Contacts of the helix formed by residues 66 - 76 (chain C) in PDB entry 2AOB
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 66 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LYS 3.3 7.2 - - - +
65C ILE* 1.3 92.9 - - + +
67C ARG* 1.3 65.6 + - - +
68C ALA* 4.2 9.2 - - + +
69C LYS* 3.1 25.1 + - + +
70C ALA* 2.9 22.1 + - - +
89C GLU* 6.2 1.8 - - + -
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Residues in contact with ARG 67 (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 ILE 3.6 1.4 + - - -
66C PRO* 1.3 69.8 - - - +
68C ALA* 1.4 58.1 + - - +
70C ALA* 3.1 4.7 + - - +
71C GLU* 2.9 39.4 + - - +
86C ARG* 3.7 27.6 - - - +
89C GLU* 3.7 29.3 + - - +
107C HIS* 3.3 36.2 + - + +
2201C S1S 2.7 83.4 + - - +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PRO* 3.2 6.2 - - + +
67C ARG* 1.4 78.4 - - - +
69C LYS* 1.3 60.4 + - + +
71C GLU* 3.2 14.7 + - - +
72C GLU* 2.9 26.2 + - - +
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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 ILE* 3.8 13.3 - - + +
66C PRO* 3.1 33.5 + - + +
68C ALA* 1.3 77.4 - - + +
70C ALA* 1.4 61.6 + - - +
72C GLU* 3.3 10.6 + - + +
73C MET* 3.0 31.0 + - + +
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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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65C ILE* 4.1 11.1 - - + +
66C PRO 2.9 11.9 + - - +
67C ARG 3.1 9.6 + - - +
69C LYS* 1.4 76.5 - - - +
71C GLU* 1.3 61.0 + - - +
73C MET* 3.4 1.3 + - - +
74C LEU* 3.0 31.9 + - - +
84C LEU* 4.0 19.3 - - + -
86C ARG* 3.8 26.9 - - - +
98C SER* 4.1 8.7 - - - +
105C VAL* 5.1 0.4 - - - -
107C HIS* 5.1 0.2 - - + -
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Residues in contact with GLU 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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67C ARG* 2.9 27.7 + - - +
68C ALA* 3.4 14.8 - - - +
69C LYS 3.2 0.4 - - - -
70C ALA* 1.3 77.6 - - - +
72C GLU* 1.3 56.7 + - - +
75C SER* 2.9 36.0 + - - -
105C VAL* 3.8 24.1 - - + +
107C HIS* 2.8 37.6 + - + +
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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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68C ALA 2.9 13.2 + - - +
69C LYS* 3.3 17.2 + - + +
71C GLU* 1.3 78.0 - - - +
73C MET* 1.3 61.1 + - - +
75C SER* 3.9 5.9 + - - -
76C LYS* 2.9 37.3 + - - +
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Residues in contact with MET 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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62C PHE* 3.5 36.1 - - + -
65C ILE* 3.6 22.4 - - + -
69C LYS* 3.0 15.6 + - + +
70C ALA* 3.4 4.0 + - - +
72C GLU* 1.3 76.1 - - - +
74C LEU* 1.3 66.2 + - + +
76C LYS* 3.1 25.9 + - - +
77C GLN* 3.9 8.0 - - - +
84C LEU* 4.1 14.4 - - + -
151D ILE* 4.9 15.5 - - + -
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Residues in contact with LEU 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 ALA 3.0 16.5 + - - +
73C MET* 1.3 70.4 - - + +
75C SER* 1.3 58.9 + - - +
76C LYS 2.9 5.6 - - - -
77C GLN* 2.8 36.9 + - + +
82C ALA* 3.7 19.5 - - + +
83C PHE 3.9 0.4 - - - +
84C LEU* 4.2 11.7 - - + -
98C SER* 3.3 45.8 - - - +
99C VAL* 3.9 3.4 - - - +
100C LYS* 3.4 13.8 - - + +
105C VAL* 3.9 15.5 - - + -
151D ILE* 3.2 34.8 - - + -
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Residues in contact with SER 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 GLU 2.9 22.4 + - - -
72C GLU* 3.9 7.5 + - - -
73C MET 3.3 0.2 - - - -
74C LEU* 1.3 76.1 - - - +
76C LYS* 1.3 57.7 + - - +
77C GLN 3.1 5.9 + - - +
100C LYS* 4.8 9.1 + - - +
105C VAL* 4.0 10.2 - - - +
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Residues in contact with LYS 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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72C GLU* 2.9 41.0 + - - +
73C MET* 3.1 12.5 + - - +
74C LEU 2.9 2.0 + - - -
75C SER* 1.3 78.9 - - - +
77C GLN* 1.3 65.1 + - - +
78C ARG 3.9 1.2 + - - -
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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