Contacts of the helix formed by residues 71 - 85 (chain B) in PDB entry 3BQT
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 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLN* 5.7 1.7 + - - +
69B GLY 3.8 2.6 + - - -
70B LEU* 1.3 76.0 - - - +
72B GLU* 1.3 62.6 + - + +
73B ALA* 2.8 34.7 + - - +
74B LYS* 2.8 33.3 + - - +
75B LYS* 3.4 9.2 + - - +
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Residues in contact with GLU 72 (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 LEU 3.4 3.1 + - - -
71B ASP* 1.3 69.5 - - + +
73B ALA* 1.3 72.6 + - + +
75B LYS* 3.9 11.1 - - - +
76B ILE* 3.2 21.0 + - - +
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Residues in contact with ALA 73 (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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71B ASP* 2.8 12.2 + - - +
72B GLU* 1.3 83.1 - - + +
74B LYS* 1.3 60.5 + - - +
76B ILE* 2.5 34.6 + - + +
77B GLU* 3.0 5.0 + - - +
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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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59B GLU* 3.3 42.7 + - + +
63B GLN* 3.9 11.9 - - - +
70B LEU* 5.4 4.3 - - + -
71B ASP* 2.8 26.5 + - - +
73B ALA* 1.3 78.3 - - - +
75B LYS* 1.3 62.0 + - - +
77B GLU* 3.2 24.0 + - - +
78B LEU* 2.9 34.7 + - + +
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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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15A VAL* 5.1 4.6 - - - +
56B TYR* 3.5 39.4 + - + +
67B TRP* 3.5 15.7 + - + -
68B HIS* 3.4 27.3 + - - +
70B LEU* 3.2 42.0 - - + -
71B ASP 3.4 7.4 + - - +
72B GLU* 3.5 11.2 + - - +
73B ALA 3.3 0.8 - - - -
74B LYS* 1.3 77.2 - - - +
76B ILE* 1.3 53.7 + - - +
78B LEU* 3.5 2.2 - - - +
79B LYS* 2.7 37.6 + - - +
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Residues in contact with ILE 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 GLU 3.2 10.1 + - - +
73B ALA* 2.5 37.1 + - + +
75B LYS* 1.3 80.2 - - - +
77B GLU* 1.3 62.4 + - + +
79B LYS* 3.7 11.9 - - + +
80B LYS* 3.1 25.6 + - - +
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Residues in contact with GLU 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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37B LYS* 3.3 33.8 - - - +
73B ALA 3.0 10.7 + - - +
74B LYS* 3.5 32.6 - - - +
75B LYS 3.2 0.2 - - - -
76B ILE* 1.3 79.9 - - + +
78B LEU* 1.3 64.1 + - - +
80B LYS* 3.3 13.6 + - + +
81B PHE* 3.0 20.8 + - - +
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Residues in contact with LEU 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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36B SER* 4.5 9.0 - - - +
37B LYS* 4.3 23.8 - - + +
52B MSE 4.1 0.4 - - + -
55B LEU* 3.3 41.6 - - + +
56B TYR* 4.0 24.7 - - + -
59B GLU* 4.0 16.8 - - + +
70B LEU* 4.7 4.3 - - + -
74B LYS* 2.9 48.6 + - + +
75B LYS* 3.5 4.3 - - - +
77B GLU* 1.3 77.7 - - + +
79B LYS* 1.3 69.3 + - - +
81B PHE* 3.1 5.1 + - - +
82B HIS* 3.0 14.6 + - - +
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Residues in contact with LYS 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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47A ASP* 6.1 1.7 - - - +
49A SER* 4.3 23.4 - - - -
52B MSE 3.7 20.9 - - - +
56B TYR* 4.1 14.8 - - - +
75B LYS 2.7 21.6 + - - +
76B ILE* 3.7 13.5 - - + +
78B LEU* 1.3 71.5 - - - +
80B LYS* 1.3 56.0 + - - +
82B HIS* 2.7 27.7 + - - +
83B GLN* 3.0 36.8 + - + +
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Residues in contact with LYS 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 ILE* 3.1 13.5 + - - +
77B GLU* 3.4 13.9 - - + +
79B LYS* 1.3 79.4 - - - +
81B PHE* 1.3 59.2 + - - +
83B GLN* 3.3 17.8 + - - +
84B SER* 3.0 31.0 + - - +
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Residues in contact with PHE 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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37B LYS* 3.5 68.9 - - + +
40B PHE* 4.1 19.3 - + - -
41B LEU* 4.4 16.8 - - + -
55B LEU* 3.9 17.0 - - + -
77B GLU 3.0 9.0 + - - +
78B LEU 3.4 6.3 - - - +
79B LYS 3.1 0.2 - - - -
80B LYS* 1.3 75.6 - - + +
82B HIS* 1.3 68.7 + - - +
84B SER* 3.3 10.4 + - - +
85B LEU* 3.1 31.9 + - + +
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Residues in contact with HIS 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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49A SER* 6.3 2.2 - - - -
40B PHE* 3.5 29.4 - + - -
44B TRP* 6.1 1.9 - + - -
50B VAL 3.9 13.3 + - - -
51B CYS* 5.0 0.2 - - - -
52B MSE 3.0 43.6 + - + +
55B LEU* 4.5 3.6 - - + -
78B LEU 3.0 9.2 + - - +
79B LYS 2.7 13.6 + - - +
81B PHE* 1.3 77.8 - - - +
83B GLN* 1.3 69.3 + - - +
85B LEU* 2.9 29.2 + - + +
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Residues in contact with GLN 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 LYS* 3.0 43.5 + - + +
80B LYS* 3.5 17.3 - - - +
82B HIS* 1.3 79.9 - - - +
84B SER* 1.3 65.6 + - - +
85B LEU 2.9 8.9 - - - +
86B GLU 3.9 6.4 - - - +
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Residues in contact with SER 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 LYS* 3.0 19.7 + - - +
81B PHE* 3.6 14.9 - - - -
82B HIS 3.2 0.4 - - - -
83B GLN* 1.3 73.4 - - - +
85B LEU* 1.3 69.5 + - - +
86B GLU* 3.1 9.4 + - - +
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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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40B PHE* 4.2 16.8 - - + -
41B LEU* 4.9 11.2 - - + -
44B TRP* 3.2 63.0 - - + +
81B PHE* 3.1 27.3 + - + +
82B HIS* 2.9 23.7 + - + +
83B GLN* 2.9 10.2 - - - +
84B SER* 1.3 75.6 - - - +
86B GLU* 1.3 73.3 + - - +
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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