Contacts of the helix formed by residues 82 - 100 (chain C) in PDB entry 1KVO
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 SER 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ARG* 2.9 30.6 + - - -
81C ASP* 1.3 72.2 - - - +
83C CYS* 1.3 60.4 + - - +
85C SER* 3.7 7.1 - - - -
86C GLN* 2.8 32.1 + - - +
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Residues in contact with CYS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.7 5.5 - - - +
57C ARG* 3.9 9.2 - - - -
58C GLY 5.0 0.9 - - - -
59C CYS* 2.0 57.7 - - + -
64C LEU* 4.0 4.5 - - + -
81C ASP* 3.1 11.4 + - - +
82C SER* 1.3 79.7 + - - +
84C ARG* 1.3 58.2 + - - +
87C LEU* 2.8 31.6 + - - +
57D ARG 4.9 2.7 - - - -
58D GLY* 3.6 23.6 - - - +
59D CYS* 5.3 0.4 - - - -
83D CYS* 5.7 3.6 - - - -
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.5 29.4 - - + +
65C SER* 2.9 44.0 + - - +
66C TYR* 3.8 9.3 - - + +
80C GLN* 3.9 25.4 - - + +
81C ASP* 2.9 24.0 + - - +
83C CYS* 1.3 78.6 - - - +
85C SER* 1.3 58.4 + - - +
87C LEU* 3.7 7.1 - - - +
88C CYS* 3.0 30.7 + - - +
55D GLU* 2.6 30.0 + - - +
56D LYS* 3.0 25.1 + - - +
58D GLY 3.7 1.8 - - - +
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C CYS* 4.9 3.9 - - - +
78C ALA 4.2 6.1 + - - -
79C LYS* 5.3 0.5 - - - -
80C GLN* 3.6 26.6 + - - +
81C ASP 2.9 22.1 + - - -
82C SER* 3.9 6.7 - - - -
84C ARG* 1.3 79.8 - - - +
86C GLN* 1.3 59.9 + - - +
88C CYS* 3.5 3.8 + - - +
89C GLU* 3.4 24.5 + - - +
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C CYS* 4.8 3.2 + - - -
53C ARG* 4.3 32.5 - - - +
54C LEU* 3.8 18.4 - - + +
57C ARG* 2.5 38.6 + - - +
82C SER 2.8 17.2 + - - +
83C CYS 4.1 1.3 - - - +
85C SER* 1.3 74.5 - - - +
87C LEU* 1.3 61.1 + - - +
89C GLU* 3.4 9.1 + - + +
90C CYS* 3.0 32.2 + - - -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ASN 4.3 0.4 - - - +
51C TYR* 3.3 41.1 - - + +
54C LEU* 3.7 19.7 - - + +
60C GLY 4.4 1.1 - - - +
61C THR* 3.4 20.6 - - - +
64C LEU* 3.2 45.5 - - + +
66C TYR* 3.7 18.8 - - + -
83C CYS 2.8 18.7 + - - +
84C ARG* 3.7 4.3 - - - +
85C SER 3.3 0.2 - - - -
86C GLN* 1.3 72.9 - - - +
88C CYS* 1.3 67.2 + - - +
90C CYS* 3.0 4.7 + - - +
91C ASP* 3.0 22.5 + - - +
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Residues in contact with CYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 4.1 3.8 - - - -
66C TYR* 3.7 38.6 - - + -
67C LYS 4.3 1.1 - - - -
68C PHE* 3.9 8.3 - - - -
77C CYS* 2.0 51.6 - - + -
80C GLN* 4.3 2.5 - - - +
84C ARG 3.0 18.1 + - - +
85C SER 3.7 4.5 - - - +
87C LEU* 1.3 77.7 - - - +
89C GLU* 1.3 49.1 + - - +
91C ASP* 3.2 3.8 + - - +
92C LYS* 2.7 36.2 + - - +
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Residues in contact with GLU 89 (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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50C CYS* 5.1 0.4 - - - -
77C CYS* 3.6 20.5 + - - +
85C SER* 3.4 14.1 + - - +
86C GLN* 3.4 13.6 + - + +
87C LEU 3.2 0.6 - - - -
88C CYS* 1.3 74.3 - - - +
90C CYS* 1.3 64.5 + - - +
92C LYS* 3.5 29.0 + - - +
93C ALA* 2.9 27.2 + - - +
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Residues in contact with CYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C HIS* 3.5 13.1 - - + -
50C CYS* 2.0 67.0 - - + +
51C TYR* 3.9 14.8 - - + -
54C LEU* 3.6 12.8 - - - -
86C GLN* 3.0 24.7 + - - -
87C LEU 3.0 8.8 + - - +
89C GLU* 1.3 75.4 - - - +
91C ASP* 1.3 63.6 + - - +
93C ALA* 3.4 4.5 + - - +
94C ALA* 3.1 17.5 + - - +
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Residues in contact with ASP 91 (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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1C ASN 4.2 1.6 + - - +
5C PHE* 3.5 37.4 - - + +
8C MET* 3.6 5.2 - - - -
47C HIS* 3.0 11.5 + - - -
51C TYR* 2.6 31.7 + - - -
66C TYR* 2.5 38.8 + - - +
87C LEU 3.0 9.4 + - - +
88C CYS 3.5 5.4 - - - +
90C CYS* 1.3 74.5 - - - +
92C LYS* 1.3 60.1 + - - +
94C ALA 3.1 1.6 + - - -
95C ALA* 2.8 29.1 + - - +
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Residues in contact with LYS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 3.4 15.2 - - + -
75C ILE* 3.0 44.3 + - + +
76C THR* 4.6 4.4 + - - +
77C CYS* 4.2 10.7 - - - +
88C CYS 2.7 21.4 + - - +
89C GLU* 3.5 32.5 + - - +
91C ASP* 1.3 72.1 - - - +
93C ALA* 1.3 63.3 + - - +
95C ALA* 3.6 1.6 - - - +
96C THR* 3.1 32.4 + - - +
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 6.1 4.7 - - + -
50C CYS* 6.1 1.1 - - - -
89C GLU* 2.9 20.2 + - - +
90C CYS* 3.5 6.7 - - - +
92C LYS* 1.3 78.8 - - - +
94C ALA* 1.3 55.7 + - - +
96C THR* 3.6 7.9 - - - +
97C CYS* 3.0 27.7 + - - +
100C ARG* 4.8 1.4 + - - -
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Residues in contact with ALA 94 (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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5C PHE* 3.8 11.0 - - + -
43C CYS* 4.7 7.4 - - - +
47C HIS* 3.5 40.2 - - + -
90C CYS 3.1 3.4 + - - +
91C ASP 3.6 4.9 - - - +
93C ALA* 1.3 75.6 - - - +
95C ALA* 1.3 66.6 + - - +
97C CYS* 3.0 8.4 + - - +
98C PHE* 2.9 36.5 + - + -
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Residues in contact with ALA 95 (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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5C PHE* 4.2 1.0 - - - -
8C MET* 4.0 24.0 - - + +
9C ILE* 4.3 20.4 - - + -
12C THR* 3.0 34.9 + - + +
75C ILE* 4.9 1.1 - - + -
91C ASP 2.8 19.0 + - - +
92C LYS 3.6 4.7 - - - +
94C ALA* 1.3 73.6 - - - +
96C THR* 1.3 62.8 + - - +
98C PHE* 3.3 6.1 + - - +
99C ALA 3.2 13.3 + - - -
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Residues in contact with THR 96 (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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12C THR* 4.5 9.9 - - - +
73C SER 5.5 1.9 + - - -
75C ILE* 5.8 1.4 - - - +
92C LYS* 3.1 22.5 + - - +
93C ALA* 3.6 7.0 - - - +
95C ALA* 1.3 77.4 - - - +
97C CYS* 1.3 59.9 + - - +
99C ALA* 3.1 9.7 + - - +
100C ARG* 2.9 50.3 + - + +
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Residues in contact with CYS 97 (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 ALA 4.6 0.7 - - - -
43C CYS* 2.0 52.9 - - + -
46C THR* 6.4 0.7 - - - -
93C ALA 3.0 17.1 + - - +
94C ALA* 3.0 7.3 + - - +
96C THR* 1.3 72.3 - - - +
98C PHE* 1.3 63.2 + - - +
100C ARG* 3.3 26.8 + - - +
101C ASN* 3.0 40.3 + - - +
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Residues in contact with PHE 98 (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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5C PHE* 4.7 2.5 - + - -
9C ILE* 4.1 25.6 - - + -
13C THR* 3.6 16.4 - - + +
21C TYR* 3.9 35.0 + + - +
40C THR* 3.7 21.9 + - + -
43C CYS* 3.4 31.0 - - + -
44C CYS* 3.4 29.8 - - - -
94C ALA* 2.9 21.1 + - + -
95C ALA 3.4 8.1 - - - +
97C CYS* 1.3 76.7 - - - +
99C ALA* 1.3 57.1 + - - +
101C ASN* 3.7 2.2 - - - -
102C LYS* 3.0 26.3 + - - +
190C OAP 4.0 24.0 - - + -
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C THR* 3.4 30.1 - - - +
13C THR* 3.6 8.2 - - - +
95C ALA 3.2 9.1 + - - +
96C THR* 3.1 10.9 + - - +
98C PHE* 1.3 76.5 - - - +
100C ARG* 1.3 65.9 + - - +
102C LYS* 2.9 26.9 + - - +
103C THR 4.6 0.2 + - - -
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA 4.8 1.4 + - - -
96C THR* 2.9 38.4 + - + +
97C CYS* 3.5 37.4 - - - +
99C ALA* 1.3 76.3 - - - +
101C ASN* 1.3 69.7 + - - +
102C LYS 3.8 0.3 + - - -
103C THR* 4.7 6.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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