Contacts of the helix formed by residues 69 - 76 (chain A) in PDB entry 4O7C
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 VAL 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A TYR* 2.9 46.8 + - + +
68A ARG* 1.3 117.6 - - - +
70A VAL* 1.3 62.0 + - - +
71A LEU 3.6 0.2 - - - -
73A THR* 2.7 41.1 + - - +
160A LYS* 4.2 21.1 - - + +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TYR* 3.2 36.0 + - + -
66A LEU* 3.4 25.8 - - + +
69A VAL* 1.3 75.4 - - - +
71A LEU* 1.3 62.8 + - - +
73A THR* 3.8 0.3 - - - -
74A LEU* 3.1 30.0 + - + +
129A PHE* 4.3 6.7 - - + -
157A PHE* 3.4 38.6 - - + -
160A LYS* 4.0 22.4 - - + -
161A ILE* 4.2 5.4 - - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU 2.8 19.9 + - - +
67A LEU* 3.7 12.1 - - + +
70A VAL* 1.3 72.5 - - - +
72A LYS* 1.3 62.5 + - + +
74A LEU* 3.3 2.9 + - - +
75A TRP* 2.8 42.7 + - + +
107A MET* 4.0 36.8 - - + +
110A ILE* 4.3 2.0 - - + -
111A LYS* 3.8 43.1 - - + +
114A LEU* 4.1 13.2 - - + -
129A PHE* 4.1 20.9 - - + -
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.3 11.0 + - - +
68A ARG* 3.3 40.1 + - - +
69A VAL 3.7 0.4 + - - +
70A VAL 3.4 0.4 - - - -
71A LEU* 1.3 83.9 - - - +
73A THR* 1.3 64.2 + - - +
75A TRP* 3.5 4.2 + - - +
76A LYS* 3.3 53.5 + - + +
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 2.7 27.0 + - - +
70A VAL 3.8 3.1 - - - -
72A LYS* 1.3 80.6 - - - +
74A LEU* 1.3 63.6 + - - +
75A TRP 3.4 0.2 + - - -
76A LYS* 3.5 11.8 + - - +
77A HIS* 3.6 10.6 + - - +
156A LEU* 3.7 27.2 - - + +
160A LYS* 3.9 28.5 + - + -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.1 23.4 + - + +
71A LEU* 4.0 1.6 - - - +
73A THR* 1.3 79.6 - - + +
75A TRP* 1.3 63.0 + - - +
77A HIS* 3.2 13.9 + - - +
80A ALA* 3.1 17.5 - - - +
107A MET* 3.7 22.4 - - + +
129A PHE* 3.9 24.0 - - + -
133A PHE* 4.1 16.2 - - + -
153A LEU* 3.9 31.7 - - + +
156A LEU* 3.9 17.0 - - + +
157A PHE* 3.9 30.5 - - + +
160A LYS* 5.2 1.8 - - + -
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Residues in contact with TRP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 2.8 29.0 + - + +
72A LYS* 3.7 6.7 - - - +
73A THR 3.3 0.2 - - - -
74A LEU* 1.3 77.9 - - - +
76A LYS* 1.3 64.4 + - + +
77A HIS 3.3 0.7 - - - +
80A ALA* 3.3 9.9 - - - +
84A GLN* 3.1 75.2 + - + +
107A MET* 3.6 42.8 - - + +
108A GLY* 3.7 4.9 - - - -
111A LYS* 3.9 34.0 - - + +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 3.3 43.9 + - + +
73A THR* 4.0 7.2 - - - +
74A LEU 3.2 0.8 - - - -
75A TRP* 1.3 82.9 - - + +
77A HIS* 1.3 64.4 + - - +
78A GLN 3.8 1.0 + - - -
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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