Contacts of the strand formed by residues 69 - 77 (chain C) in PDB entry 1KJ4
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 HIS 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C PRO* 4.6 5.6 - - + +
64C VAL 3.7 0.7 - - - +
65C GLU* 3.2 3.1 - - - -
66C ILE* 2.6 45.6 + - - +
67C CYS 3.0 23.3 + - - -
68C GLY* 1.3 75.6 + - - +
70C LYS* 1.3 62.6 + - - +
71C ALA 4.0 0.2 + - - -
93C ILE* 3.8 30.1 + - + +
99D PHE* 3.7 47.3 + + - -
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Residues in contact with LYS 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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64C VAL 3.6 5.4 - - - +
65C GLU* 4.3 7.4 - - + +
68C GLY 4.0 3.0 + - - +
69C HIS* 1.3 71.7 - - - +
71C ALA* 1.3 63.4 + - - +
92C GLN 5.1 3.3 - - - +
93C ILE* 5.0 2.8 - - - +
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Residues in contact with ALA 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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62C ILE 3.7 0.2 - - - +
63C PRO* 3.6 1.0 - - - +
64C VAL* 2.7 44.3 + - + +
66C ILE* 5.7 2.5 - - + -
70C LYS* 1.3 76.2 - - - +
72C ILE* 1.3 62.2 + - - +
89C LEU* 4.1 14.4 - - + -
92C GLN* 3.6 30.1 - - + +
93C ILE* 4.3 14.4 - - + -
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Residues in contact with ILE 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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61C GLN* 3.4 38.4 - - + +
62C ILE 3.3 6.5 - - - +
63C PRO* 4.1 15.9 - - + -
71C ALA* 1.3 78.4 - - - +
73C GLY* 1.3 59.3 + - - +
89C LEU* 4.4 2.0 - - - -
92C GLN* 2.5 37.8 + - - +
516C ACT 4.4 0.5 + - - -
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Residues in contact with GLY 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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60C ASP 4.0 0.2 - - - -
61C GLN* 3.3 9.9 + - - -
62C ILE* 2.6 40.5 + - - +
72C ILE* 1.3 79.2 - - - +
74C THR* 1.3 61.9 + - - -
75C VAL* 4.5 2.1 - - - +
89C LEU* 4.5 6.2 - - - +
92C GLN* 4.2 1.1 - - - -
516C ACT 3.2 15.9 - - - -
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Residues in contact with THR 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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30C ASP* 5.3 9.1 - - - +
31C THR* 4.1 9.9 + - - +
58C GLN* 3.5 30.0 + - + +
59C TYR 3.4 13.5 - - - +
60C ASP* 2.9 17.9 + - - +
61C GLN 4.8 0.5 + - - -
73C GLY* 1.3 73.3 - - - -
75C VAL* 1.3 66.9 + - - +
76C LEU* 4.0 11.8 + - + +
88C ASN* 3.6 16.1 + - - +
89C LEU* 4.8 1.4 - - - +
516C ACT 2.4 34.0 + - - +
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Residues in contact with VAL 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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15C ILE* 3.4 26.2 - - + -
31C THR* 3.8 13.9 - - + +
33C LEU* 4.1 29.2 - - + -
38C LEU* 4.1 23.6 - - + -
59C TYR* 3.0 33.8 + - - +
62C ILE* 4.0 13.0 - - + -
64C VAL* 4.2 9.0 - - + -
73C GLY 3.8 1.1 + - - +
74C THR* 1.3 79.6 - - - +
76C LEU* 1.3 70.8 + - - +
77C VAL* 4.1 3.8 - - + -
89C LEU* 4.9 2.9 - - + -
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Residues in contact with LEU 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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30C ASP* 3.5 33.4 - - + +
31C THR 2.7 15.9 + - - +
32C VAL* 3.0 21.3 - - + +
33C LEU* 2.7 32.6 + - - +
45C LYS* 4.2 5.6 - - + -
47C ILE* 3.9 26.7 - - + -
56C VAL* 4.0 15.5 - - + -
57C ARG 3.4 4.5 - - - +
58C GLN* 3.4 42.6 - - + +
74C THR* 4.0 7.6 - - + -
75C VAL* 1.3 76.3 - - - +
77C VAL* 1.3 55.9 + - - +
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Residues in contact with VAL 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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33C LEU* 3.0 14.4 - - + +
34C GLU 3.9 0.9 - - - +
35C GLU* 3.5 10.1 - - - +
36C MET* 3.3 46.0 - - + +
38C LEU* 4.4 7.9 - - + -
56C VAL* 3.6 3.5 - - - +
57C ARG* 2.9 54.7 + - - +
59C TYR* 3.4 29.4 - - + -
75C VAL* 4.5 4.9 - - + -
76C LEU* 1.3 76.8 - - - +
78C GLY* 1.3 57.5 + - - +
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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