.4 - - + -
210B PHE* 5.6 0.2 - - + -
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Residues in contact with GLY 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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77B HIS* 3.1 20.6 + - - -
78B VAL 3.7 2.2 - - - -
79B LEU 3.2 0.4 - - - -
80B ILE* 1.3 78.3 - - - +
82B LYS* 1.3 60.8 + - - +
84B VAL* 4.1 10.4 - - - +
111B ALA* 3.9 17.3 - - - +
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Residues in contact with LYS 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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78B VAL* 3.3 24.9 - - + +
79B LEU* 2.9 10.8 + - + +
81B GLY* 1.3 79.3 - - - +
83B VAL* 1.3 67.6 + - + +
84B VAL* 3.6 1.7 + - - +
85B LEU* 5.2 1.0 + - - +
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Residues in contact with VAL 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 LEU* 3.0 39.7 + - + +
80B ILE* 4.1 17.9 - - + -
82B LYS* 1.3 83.8 - - + +
84B VAL* 1.3 66.2 + - - +
85B LEU 3.1 3.1 - - - -
86B GLU* 3.0 12.8 + - + +
87B LEU* 2.9 20.7 + - + +
210B PHE* 4.3 21.8 - - + -
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Residues in contact with VAL 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 ILE* 2.9 26.8 + - + +
81B GLY 4.1 10.8 - - - +
82B LYS 3.6 0.9 - - - +
83B VAL* 1.3 77.6 - - - +
85B LEU* 1.3 73.2 + - + +
87B LEU* 3.2 6.5 + - - +
88B GLU* 2.8 29.9 + - + +
110B LEU* 4.0 22.2 - - + +
111B ALA* 3.9 34.1 - - + +
114B LEU* 4.8 10.8 - - + -
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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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82B LYS 5.2 1.5 + - - +
83B VAL 3.1 0.8 - - - -
84B VAL* 1.3 95.6 - - + +
86B GLU* 1.3 60.2 + - - +
88B GLU* 3.5 29.1 + - - +
89B ARG* 4.0 9.2 + - - +
100B ARG* 5.1 4.0 - - - +
110B LEU* 4.9 9.4 - - + -
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Residues in contact with GLU 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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83B VAL* 3.0 16.7 + - + +
85B LEU* 1.3 78.8 - - - +
87B LEU* 1.3 61.8 + - - +
88B GLU 3.6 0.2 + - - -
89B ARG* 3.0 40.0 + - - +
90B PHE* 3.2 23.2 - - - -
210B PHE* 4.1 15.9 - - + -
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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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80B ILE* 4.2 27.8 - - + -
83B VAL* 2.9 15.7 + - + +
84B VAL* 3.6 5.8 - - - +
86B GLU* 1.3 75.9 - - - +
88B GLU* 1.3 64.5 + - - +
90B PHE* 3.0 16.6 + - - +
91B LEU* 3.7 12.7 + - + +
114B LEU* 3.9 26.0 - - + -
206B ILE* 4.9 1.6 - - + +
209B LEU* 3.8 39.5 - - + +
210B PHE* 3.8 39.4 - - + +
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Residues in contact with GLU 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 VAL* 2.8 17.5 + - + +
85B LEU* 3.6 18.1 - - - +
86B GLU 3.3 0.4 - - - -
87B LEU* 1.3 76.7 - - - +
89B ARG* 1.3 63.8 + - - +
91B LEU* 3.0 30.3 + - + +
96B THR* 4.7 16.7 - - + +
100B ARG* 2.7 45.1 + - - -
110B LEU* 3.9 17.2 - - + +
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Residues in contact with ARG 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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85B LEU 4.3 7.6 - - - +
86B GLU* 3.0 43.4 + - - +
87B LEU 3.1 0.6 + - - -
88B GLU* 1.3 78.9 - - - +
90B PHE* 1.3 83.7 + - + +
91B LEU 3.5 5.7 + - - +
212B ARG* 4.2 21.8 + - - +
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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