Contacts of the helix formed by residues 63 - 79 (chain C) in PDB entry 4OWW
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 HIS 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C GLN* 1.3 93.4 + - - +
64C ILE* 1.3 64.1 + - - +
65C ALA 3.5 2.5 - - - -
66C ALA* 3.6 16.7 + - + +
67C GLN* 3.2 37.7 + - + +
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Residues in contact with ILE 64 (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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62C GLN* 3.9 18.8 - - + +
63C HIS* 1.3 75.1 - - - +
65C ALA* 1.3 63.4 + - + +
67C GLN* 3.3 15.5 + - - +
68C GLN* 3.0 42.0 + - - +
87C ASP* 4.1 18.2 - - + +
88C SER 3.9 12.8 - - - +
89C ALA* 5.7 1.1 - - - -
93C LEU* 3.8 25.1 - - + -
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Residues in contact with ALA 65 (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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63C HIS 3.5 0.2 - - - -
64C ILE* 1.3 81.4 - - + +
66C ALA* 1.3 60.2 - - - +
68C GLN* 3.3 15.2 + - - +
69C LYS* 3.1 28.1 + - - +
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Residues in contact with ALA 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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63C HIS* 3.6 19.4 + - + +
64C ILE 3.4 0.4 - - - -
65C ALA* 1.3 79.1 - - - +
67C GLN* 1.3 57.4 + - + +
69C LYS* 3.5 5.5 + - - +
70C ALA* 3.0 29.6 + - - +
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Residues in contact with GLN 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLN* 5.5 6.2 + - - +
63C HIS* 3.2 31.4 + - + +
64C ILE* 3.6 21.1 - - - +
65C ALA 3.3 0.2 - - - -
66C ALA* 1.3 73.7 - - + +
68C GLN* 1.3 60.4 + - - +
70C ALA* 3.8 5.4 - - - +
71C ALA* 3.0 29.8 + - - +
93C LEU* 4.0 21.0 - - + +
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Residues in contact with GLN 68 (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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64C ILE* 3.0 40.5 + - - +
65C ALA* 3.5 14.3 - - - +
67C GLN* 1.3 76.7 - - - +
69C LYS* 1.3 57.7 + - - +
71C ALA* 3.4 4.8 + - - +
72C LEU 3.0 23.7 + - - -
85C THR* 3.4 43.9 + - + +
86C GLN* 3.3 31.4 + - - +
87C ASP* 3.7 10.5 + - - +
93C LEU* 4.2 11.9 - - + +
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Residues in contact with LYS 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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65C ALA 3.1 15.6 + - - +
66C ALA* 4.0 6.5 - - - +
68C GLN* 1.3 74.4 - - - +
70C ALA* 1.3 61.5 + - - +
72C LEU* 3.8 8.1 - - + +
73C GLN* 2.9 66.3 + - + +
85C THR* 5.0 1.3 - - - -
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Residues in contact with ALA 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 ALA 3.0 19.0 + - - +
67C GLN* 3.8 7.0 - - - +
69C LYS* 1.3 76.3 - - - +
71C ALA* 1.3 57.7 + - - +
73C GLN* 3.3 12.1 + - - +
74C HIS* 2.9 31.1 + - - +
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Residues in contact with ALA 71 (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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385A ASN* 5.9 9.0 - - + +
67C GLN 3.0 19.5 + - - +
68C GLN 3.7 4.0 - - - +
69C LYS 3.3 0.2 - - - -
70C ALA* 1.3 76.0 - - - +
72C LEU* 1.3 58.5 + - - +
74C HIS* 3.5 6.2 + - - +
75C ALA* 3.0 26.9 + - - +
93C LEU* 4.1 19.7 - - + -
94C ILE* 4.0 21.6 - - + +
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Residues in contact with LEU 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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68C GLN 3.0 17.2 + - - +
69C LYS* 3.8 7.4 - - + +
71C ALA* 1.3 74.5 - - - +
73C GLN* 1.3 62.2 + - + +
75C ALA* 3.4 3.9 + - + +
76C HIS* 3.0 59.0 + - + +
83C PHE* 3.7 36.6 - - + +
84C ILE* 4.6 0.9 - - - +
85C THR* 3.8 21.3 - - + +
94C ILE* 4.0 8.0 - - + +
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Residues in contact with GLN 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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69C LYS* 2.9 57.7 + - + +
70C ALA* 3.8 7.8 - - - +
72C LEU* 1.3 77.9 - - + +
74C HIS* 1.3 62.8 + - - +
76C HIS* 3.4 10.6 + - - +
77C ALA* 3.2 21.8 + - - +
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Residues in contact with HIS 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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384A SER* 5.8 9.0 - - - -
385A ASN* 6.1 4.9 + - - +
386A VAL* 5.6 3.8 - - - +
70C ALA 2.9 17.5 + - - +
71C ALA* 3.8 7.2 - - - +
73C GLN* 1.3 75.2 - - - +
75C ALA* 1.3 65.6 + - - +
77C ALA* 3.2 10.1 + - + +
78C HIS* 3.1 59.5 + + + +
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Residues in contact with ALA 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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386A VAL* 3.5 28.9 - - + -
71C ALA 3.0 18.1 + - - +
72C LEU* 3.5 8.3 - - - +
74C HIS* 1.3 77.6 + - - +
76C HIS* 1.3 57.8 + - + +
78C HIS 3.1 0.7 + - - -
79C SER* 2.8 35.9 + - - +
83C PHE* 4.1 16.2 - - + -
94C ILE* 4.1 13.0 - - + -
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Residues in contact with HIS 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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263A ARG* 3.3 60.9 + - - +
72C LEU* 3.0 53.1 + - + +
73C GLN* 3.8 9.2 - - - +
74C HIS 3.3 0.2 - - - -
75C ALA* 1.3 78.4 - - + +
77C ALA* 1.3 60.6 + - - +
78C HIS 3.6 0.2 + - - -
79C SER 3.7 4.7 - - - +
81C GLY 4.9 3.6 - - - -
83C PHE* 4.7 10.4 + + - -
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Residues in contact with ALA 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 GLN 3.2 13.4 + - - +
74C HIS* 3.6 11.0 - - - +
75C ALA 3.2 0.8 - - - -
76C HIS* 1.3 77.8 - - - +
78C HIS* 1.3 74.9 + - + +
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Residues in contact with HIS 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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220A HIS* 4.8 16.2 + - - -
386A VAL* 5.3 5.9 - - + +
74C HIS* 3.1 58.7 + + + +
75C ALA* 3.1 4.0 + - - +
77C ALA* 1.3 92.8 - - + +
79C SER* 1.3 59.4 + - - +
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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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260A ASN 5.0 0.2 + - - -
263A ARG* 3.4 20.3 + - - -
386A VAL* 3.7 27.6 - - - +
390A ASN* 4.9 2.4 + - - -
75C ALA 2.8 16.3 + - - +
76C HIS* 3.7 3.8 - - - +
77C ALA 3.7 1.0 - - - -
78C HIS* 1.3 81.6 - - - +
80C SER* 1.3 64.0 + - - +
81C GLY* 3.0 14.0 + - - +
83C PHE* 3.6 13.3 - - - -
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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