Contacts of the helix formed by residues 65 - 79 (chain C) in PDB entry 3HUU
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 ASN 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C LYS 5.2 4.3 - - - -
29C SER* 5.6 0.2 - - - -
63C SER* 3.5 0.9 - - - -
64C GLU* 1.3 84.5 - - + +
66C SER* 1.3 63.6 + - - +
67C GLY* 3.2 6.8 + - - +
68C ASP* 2.7 54.0 + - - +
69C LEU* 3.0 21.0 + - - +
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LYS 5.1 5.0 + - - -
65C ASN* 1.3 72.2 - - - +
67C GLY* 1.3 66.4 + - - +
69C LEU* 3.3 12.9 + - - +
70C TYR* 3.1 22.9 + - - +
91C LEU* 5.7 4.3 - - - +
95C PRO* 6.3 4.7 - - - -
96C ILE* 5.2 1.6 - - - +
154C TYR* 5.0 7.6 + - - -
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASN* 3.2 6.8 + - - -
66C SER* 1.3 79.6 - - - +
68C ASP* 1.3 63.5 + - - +
70C TYR* 3.3 10.9 + - - +
71C HIS* 3.4 24.3 + - - -
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C SER* 3.3 18.1 + - - +
64C GLU 5.2 1.4 + - - -
65C ASN* 2.7 39.1 + - - +
67C GLY* 1.3 72.2 - - - -
69C LEU* 1.3 52.5 + - - +
71C HIS* 3.3 7.0 + - - +
72C GLU* 2.7 35.3 + - - +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 4.1 12.8 - - + -
27C GLN 3.7 18.8 - - - +
28C LYS* 4.0 13.9 - - - +
61C THR* 3.6 40.4 - - + +
63C SER* 3.4 14.7 + - - +
65C ASN 3.0 17.9 + - - +
66C SER* 3.5 11.9 - - - +
67C GLY 3.2 0.2 - - - -
68C ASP* 1.3 77.0 - - - +
70C TYR* 1.3 53.1 + - - +
72C GLU* 3.4 5.5 - - - +
73C VAL* 2.8 41.2 + - + +
89C TYR* 4.3 7.2 - - + +
96C ILE* 4.1 20.0 - - + -
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Residues in contact with TYR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER 3.1 12.4 + - - +
67C GLY* 3.3 11.0 + - - +
69C LEU* 1.3 76.0 - - - +
71C HIS* 1.3 86.8 + + + +
74C LYS* 2.8 40.4 + - + +
95C PRO* 3.8 34.8 - - + -
96C ILE* 3.5 12.0 - - + +
98C HIS* 6.0 0.4 - - + -
99C LEU* 3.4 50.5 - - + +
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY* 3.4 22.4 + - - -
68C ASP* 3.3 8.8 + - - +
69C LEU 3.3 0.4 - - - -
70C TYR* 1.3 98.2 - + - +
72C GLU* 1.3 63.5 + - - +
74C LYS* 3.8 17.1 + - + +
75C THR* 2.8 29.3 + - - -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C THR* 3.4 19.1 - - + -
62C VAL* 2.8 35.2 + - - +
63C SER* 2.5 40.3 + - - +
68C ASP 2.7 16.8 + - - +
69C LEU* 3.0 5.2 + - + +
71C HIS* 1.3 77.7 - - - +
73C VAL* 1.3 58.5 + - - +
75C THR* 3.2 7.3 + - - -
76C MET* 3.0 45.9 + - + +
52D ASN* 4.3 4.0 + - - +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 4.0 24.7 - - + -
61C THR* 4.2 18.8 - - + -
69C LEU* 2.8 22.9 + - + +
70C TYR 3.8 3.4 - - - +
72C GLU* 1.3 74.1 - - - +
74C LYS* 1.3 64.6 + - - +
76C MET* 3.2 9.8 + - - +
77C ILE* 3.0 24.2 + - + +
85C PHE* 4.3 7.0 - - + -
96C ILE* 4.2 13.5 - - + -
99C LEU* 3.5 19.7 - - + -
100C LEU* 4.0 23.1 - - + -
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Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C TYR* 2.8 36.8 + - + +
71C HIS* 4.0 17.1 + - - +
73C VAL* 1.3 77.5 - - - +
75C THR* 1.3 63.9 + - - +
77C ILE* 3.2 6.4 + - + +
78C GLN* 3.0 55.9 + - + +
99C LEU* 4.0 21.8 - - + -
103C PHE* 4.4 15.7 - - + -
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Residues in contact with THR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C HIS 2.8 23.1 + - - -
72C GLU* 3.2 6.5 + - - -
74C LYS* 1.3 77.3 - - - +
76C MET* 1.3 57.4 + - + +
78C GLN* 4.3 7.7 + - - +
79C SER* 2.7 47.9 + - - +
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Residues in contact with MET 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLY* 5.4 2.7 - - - -
59C ARG* 3.7 29.2 - - + +
60C MET 4.2 3.1 - - - +
61C THR* 4.1 21.8 - - + -
72C GLU* 3.0 36.6 + - + +
73C VAL* 3.5 10.8 - - - +
74C LYS 3.2 0.2 - - - -
75C THR* 1.3 78.3 - - - +
77C ILE* 1.3 57.0 + - - +
79C SER* 4.6 0.7 - - - -
80C LYS* 3.0 21.8 + - - -
81C SER* 3.2 28.2 + - - +
82C VAL* 4.4 6.8 + - + -
85C PHE* 4.0 28.0 - - + -
52D ASN* 3.9 19.5 - - + +
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C VAL* 3.0 19.8 + - + +
74C LYS* 3.6 7.4 - - + +
76C MET* 1.3 77.4 - - - +
78C GLN* 1.3 61.5 + - + +
80C LYS* 3.2 19.0 + - - +
82C VAL 6.1 0.7 - - - -
85C PHE* 3.8 19.7 - - + -
99C LEU* 4.2 16.4 - - + +
100C LEU* 3.9 25.8 - - + -
103C PHE* 4.0 38.6 - - + +
105C VAL* 4.1 15.9 - - + -
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Residues in contact with GLN 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LYS* 3.0 51.8 + - + +
75C THR* 4.3 5.9 - - - +
77C ILE* 1.3 76.3 - - + +
79C SER* 1.3 60.0 + - - +
80C LYS* 3.2 11.1 + - - +
103C PHE* 4.2 25.1 - - + -
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Residues in contact with SER 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C THR* 2.7 35.7 + - - +
76C MET* 4.0 3.4 - - - -
78C GLN* 1.3 75.4 - - - +
80C LYS* 1.3 72.4 + - - +
81C SER* 3.2 11.7 + - - -
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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