Contacts of the helix formed by residues 68 - 78 (chain C) in PDB entry 4OA5
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 GLY 68 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C THR* 3.1 25.8 + - - +
66C CYS 3.4 1.0 + - - -
67C VAL* 1.3 80.1 - - - +
69C PHE* 1.3 59.8 + - - +
70C SER 3.5 2.2 - - - -
71C ALA* 3.4 8.9 + - - +
72C ILE* 2.9 42.0 + - - +
97C ALA* 4.4 4.0 - - - -
101C ILE* 5.2 5.2 - - - -
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Residues in contact with PHE 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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19C VAL* 5.0 0.9 - - + -
24C ALA* 3.3 36.6 - - + -
25C LEU* 4.7 0.4 - - - -
27C ALA* 4.6 7.6 - - + +
28C HIS* 3.6 26.9 - + + +
39C GLN* 3.6 15.5 - - + +
40C LEU* 3.2 33.2 - - + -
41C GLY 3.6 21.5 - - - -
42C THR* 4.1 16.6 - - + -
45C GLY* 4.9 0.7 - - - -
67C VAL 3.5 2.6 + - - -
68C GLY* 1.3 79.0 - - - +
70C SER* 1.3 67.2 + - - +
72C ILE* 3.3 2.2 + - - +
73C CYS* 3.0 48.3 + - - -
301C SAH 3.4 15.7 + - - +
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Residues in contact with SER 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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40C LEU* 4.1 12.3 - - - -
48C LEU* 4.8 1.7 - - - +
62C GLU* 2.5 27.9 + - - -
65C THR 4.7 0.5 + - - -
69C PHE* 1.3 84.0 - - - +
71C ALA* 1.3 56.4 + - - +
73C CYS* 3.3 6.7 + - - +
74C MET* 2.9 34.1 + - - +
134C PHE* 4.0 13.0 - - - -
301C SAH 2.7 38.8 + - - -
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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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62C GLU* 3.5 20.1 + - - +
68C GLY* 3.4 13.8 + - - +
69C PHE 3.2 0.6 - - - -
70C SER* 1.3 78.8 + - - +
72C ILE* 1.3 60.6 + - - +
74C MET* 3.3 8.9 + - - -
75C ALA* 2.9 27.0 + - - +
84C ILE* 3.3 15.8 - - + +
86C THR* 4.4 7.0 - - + -
101C ILE* 5.6 0.4 - - + -
110C ILE* 3.7 26.6 - - + +
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Residues in contact with ILE 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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24C ALA* 3.9 18.2 - - + -
27C ALA* 3.8 27.1 - - + -
68C GLY 2.9 23.5 + - - +
69C PHE* 3.7 3.6 - - - +
71C ALA* 1.3 72.7 - - - +
73C CYS* 1.3 66.9 - - - +
75C ALA* 3.3 2.3 + - - +
76C HIS* 3.2 43.6 + - + +
100C ASN* 4.1 16.8 - - + +
101C ILE* 4.4 7.9 - - + +
104C CYS* 3.8 21.8 - - + -
106C LEU* 3.9 16.7 - - + +
110C ILE* 4.1 13.0 - - + -
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Residues in contact with CYS 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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19C VAL* 3.9 23.1 - - - -
24C ALA* 4.3 2.7 - - - -
45C GLY* 4.1 21.3 - - - +
48C LEU* 6.0 0.4 - - + -
49C GLN* 2.9 34.0 + - - +
69C PHE* 3.0 54.1 + - - -
70C SER* 3.6 8.7 - - - +
72C ILE* 1.3 79.3 - - - +
74C MET* 1.3 63.3 + - + +
75C ALA 3.4 0.2 + - - -
76C HIS* 3.4 7.5 + - - +
77C ALA 3.7 0.3 + - - -
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Residues in contact with MET 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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48C LEU* 3.9 29.2 - - + -
49C GLN* 4.8 2.5 - - - -
52C ILE* 3.5 29.6 - - + +
60C ILE* 4.1 24.5 - - + -
62C GLU* 3.3 35.4 - - + +
70C SER* 2.9 19.1 + - - +
71C ALA* 4.0 5.6 - - - -
73C CYS* 1.3 76.7 - - - +
75C ALA* 1.3 58.5 + - - +
77C ALA* 2.9 21.5 + - - +
78C LEU* 3.3 12.7 + - - +
84C ILE* 3.7 15.0 - - + -
132C MET* 4.1 12.3 - - - -
134C PHE* 4.0 10.5 - - + -
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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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71C ALA 2.9 17.3 + - - +
72C ILE 3.7 4.7 - - - +
73C CYS 3.3 0.4 - - - -
74C MET* 1.3 76.6 - - - +
76C HIS* 1.3 58.2 + - - +
78C LEU* 3.0 28.0 + - - +
84C ILE* 3.5 14.6 - - + +
106C LEU* 4.1 14.5 - - + +
109C LYS* 3.8 21.2 - - + +
110C ILE* 3.8 20.2 - - + -
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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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19C VAL* 5.8 0.4 - - + -
21C THR* 3.8 33.2 + - + -
24C ALA* 5.1 0.9 + - + -
49C GLN* 3.9 11.2 - - - +
72C ILE* 3.2 30.8 + - + +
73C CYS* 3.7 11.2 - - - +
74C MET 3.3 0.2 - - - -
75C ALA* 1.3 77.6 - - - +
77C ALA* 1.3 58.7 + - - +
78C LEU 4.4 3.2 - - - +
104C CYS 5.1 1.8 - - - -
106C LEU* 3.7 29.7 - - + +
304C IOD 4.1 23.5 - - + +
309C IOD 3.6 13.8 - - + +
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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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49C GLN* 3.7 45.1 - - + +
52C ILE* 3.8 16.5 - - + +
53C ARG* 4.9 10.9 - - + +
73C CYS 3.7 1.2 + - - -
74C MET 2.9 11.2 + - - +
76C HIS* 1.3 77.5 - - - +
78C LEU* 1.3 64.9 + - - +
79C PRO* 3.8 2.6 - - - +
309C IOD 3.9 9.9 - - + -
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Residues in contact with LEU 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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52C ILE* 3.8 13.9 - - + -
57C ILE 3.4 22.7 - - - +
58C HIS 3.6 13.2 - - - +
60C ILE* 3.8 13.9 - - + -
74C MET 3.6 9.2 - - - +
75C ALA* 3.0 18.5 + - + +
76C HIS 4.4 3.3 - - - +
77C ALA* 1.3 80.5 - - - +
79C PRO* 1.3 75.4 - - + +
82C GLY* 3.9 2.7 - - - -
83C HIS* 3.6 23.1 - - - +
84C ILE* 3.6 34.8 - - + -
109C LYS* 4.1 10.0 - - - +
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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