Contacts of the helix formed by residues 59 - 68 (chain A) in PDB entry 7KAC
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 LEU 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASP* 3.7 18.5 - - + +
54A ASP 5.5 0.2 - - - +
55A ASP* 4.1 26.0 - - + +
57A SER 3.1 1.4 - - - +
58A THR* 1.3 79.9 - - - +
60A GLN* 1.3 65.7 + - - +
61A LYS 3.6 0.2 - - - -
62A GLU* 4.2 1.2 - - - +
63A ILE* 3.3 26.0 + - - +
82A LEU* 6.4 3.1 - - + -
87A LEU* 6.0 9.4 - - + -
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Residues in contact with GLN 60 (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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7A ASP* 4.9 6.5 - - + -
55A ASP 4.7 2.2 + - - +
56A VAL 3.5 18.8 + - - +
57A SER 3.8 0.8 + - - -
59A LEU* 1.3 79.4 - - - +
61A LYS* 1.3 57.8 + - - +
63A ILE* 4.0 2.0 - - - +
64A LEU* 3.1 27.1 + - - +
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Residues in contact with LYS 61 (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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56A VAL 4.3 0.4 + - - +
57A SER* 3.2 27.3 + - - +
60A GLN* 1.3 75.4 - - - +
62A GLU* 1.3 67.8 + - - +
64A LEU* 3.4 7.6 + - - +
65A ILE* 3.1 22.0 + - - +
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Residues in contact with GLU 62 (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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57A SER* 3.0 23.6 + - - +
58A THR* 3.6 26.5 - - - +
59A LEU* 3.9 1.1 + - - +
60A GLN 3.4 0.4 - - - -
61A LYS* 1.3 79.5 - - - +
63A ILE* 1.3 61.5 + - - +
65A ILE* 3.3 8.5 + - - +
66A LEU* 3.1 22.6 + - - +
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Residues in contact with ILE 63 (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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7A ASP* 4.4 14.1 - - + -
8A ILE* 5.8 1.6 - - + +
59A LEU 3.3 19.0 + - - +
60A GLN 4.2 2.0 - - - +
62A GLU* 1.3 76.0 - - - +
64A LEU* 1.3 60.5 + - - +
66A LEU* 3.3 10.8 + - + +
67A LYS* 3.0 30.8 + - - +
77A TYR* 4.3 17.3 - - + +
80A SER* 4.9 5.2 - - - +
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Residues in contact with LEU 64 (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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60A GLN 3.1 18.1 + - - +
61A LYS* 3.6 10.1 - - - +
62A GLU 3.3 0.4 - - - -
63A ILE* 1.3 76.5 - - - +
65A ILE* 1.3 59.4 + - - +
67A LYS* 3.5 4.5 + - - +
68A THR* 2.9 33.9 + - + +
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Residues in contact with ILE 65 (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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61A LYS 3.1 12.9 + - - +
62A GLU* 3.3 10.5 + - - +
64A LEU* 1.3 75.6 - - - +
66A LEU* 1.3 61.9 + - - +
68A THR* 3.1 20.8 + - - -
69A CYS* 3.4 12.0 + - - +
133A LYS* 4.6 16.2 - - + +
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Residues in contact with LEU 66 (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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62A GLU 3.1 13.4 + - - +
63A ILE* 3.3 13.2 + - + +
65A ILE* 1.3 75.6 - - - +
67A LYS* 1.3 61.4 + - - +
69A CYS* 3.6 18.8 + - + +
75A VAL* 5.7 4.3 - - + +
77A TYR* 4.0 33.6 - - + +
80A SER* 5.6 0.4 - - - +
89A ILE* 4.0 34.8 - - + -
91A MET* 5.1 11.7 - - + -
156A PHE* 5.2 16.8 - - + -
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Residues in contact with LYS 67 (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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63A ILE 3.0 16.8 + - - +
64A LEU* 3.9 5.6 - - - +
66A LEU* 1.3 76.8 - - - +
68A THR* 1.3 60.9 + - + +
69A CYS 3.2 8.0 + - - +
70A ARG* 5.0 4.3 + - - +
77A TYR* 3.8 25.6 - - + +
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Residues in contact with THR 68 (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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64A LEU* 2.9 21.5 + - + +
65A ILE* 3.1 13.0 + - - -
67A LYS* 1.3 78.2 - - + +
69A CYS* 1.3 56.2 + - - -
70A ARG* 3.5 4.0 + - - +
127A TYR* 3.1 14.0 + - - -
131A GLN* 4.7 4.7 - - - +
133A LYS* 4.4 7.7 + - - -
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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