Contacts of the helix formed by residues 67 - 72 (chain A) in PDB entry 1KI1
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLN* 4.6 4.0 - - + -
64A TYR* 2.9 21.5 + - + +
66A ARG* 1.3 78.3 - - - +
68A ARG* 1.3 67.1 + - - +
69A PRO 3.4 0.4 - - - -
70A LEU* 3.0 31.8 + - + +
1333B CYS* 4.7 0.7 - - + -
1379B MET* 3.9 24.3 - - + +
1382B VAL* 5.4 0.9 - - + -
1383B THR* 3.6 27.6 - - + -
1417B CYS* 4.1 18.8 - - + +
1420B VAL* 3.9 20.0 - - + -
1421B ASN* 3.5 14.6 - - - +
1424B VAL* 3.8 27.8 - - + -
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Residues in contact with ARG 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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58A THR* 5.9 3.1 - - + -
61A GLN* 2.8 49.9 + - + +
62A GLU* 3.5 14.0 + - - +
64A TYR 3.2 8.0 + - - +
65A ASP* 3.4 27.8 - - - +
67A LEU* 1.3 76.0 - - - +
69A PRO* 1.3 68.1 - - + +
70A LEU 3.0 1.4 + - - -
71A SER* 3.1 15.1 + - - -
72A TYR* 3.5 23.9 - - + +
96A LYS* 3.5 22.9 - - - +
97A TRP* 3.2 29.6 - - - -
100A GLU* 2.5 44.2 + - - +
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Residues in contact with PRO 69 (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 ASP 3.1 24.2 - - - +
66A ARG* 3.9 21.1 - - - +
67A LEU 3.5 1.3 - - - -
68A ARG* 1.3 91.4 - - + +
70A LEU* 1.3 63.6 + - + +
71A SER 3.1 1.3 - - - -
72A TYR* 3.1 28.0 + - + +
73A PRO* 3.3 11.1 - - - +
100A GLU* 5.0 4.3 - - - +
104A HIS* 3.5 40.0 + - + +
1337B LEU* 5.1 3.3 - - + +
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Residues in contact with LEU 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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66A ARG 3.7 17.3 - - - +
67A LEU* 3.0 34.4 + - + +
68A ARG 3.0 1.4 + - - -
69A PRO* 1.3 80.6 - - + +
71A SER* 1.3 57.9 + - - +
72A TYR 3.4 0.2 - - - -
73A PRO* 3.8 9.9 - - - +
1333B CYS* 4.3 12.1 - - + +
1336B GLN* 4.1 32.9 + - + +
1337B LEU* 3.9 42.7 - - + +
1376B LEU* 3.0 20.4 - - - +
1379B MET* 4.3 12.8 - - + -
1424B VAL* 4.7 8.7 - - + -
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Residues in contact with SER 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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5A LYS* 2.8 30.5 + - - -
7A VAL* 4.0 8.1 - - - +
56A PHE* 5.7 4.5 - - - -
57A ASP 5.0 1.4 + - - -
58A THR* 4.4 12.1 - - - +
61A GLN* 3.3 23.6 + - - -
68A ARG 3.1 8.8 + - - -
69A PRO 3.1 0.8 - - - -
70A LEU* 1.3 79.2 - - - +
72A TYR* 1.3 64.5 + - - +
73A PRO* 3.7 1.1 - - - -
75A THR* 3.9 1.0 + - - -
1376B LEU* 4.0 16.5 - - - +
1379B MET* 3.6 12.6 - - - +
1380B GLN* 5.0 2.4 + - - -
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Residues in contact with TYR 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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7A VAL* 4.6 4.7 - - + -
9A VAL* 4.1 20.4 - - + +
58A THR* 5.0 3.0 - - + +
68A ARG* 3.5 20.1 - - + +
69A PRO* 3.1 25.5 + - + +
71A SER* 1.3 83.6 - - - +
73A PRO* 1.3 67.7 - - + +
74A GLN 3.3 0.2 + - - -
75A THR* 2.5 27.4 + - - -
78A PHE* 3.7 25.4 - + + -
97A TRP* 4.2 7.3 - - - -
100A GLU* 2.7 42.1 + - + +
101A ILE* 4.4 12.8 - - + +
104A HIS* 3.8 23.3 - + + +
105A CYS* 3.7 20.2 - - - -
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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