Contacts of the helix formed by residues 58 - 75 (chain C) in PDB entry 1CUN
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 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C GLU* 2.7 42.1 + - - -
21C TRP* 3.2 50.3 + + + -
54C GLU* 3.0 15.7 + - + +
55C LEU 3.7 5.8 - - - +
56C ALA 3.1 0.4 - - - -
57C ALA* 1.3 77.3 - - - +
59C GLU* 1.3 65.1 + - - +
60C PRO* 3.4 3.6 - - - -
61C ALA* 3.6 13.2 + - + +
62C ILE* 3.2 21.3 - - + +
94C TRP* 5.1 0.7 - - + -
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Residues in contact with GLU 59 (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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55C LEU 3.3 10.3 + - - +
56C ALA* 3.6 17.5 - - - +
58C HIS* 1.3 77.2 - - - +
60C PRO* 1.3 65.7 - - + +
62C ILE* 3.1 4.7 + - + +
63C GLN* 2.9 35.9 + - + +
94C TRP* 3.9 33.0 + - + +
98C LYS* 4.2 11.4 + - - +
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Residues in contact with PRO 60 (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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56C ALA 4.1 5.2 - - - +
57C ALA* 4.2 4.9 - - - +
58C HIS* 3.4 10.3 - - - +
59C GLU* 1.3 95.6 - - + +
61C ALA* 1.3 50.8 + - - +
63C GLN* 3.3 6.8 + - + +
64C SER* 2.8 35.9 + - - -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.5 23.9 - - - +
58C HIS* 3.6 17.1 + - + +
59C GLU 3.3 0.6 - - - -
60C PRO* 1.3 79.0 - - - +
62C ILE* 1.3 63.5 + - - +
64C SER* 3.4 8.7 + - - -
65C VAL* 3.2 25.9 + - - +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.5 13.0 - - + +
21C TRP* 4.7 3.1 - - + -
22C ILE* 4.6 3.6 - - + -
58C HIS* 3.2 41.5 - - + +
59C GLU* 3.1 8.8 + - + +
61C ALA* 1.3 72.8 - - - +
63C GLN* 1.3 67.1 + - + +
65C VAL* 3.1 14.1 + - - +
66C LEU* 3.1 24.0 + - + +
90C PHE* 4.0 27.4 - - + -
94C TRP* 4.0 54.5 - - + +
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Residues in contact with GLN 63 (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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59C GLU* 2.9 21.8 + - + +
60C PRO* 3.7 8.1 - - + +
62C ILE* 1.3 74.5 - - + +
64C SER* 1.3 65.0 + - - +
66C LEU* 3.4 25.5 + - - +
67C ASP* 2.7 62.1 + - - +
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PRO 2.8 18.2 + - - -
61C ALA* 3.4 10.8 - - - -
62C ILE 3.1 0.2 - - - -
63C GLN* 1.3 78.7 - - - +
65C VAL* 1.3 61.5 + - - +
67C ASP* 3.4 9.6 + - - +
68C THR* 3.1 27.8 + - - -
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 3.4 25.0 - - + -
14C ASP* 4.3 23.1 - - + -
15C MET* 4.2 13.2 - - + -
18C GLU* 4.3 19.3 - - + -
61C ALA 3.4 13.5 - - - +
62C ILE 3.1 8.4 + - - +
64C SER* 1.3 76.9 - - - +
66C LEU* 1.3 61.2 + - - +
68C THR* 3.2 5.0 + - - -
69C GLY 2.9 25.3 + - - -
87C LEU* 4.9 0.9 - - + -
90C PHE* 3.5 26.9 - - + -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 3.1 23.5 + - + +
63C GLN* 3.4 31.4 + - - +
65C VAL* 1.3 76.9 - - - +
67C ASP* 1.3 57.1 + - - +
69C GLY* 3.3 1.0 + - - -
70C LYS* 2.9 29.3 + - - +
87C LEU* 3.7 16.6 - - + +
90C PHE* 3.7 21.8 - - + -
91C VAL* 3.5 33.2 - - + -
94C TRP* 5.7 4.3 - - + -
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLN* 2.7 50.5 + - - +
64C SER* 3.6 9.6 - - - +
65C VAL 3.2 0.2 - - - -
66C LEU* 1.3 73.6 - - - +
68C THR* 1.3 65.6 + - - +
70C LYS* 3.2 7.4 + - - +
71C LYS* 3.0 23.9 + - - +
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Residues in contact with THR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C MET* 4.0 19.2 - - + -
11C PHE* 3.7 26.7 - - + -
64C SER* 3.1 14.0 + - - -
65C VAL* 3.7 7.8 - - - -
67C ASP* 1.3 77.5 - - - +
69C GLY* 1.3 59.0 + - - +
71C LYS* 3.2 6.6 + - - +
72C LEU* 2.8 50.8 + - + +
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Residues in contact with GLY 69 (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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11C PHE* 3.5 24.3 - - - -
65C VAL 2.9 11.6 + - - -
66C LEU 3.7 3.1 - - - -
68C THR* 1.3 77.3 - - - +
70C LYS* 1.3 51.6 + - - +
72C LEU* 3.7 2.6 - - - +
73C SER* 2.8 37.4 + - - -
83C ILE* 4.1 4.4 - - - +
87C LEU* 3.8 18.8 - - - +
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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
----------------------------------------------------------
66C LEU 2.9 13.7 + - - +
67C ASP* 3.4 12.8 - - - +
68C THR 3.2 0.2 - - - -
69C GLY* 1.3 75.7 - - - +
71C LYS* 1.3 58.0 + - - +
73C SER* 3.3 4.6 + - - -
74C ASP* 2.8 65.0 + - - +
87C LEU* 4.1 4.2 - - - +
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Residues in contact with LYS 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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7C MET* 4.7 22.0 - - - -
67C ASP 3.0 10.5 + - - +
68C THR* 3.6 9.6 - - - +
70C LYS* 1.3 81.2 - - - +
72C LEU* 1.3 63.1 + - + +
74C ASP* 3.6 6.0 + - - +
75C ASP* 3.2 48.0 + - - +
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Residues in contact with LEU 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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7C MET* 3.5 33.7 - - + -
8C VAL* 4.0 21.1 - - + +
11C PHE* 3.6 42.6 - - + -
68C THR* 2.8 30.7 + - + +
69C GLY 3.8 3.4 - - - +
71C LYS* 1.3 71.6 - - + +
73C SER* 1.3 66.6 + - - +
75C ASP* 3.7 3.5 + - - +
77C THR* 3.1 42.7 + - + +
83C ILE* 4.3 13.5 - - + -
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Residues in contact with SER 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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69C GLY 2.8 20.1 + - - -
70C LYS* 3.7 6.1 - - - -
72C LEU* 1.3 75.2 - - - +
74C ASP* 1.3 67.2 + - - +
76C ASN* 3.0 22.3 + - - -
80C LYS* 3.5 14.0 - - - +
83C ILE* 4.6 14.1 - - - +
84C GLN* 3.3 32.6 + - - +
87C LEU* 5.3 4.0 - - - -
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Residues in contact with ASP 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS* 2.8 60.9 + - - +
71C LYS* 3.9 5.9 + - - +
73C SER* 1.3 74.4 + - - +
75C ASP* 1.3 57.4 + - - +
76C ASN* 2.5 31.1 + - - +
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Residues in contact with ASP 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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71C LYS* 3.2 37.9 + - - +
72C LEU* 5.2 1.6 - - - +
73C SER 3.4 0.6 - - - -
74C ASP* 1.3 77.7 - - - +
76C ASN* 1.3 55.7 + - - +
77C THR* 2.6 36.9 + - + +
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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
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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