Contacts of the helix formed by residues 72 - 79 (chain C) in PDB entry 3ORH
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 ALA 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C PHE* 3.0 49.5 + - + -
70C GLY 3.4 1.6 + - - -
71C MET* 1.4 77.7 - - - +
73C ILE* 1.4 58.4 + - - +
74C ALA 3.6 1.8 - - - -
75C ALA* 3.9 5.2 - - - -
76C SER* 2.8 36.1 + - - +
102C TRP* 4.1 17.9 - - + +
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Residues in contact with ILE 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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42C MET* 3.8 18.6 - - + -
44C ARG* 3.9 36.8 - - + +
47C THR* 3.8 37.7 - - + +
50C MET* 3.7 18.8 - - + -
51C HIS* 4.2 8.7 + - - +
71C MET* 3.2 29.3 - - + +
72C ALA* 1.4 76.5 - - - +
74C ALA* 1.4 66.5 + - - +
76C SER* 3.5 4.0 + - - -
77C LYS* 3.4 18.0 + - - +
4002C SAH 3.2 8.8 + - - +
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Residues in contact with ALA 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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50C MET* 3.9 25.1 - - + +
54C ALA* 3.4 4.7 - - - +
66C GLU* 3.6 15.7 - - - +
73C ILE* 1.4 71.2 - - - +
75C ALA* 1.3 57.3 + - - +
77C LYS* 3.2 2.3 + - - -
78C VAL* 2.9 31.5 + - - +
133C LEU* 3.8 22.0 - - + -
4002C SAH 2.8 27.5 + - - +
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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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66C GLU* 3.3 27.3 + - - +
69C PHE* 3.8 22.4 - - + -
72C ALA* 3.7 7.7 + - - +
73C ILE 3.3 0.6 - - - -
74C ALA* 1.3 78.9 - - - +
76C SER* 1.3 61.7 + - - +
78C VAL* 3.3 1.5 + - - -
79C GLN* 3.1 27.4 + - - +
86C HIS* 3.5 6.4 - - + -
88C ILE* 4.4 0.4 - - + -
102C TRP* 3.8 24.2 - - + -
4002C SAH 5.4 0.2 - - - -
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Residues in contact with SER 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 ALA* 2.8 24.5 + - - +
73C ILE* 3.9 4.5 - - - -
74C ALA 3.3 0.2 - - - -
75C ALA* 1.3 75.9 - - - +
77C LYS* 1.3 60.3 + - - +
79C GLN* 3.5 16.7 + - - +
80C GLU* 3.5 16.4 + - - +
102C TRP* 3.4 23.4 + - - -
106C GLN* 5.3 1.3 - - - -
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Residues in contact with LYS 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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51C HIS* 3.6 55.1 + - + +
54C ALA* 3.5 24.2 - - + -
55C ALA* 4.8 8.7 - - - +
58C SER* 5.0 1.2 + - - -
73C ILE 3.4 4.2 + - - +
74C ALA 3.2 3.8 + - - +
76C SER* 1.3 76.2 - - - +
78C VAL* 1.4 64.9 + - - +
80C GLU* 3.1 45.5 + - - +
81C ALA* 3.9 4.0 + - - +
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Residues in contact with VAL 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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54C ALA* 3.8 25.5 - - + +
57C ALA* 5.1 0.4 - - + -
58C SER* 4.3 12.3 - - - -
64C VAL* 4.1 20.4 - - + -
66C GLU* 4.1 12.1 - - - +
74C ALA 2.9 19.1 + - - +
75C ALA 3.3 7.8 + - - +
77C LYS* 1.4 73.9 - - - +
79C GLN* 1.3 56.8 + - - +
81C ALA* 3.1 28.1 + - - +
83C ILE* 3.8 21.3 - - + +
86C HIS* 3.7 24.0 - - + +
133C LEU* 4.4 7.6 - - + -
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Residues in contact with GLN 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 ALA 3.1 17.4 + - - +
76C SER* 3.5 12.6 - - - +
78C VAL* 1.3 76.5 - - - +
80C GLU* 1.4 56.5 + - - +
81C ALA 3.3 0.4 - - - -
83C ILE* 4.3 1.0 - - - +
86C HIS* 3.1 31.8 + - - +
102C TRP* 3.8 8.1 - - + -
106C GLN* 3.4 30.8 - - - +
107C THR* 3.5 8.1 + - - +
108C HIS* 2.9 76.9 + - - +
110C VAL* 3.6 6.1 - - - +
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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