Contacts of the helix formed by residues 61 - 78 (chain F) in PDB entry 3CHB
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 GLN 61 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GAL 3.0 24.6 + - - -
4C SIA 4.1 2.9 + - - -
56F GLN 4.0 0.7 - - - +
57F HIS* 3.2 24.2 - - + -
58F ILE* 2.9 38.9 + - + +
60F SER* 1.3 78.1 - - - +
62F LYS* 1.3 59.0 - - - +
63F LYS 3.4 0.2 - - - -
64F ALA* 3.1 3.1 + - - +
65F ILE* 2.8 35.3 + - + +
88F TRP* 4.4 0.2 - - - -
31G LEU* 2.9 30.8 + - - +
32G ALA* 3.9 2.6 - - - +
33G GLY* 3.3 19.2 - - - +
36G GLU* 3.5 18.8 - - - +
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Residues in contact with LYS 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LYS* 6.6 0.4 - - - -
53F PRO* 4.1 21.7 - - + +
54F GLY* 3.4 33.3 + - - +
57F HIS* 3.9 28.4 + - + -
58F ILE 4.2 4.7 - - - -
59F ASP* 3.1 27.1 + - - +
61F GLN* 1.3 80.5 - - - +
63F LYS* 1.3 61.3 + - - +
65F ILE* 3.3 7.6 + - + +
66F GLU* 3.3 25.5 + - - +
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Residues in contact with LYS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ASP 4.5 1.8 + - - -
60F SER* 4.2 13.4 + - - +
61F GLN 3.4 0.4 - - - -
62F LYS* 1.3 77.1 - - - +
64F ALA* 1.3 58.0 + - - +
66F GLU* 3.3 9.0 + - - +
67F ARG* 2.9 27.4 + - - +
53G PRO* 5.0 10.5 - - - +
62G LYS* 6.1 3.0 - - - +
66G GLU* 3.4 44.7 + - + +
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Residues in contact with ALA 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F SER 4.1 2.1 + - - +
61F GLN 3.1 9.4 + - - +
63F LYS* 1.3 77.3 - - - +
65F ILE* 1.3 57.6 + - - +
67F ARG* 3.3 12.1 + - - +
68F MET* 2.9 29.6 + - - +
29G GLU* 4.9 0.9 - - - +
30G SER 4.2 3.6 - - - +
31G LEU* 3.7 29.4 - - + +
36G GLU* 4.1 23.8 - - + -
69G LYS* 6.3 0.7 - - - +
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Residues in contact with ILE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F VAL* 3.9 18.1 - - + +
51F GLU* 4.2 9.0 - - + +
53F PRO* 4.2 15.9 - - + -
57F HIS* 3.7 43.7 - - + +
61F GLN* 2.8 27.9 + - + +
62F LYS* 3.3 9.4 + - + +
64F ALA* 1.3 71.8 - - - +
66F GLU* 1.3 76.8 + - - +
68F MET* 3.2 4.5 + - - +
69F LYS* 3.2 30.5 + - - +
31G LEU* 4.1 26.2 - - + -
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Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LYS* 4.3 40.4 - - + +
67E ARG* 2.9 44.9 + - - +
53F PRO* 4.4 8.3 - - - +
62F LYS 3.3 14.2 + - - +
63F LYS* 3.3 9.8 + - - +
65F ILE* 1.3 81.5 - - - +
67F ARG* 1.3 62.3 + - - +
69F LYS* 2.8 27.6 + - - -
70F ASP* 3.1 17.0 + - - +
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Residues in contact with ARG 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F LYS 2.9 16.4 + - - +
64F ALA* 3.6 11.5 - - - +
65F ILE 3.3 0.2 - - - -
66F GLU* 1.3 76.3 - - - +
68F MET* 1.3 58.7 + - - +
70F ASP* 3.0 12.5 + - - +
71F THR* 2.8 30.8 + - - -
27G TYR* 4.7 0.2 - - - -
29G GLU* 3.4 30.2 + - - +
66G GLU* 2.9 55.2 + - - +
69G LYS* 3.5 27.5 + - - +
70G ASP* 2.7 36.7 + - - +
73G ARG* 3.8 11.7 - - - +
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Residues in contact with MET 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F VAL* 3.9 20.9 - - + -
64F ALA 2.9 17.4 + - - +
65F ILE 3.2 5.6 + - - +
67F ARG* 1.3 77.8 - - - +
69F LYS* 1.3 58.3 + - - +
71F THR* 3.1 3.1 + - - -
72F LEU* 2.9 38.3 + - + +
96F ILE* 4.1 23.8 - - + -
97F ALA 4.3 2.2 - - - +
98F ALA* 4.1 6.1 - - - -
99F ILE* 3.7 24.5 - - + -
29G GLU* 3.5 40.9 + - + +
31G LEU* 3.8 25.8 - - + +
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Residues in contact with LYS 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ARG* 3.6 27.8 + - - +
27F TYR* 3.7 12.1 + - - +
29F GLU* 6.5 0.2 - - + -
36F GLU* 4.2 17.8 + - - +
37F MET* 4.6 4.2 - - - +
38F ALA* 3.9 30.7 - - + +
50F VAL* 4.0 17.9 - - + +
51F GLU 5.3 0.4 + - - -
53F PRO* 4.8 4.8 - - - +
65F ILE* 3.2 26.8 + - - +
66F GLU* 2.8 37.6 + - - +
67F ARG 3.2 0.2 - - - -
68F MET* 1.3 75.7 - - - +
70F ASP* 1.3 63.5 + - - +
72F LEU* 3.4 6.3 + - - +
73F ARG* 3.1 24.4 + - - +
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Residues in contact with ASP 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ARG* 2.7 32.5 + - - +
70E ASP* 5.7 0.3 - - - +
66F GLU* 3.1 16.3 + - - +
67F ARG* 3.0 13.7 + - - +
69F LYS* 1.3 77.2 - - - +
71F THR* 1.3 62.5 + - - +
73F ARG* 3.4 22.6 + - - +
74F ILE* 3.1 25.9 + - - +
70G ASP* 5.7 0.5 - - - +
73G ARG* 3.7 21.4 + - - +
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Residues in contact with THR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ARG 2.8 7.5 + - - -
68F MET* 3.1 10.1 + - - -
70F ASP* 1.3 77.8 - - - +
72F LEU* 1.3 58.3 + - - +
74F ILE* 3.4 7.0 - - + +
75F ALA* 2.8 31.2 + - - +
99F ILE* 4.3 21.8 - - + -
101F MET* 4.1 25.6 - - + -
27G TYR* 4.9 0.9 - - + -
29G GLU* 2.8 31.0 + - - +
73G ARG* 3.0 27.3 + - - +
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 3.8 7.9 - - + +
27F TYR* 4.0 13.6 - - + -
38F ALA* 5.0 5.8 - - + -
40F ILE* 4.1 33.4 - - + -
50F VAL* 3.6 32.3 - - + +
68F MET* 2.9 25.9 + - + +
69F LYS* 4.0 2.7 - - - +
71F THR* 1.3 75.4 - - + +
73F ARG* 1.3 57.4 + - - +
75F ALA* 3.7 3.2 - - - +
76F TYR* 2.9 31.5 + - - +
96F ILE* 3.8 17.5 - - + -
99F ILE* 3.7 29.8 - - + -
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Residues in contact with ARG 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ARG* 3.8 21.3 + - - +
70E ASP* 3.7 30.5 + - - +
71E THR* 3.1 40.6 + - - +
74E ILE* 4.2 12.6 - - - +
101E MET* 4.9 3.4 - - + -
27F TYR* 3.7 26.1 - - + +
29F GLU* 4.4 2.6 + - - -
69F LYS 3.1 16.2 + - - +
70F ASP* 3.8 27.8 + - - +
71F THR 3.3 0.2 - - - -
72F LEU* 1.3 79.0 - - - +
74F ILE* 1.3 58.2 + - - +
76F TYR* 3.3 2.7 + - - +
77F LEU* 3.0 41.3 + - + +
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Residues in contact with ILE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ILE* 5.4 8.3 - - + -
78E THR* 6.5 0.9 - - + -
70F ASP 3.1 15.0 + - - +
71F THR* 3.4 14.1 - - - +
73F ARG* 1.3 76.2 - - - +
75F ALA* 1.3 67.2 + - - +
77F LEU* 4.5 14.4 - - + -
78F THR* 2.8 47.9 + - + +
73G ARG* 4.2 12.1 - - - +
74G ILE* 5.2 10.5 - - + -
77G LEU* 3.6 25.6 - - + -
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Residues in contact with ALA 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 4.1 15.1 + - + -
71F THR* 2.8 21.8 + - + +
72F LEU* 3.7 4.7 - - - +
74F ILE* 1.3 78.0 - - - +
76F TYR* 1.3 62.8 + - - +
78F THR* 3.7 5.4 - - - -
79F GLU* 3.1 4.0 + - - -
80F ALA* 3.0 35.0 + - + +
82F VAL* 5.2 3.1 - - + -
99F ILE* 5.5 2.2 - - + -
101F MET* 4.1 23.8 - - + -
77G LEU* 5.0 2.5 - - + -
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Residues in contact with TYR 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ALA* 5.4 2.7 - - + -
81E LYS 4.8 0.7 + - - -
101E MET* 3.6 28.5 - - + +
102E ALA* 3.1 32.2 + - - -
103E ASN 3.5 7.1 + - - -
24F ILE* 3.5 41.6 - - + +
25F PHE 3.7 20.6 - - - -
26F SER* 4.0 2.7 - - - -
27F TYR* 3.7 24.2 - - + -
72F LEU 2.9 18.3 + - - +
73F ARG 3.5 3.4 - - - +
75F ALA* 1.3 76.6 - - - +
77F LEU* 1.3 83.5 + - + +
79F GLU* 3.2 17.1 + - - +
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ILE* 3.7 40.8 - - + -
75E ALA* 4.9 1.1 - - - +
78E THR* 4.0 18.8 - - + +
80E ALA* 3.7 29.8 - - + -
101E MET* 4.3 9.2 - - + -
73F ARG* 3.0 32.6 + - + +
74F ILE* 4.0 13.5 - - + +
76F TYR* 1.3 94.4 - - + +
78F THR* 1.3 59.8 + - + +
79F GLU* 3.7 5.4 + - - +
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Residues in contact with THR 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ILE* 2.8 42.6 + - + +
75F ALA* 3.4 6.2 + - - -
77F LEU* 1.3 76.6 - - + +
79F GLU* 1.3 68.9 + - - +
80F ALA* 3.2 15.1 + - - +
77G LEU* 4.0 18.6 - - + +
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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
------------------------------------------------------------
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