Contacts of the helix formed by residues 55 - 73 (chain C) in PDB entry 1C03
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 ASN 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLN* 3.3 13.4 - - - +
53C GLU* 2.7 33.6 + - + +
54C LYS* 1.3 74.8 - - - +
56C LEU* 1.3 65.1 + - - +
57C THR* 2.8 29.6 + - - -
58C GLU* 3.1 27.1 + - + +
59C LEU* 3.2 15.3 + - - +
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Residues in contact with LEU 56 (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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54C LYS 3.6 3.7 + - - +
55C ASN* 1.3 72.7 + - - +
57C THR* 1.3 57.4 + - - +
59C LEU* 3.9 6.5 - - + -
60C ASP* 3.1 24.4 + - - +
89C GLY* 3.4 32.5 - - - +
91C LYS* 4.2 15.0 - - + -
134C ASN* 4.1 32.5 - - + +
137C TYR* 4.5 13.0 - - + -
138C LEU* 3.4 35.9 - - + -
141C ILE* 3.9 19.5 - - + -
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Residues in contact with THR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASN* 2.8 14.4 + - - -
56C LEU* 1.3 75.4 - - - +
58C GLU* 1.3 63.3 + - - +
60C ASP* 3.0 11.6 + - + +
61C ASN* 2.9 45.5 + - - +
89C GLY 5.5 0.2 - - - -
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLN* 3.5 35.7 + - - +
53C GLU* 4.5 3.6 - - - +
55C ASN* 3.1 25.8 + - - +
57C THR* 1.3 79.2 - - - +
59C LEU* 1.3 57.4 + - - +
61C ASN* 3.0 19.9 + - - +
62C LEU* 2.9 44.4 + - + +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C MET* 3.6 41.6 - - + +
49C GLN* 3.9 17.9 - - + -
50C LEU* 3.9 22.7 - - + +
55C ASN 3.2 15.7 + - - +
56C LEU* 4.1 8.7 - - + +
57C THR 3.4 0.2 - - - -
58C GLU* 1.3 75.6 - - - +
60C ASP* 1.3 56.2 + - - +
62C LEU* 4.2 5.3 - - + +
63C GLY 3.1 19.4 + - - -
85C ILE* 3.4 20.1 - - + +
89C GLY* 5.9 0.2 - - - -
138C LEU* 3.9 14.6 - - + -
141C ILE* 3.9 36.3 - - + -
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU 3.1 15.3 + - - +
57C THR* 3.0 17.4 + - + +
59C LEU* 1.3 76.5 - - - +
61C ASN* 1.3 63.1 + - - +
63C GLY 3.4 0.9 + - - -
64C HIS* 2.9 24.9 + - - +
85C ILE 5.1 0.7 - - - -
86C GLN* 3.1 36.0 - - - +
89C GLY* 4.9 1.6 - - - +
90C ARG* 2.8 45.1 + - - +
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Residues in contact with ASN 61 (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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57C THR* 2.9 31.7 + - - +
58C GLU* 3.6 25.6 + - - +
60C ASP* 1.3 81.4 - - - +
62C LEU* 1.3 57.2 + - + +
64C HIS* 2.9 13.8 + - + +
65C PHE* 2.9 28.6 + - - +
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Residues in contact with LEU 62 (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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42C THR* 4.5 14.6 + - + -
45C GLN* 4.0 35.4 - - + +
46C MET* 3.5 51.5 - - + +
49C GLN* 4.8 6.3 - - - +
58C GLU* 2.9 34.4 + - - +
59C LEU* 4.2 6.1 - - + +
61C ASN* 1.3 72.1 - - + +
63C GLY* 1.3 66.3 + - - +
65C PHE* 3.4 10.0 + - + +
66C LEU* 3.2 21.0 + - - +
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Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C MET* 3.5 13.8 - - - +
59C LEU 3.1 15.9 + - - -
60C ASP 3.7 2.2 - - - -
61C ASN 3.3 0.2 - - - -
62C LEU* 1.3 79.7 - - - +
64C HIS* 1.3 58.8 + - - +
67C LYS* 3.2 25.3 + - - +
82C CYS* 3.5 18.1 - - - +
85C ILE* 4.5 3.4 - - - -
86C GLN* 3.9 11.9 - - - -
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Residues in contact with HIS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 4.3 4.0 + - - -
26A ASP 5.3 2.0 - - - -
27A PHE* 3.7 41.4 - + - -
30A GLY* 5.3 6.4 - - - -
31A LEU* 4.9 12.6 - - + +
34A GLN* 5.0 11.2 + - - -
60C ASP* 2.9 9.7 + - - +
61C ASN* 2.9 17.2 + - + +
63C GLY* 1.3 76.5 - - - +
65C PHE* 1.3 67.3 + - + +
67C LYS* 3.5 2.3 + - - +
68C GLY* 3.3 15.2 + - - -
86C GLN* 3.2 25.6 + - - +
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Residues in contact with PHE 65 (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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34A GLN* 5.6 9.9 - - - +
38C GLN* 3.4 40.8 - - + -
42C THR* 3.5 34.1 - - + -
61C ASN 2.9 11.6 + - - +
62C LEU* 3.6 12.8 - - + +
64C HIS* 1.3 80.6 - - + +
66C LEU* 1.3 69.4 + - + +
68C GLY* 3.1 13.2 + - - -
69C SER* 3.2 26.4 + - - -
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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
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35C PHE* 3.5 28.3 - - + -
39C ALA* 4.0 17.9 - - + +
42C THR* 3.1 27.1 - - + +
43C PHE* 3.4 34.5 - - + -
46C MET* 4.5 5.6 - - + -
62C LEU 3.2 12.7 + - - +
65C PHE* 1.3 83.2 - - + +
67C LYS* 1.3 51.9 + - - +
69C SER* 4.0 5.6 - - - +
70C SER* 2.5 38.3 + - - -
78C ILE* 4.7 5.2 - - + -
82C CYS* 3.7 20.6 - - - -
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Residues in contact with LYS 67 (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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20A MET* 3.2 35.3 + - + -
24A ASP* 3.1 34.1 + - - +
27A PHE* 3.9 16.8 - - + -
63C GLY 3.2 18.8 + - - +
64C HIS* 3.7 4.7 - - - +
65C PHE 3.2 0.8 - - - -
66C LEU* 1.3 76.6 - - - +
68C GLY* 1.3 58.2 + - - +
70C SER* 3.3 5.0 + - - -
71C ALA* 2.9 32.2 + - - +
79C ALA* 4.0 11.6 - - + +
82C CYS* 3.8 11.1 - - + -
83C GLU* 3.0 37.2 + - + +
86C GLN* 3.4 17.2 - - - +
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Residues in contact with GLY 68 (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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17A ILE* 5.3 0.5 - - - +
27A PHE* 4.1 18.1 - - - -
31A LEU* 4.4 20.8 - - - +
64C HIS 3.3 6.8 + - - -
65C PHE 3.1 6.8 + - - -
67C LYS* 1.3 78.8 - - - +
69C SER* 1.3 64.0 + - - +
71C ALA* 3.5 1.2 + - - +
72C ALA* 3.1 24.7 + - - +
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Residues in contact with SER 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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35C PHE* 3.8 23.3 - - - -
38C GLN* 3.4 21.8 + - - -
65C PHE* 3.2 24.8 + - - -
66C LEU* 3.9 9.0 - - - -
68C GLY* 1.3 75.0 - - - +
70C SER* 1.3 62.9 + - - +
72C ALA* 3.2 18.8 + - - +
73C LEU* 3.4 13.3 + - - +
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Residues in contact with SER 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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35C PHE* 4.0 13.9 - - - -
66C LEU 2.5 23.6 + - - -
67C LYS* 3.3 8.1 + - - -
69C SER* 1.3 78.3 - - - +
71C ALA* 1.3 62.6 + - - +
73C LEU* 3.2 2.8 + - - -
74C GLY 3.1 4.3 + - - -
75C LEU* 2.9 49.5 + - - +
78C ILE* 4.0 18.8 - - - +
79C ALA* 3.6 11.3 + - - -
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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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17A ILE* 4.1 13.4 - - + +
20A MET* 3.7 30.5 - - + -
27A PHE* 4.8 1.1 - - + -
13C ILE* 3.6 19.9 - - - +
67C LYS 2.9 23.3 + - - +
68C GLY* 3.9 4.5 - - - +
70C SER* 1.3 78.1 + - - +
72C ALA* 1.3 60.9 + - - +
74C GLY* 3.5 9.0 + - - +
75C LEU 4.7 2.5 - - - +
76C GLN* 5.8 0.9 - - - +
79C ALA* 4.3 7.4 - - + +
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Residues in contact with ALA 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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13A ILE* 5.9 0.2 - - - +
17A ILE* 4.5 8.7 - - + -
31A LEU* 6.5 0.2 - - + -
72A ALA* 3.9 30.1 - - + +
13C ILE* 3.5 16.7 - - - +
17C ILE* 4.2 13.2 - - - +
68C GLY 3.1 18.2 + - - +
69C SER* 3.4 8.3 - - - +
70C SER 3.1 0.4 - - - -
71C ALA* 1.3 78.9 - - - +
73C LEU* 1.3 64.7 + - + +
74C GLY 3.3 1.3 - - - -
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Residues in contact with LEU 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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13C ILE* 4.3 4.0 - - - -
14C LEU* 3.5 31.4 - - + +
17C ILE* 5.1 9.0 - - + -
28C SER 5.7 0.2 - - - +
31C LEU* 4.0 33.0 - - + +
32C ILE* 4.1 24.9 - - + +
35C PHE* 3.5 40.4 - - + -
69C SER 3.4 8.9 + - - +
70C SER 3.2 7.3 + - - +
72C ALA* 1.3 84.1 - - + +
74C GLY* 1.3 61.3 + - - +
75C LEU* 3.5 17.9 + - + +
159C LEU* 6.4 0.2 - - + -
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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