Contacts of the helix formed by residues 67 - 76 (chain C) in PDB entry 3PLA
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 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A PHE* 3.9 30.1 - - + -
9C TYR* 4.2 21.6 - - + +
11C LYS* 5.6 2.1 + - - -
63C GLU 3.9 2.9 + - - +
64C GLU* 3.1 28.2 + - + +
66C VAL* 1.3 78.7 - - - +
68C HIS* 1.3 56.8 - - - +
70C PRO* 3.2 18.1 - - - +
71C LEU* 4.5 4.7 + - - +
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Residues in contact with HIS 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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288A ALA 4.3 6.7 - - - +
289A LYS* 4.1 19.8 - - + +
350A ARG* 3.3 42.7 + - - -
354A PHE* 3.5 31.4 - - + -
39C THR* 3.9 4.3 - - + -
43C THR* 2.9 26.7 + - - +
65C ILE 3.7 8.8 + - - -
66C VAL* 3.0 1.8 + - - -
67C ALA* 1.3 75.9 - - - +
69C LEU* 1.3 77.5 + - + +
70C PRO 3.5 0.2 - - - -
71C LEU* 3.4 6.7 + - - +
72C LEU* 2.9 53.7 + - + +
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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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39C THR* 4.5 2.9 - - + -
42C THR* 4.3 15.3 - - + -
43C THR* 4.0 19.7 - - - +
46C VAL* 4.8 9.9 - - + -
54C VAL* 4.8 1.6 - - + -
56C ILE* 4.1 18.2 - - + -
66C VAL* 3.0 28.4 + - + +
68C HIS* 1.3 98.4 - - + +
70C PRO* 1.4 63.5 - - + +
72C LEU* 4.3 4.9 - - + -
73C CYS* 2.8 39.8 + - - +
101C SER* 3.6 33.9 - - - +
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Residues in contact with PRO 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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9C TYR* 3.9 23.1 - - + +
11C LYS* 4.3 17.5 - - + +
56C ILE* 4.4 7.2 - - + -
66C VAL 3.4 9.4 - - - +
67C ALA* 3.2 17.9 - - - +
69C LEU* 1.4 92.1 - - + +
71C LEU* 1.3 62.9 + - + +
73C CYS* 3.4 1.6 + - + +
74C ASP* 3.2 29.4 + - - -
80C TYR* 3.8 29.6 - - + +
82C TYR* 4.2 8.3 - - + +
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Residues in contact with LEU 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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289A LYS* 4.8 22.4 - - - +
354A PHE* 3.6 33.4 - - + -
11C LYS* 6.2 4.0 - - - +
67C ALA 4.7 4.0 - - - +
68C HIS 3.4 6.9 + - - +
69C LEU 3.3 0.6 - - - -
70C PRO* 1.3 81.2 - - + +
72C LEU* 1.3 63.0 + - - +
74C ASP* 3.5 5.5 + - - +
75C GLU* 3.4 28.4 + - - +
136E PHE* 5.3 0.3 - - - -
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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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289A LYS* 3.8 29.3 - - + +
43C THR* 4.0 20.2 - - + +
46C VAL* 3.7 25.4 - - + +
47C GLU* 4.5 20.0 - - + +
68C HIS* 2.9 43.5 + - + +
69C LEU* 3.8 7.0 - - + +
71C LEU* 1.3 74.1 - - - +
73C CYS* 1.3 61.2 + - - +
75C GLU* 3.4 23.7 + - - +
76C LYS* 3.3 24.7 + - + +
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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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46C VAL* 4.0 17.5 - - - -
54C VAL* 3.8 39.0 - - - -
69C LEU* 2.8 25.2 + - - +
70C PRO 3.8 0.4 - - - +
72C LEU* 1.3 72.9 - - - +
74C ASP* 1.3 59.3 + - - +
76C LYS 4.7 0.2 - - - +
77C LYS* 2.8 6.5 + - - -
78C ILE* 2.7 52.0 + - - +
80C TYR* 3.7 20.4 - - + -
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Residues in contact with ASP 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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68A GLU* 4.3 14.1 - - - +
70C PRO 3.2 18.0 + - - +
71C LEU* 3.9 5.8 - - - +
72C LEU 3.3 0.2 - - - -
73C CYS* 1.3 76.9 - - - +
75C GLU* 1.3 64.8 + - - +
77C LYS* 3.3 30.1 + - - +
78C ILE 5.1 0.9 - - - +
80C TYR* 3.5 27.0 + - - -
125C LYS* 4.4 7.6 + - - -
136E PHE* 3.6 14.1 - - + -
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Residues in contact with GLU 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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289A LYS* 3.0 29.6 + - - +
71C LEU* 3.4 15.8 + - - +
72C LEU* 3.6 29.3 - - - +
74C ASP* 1.3 79.1 - - - +
76C LYS* 1.3 61.9 + - + +
77C LYS* 3.6 11.6 + - - +
133E ASP* 5.3 0.3 - - - +
135E ARG* 3.6 52.7 + - - +
136E PHE* 3.8 27.2 - - + -
158E ASP* 4.6 2.1 - - - +
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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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46C VAL* 3.7 16.8 - - + +
47C GLU* 3.0 36.5 + - - +
49C GLY* 5.0 6.7 - - - +
72C LEU* 3.3 20.8 + - + +
75C GLU* 1.3 78.7 - - + +
77C LYS* 1.3 71.5 + - - +
78C ILE* 3.3 26.4 + - + +
135E ARG* 4.5 14.2 - - - +
156E GLN* 5.1 0.9 - - - -
157E PRO* 4.7 11.8 - - - +
158E ASP* 3.5 37.9 - - + +
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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