Contacts of the helix formed by residues 63 - 75 (chain C) in PDB entry 3IKH
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 ASP 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C GLY 3.3 0.4 - - - +
62C ASN* 1.3 77.8 - - - +
64C SER* 1.3 66.2 + - - +
65C ASN* 3.9 12.6 + - - +
66C GLY 2.8 21.0 + - - -
67C ALA* 3.1 13.2 + - - +
70C ARG* 4.9 0.7 + - - -
89C HIS* 3.5 26.0 + - + +
90C SER* 2.7 49.4 + - - +
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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
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64A SER* 4.4 18.4 - - - -
63C ASP* 1.3 75.2 - - - +
65C ASN* 1.3 67.4 + - - +
67C ALA* 3.3 7.9 + - - +
68C TRP* 3.0 23.2 + - - +
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Residues in contact with ASN 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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64A SER* 4.9 15.8 + - - -
11C VAL* 3.5 32.1 - - + +
34C GLN* 5.7 1.0 - - - +
63C ASP* 3.2 16.9 + - - +
64C SER* 1.3 86.9 + - - +
66C GLY* 1.3 57.9 + - - +
68C TRP* 3.1 13.9 + - - +
69C ILE* 2.8 35.2 + - - +
90C SER* 4.0 7.4 - - - -
92C THR* 3.8 23.6 - - + +
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Residues in contact with GLY 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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60C THR* 4.5 2.2 - - - -
61C GLY 3.6 10.1 - - - -
63C ASP* 2.8 15.8 + - - -
65C ASN* 1.3 77.4 - - - +
67C ALA* 1.3 60.6 + - - +
69C ILE* 3.3 5.1 + - - +
70C ARG* 3.0 38.4 + - - +
90C SER* 3.1 19.5 + - - -
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Residues in contact with ALA 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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63C ASP 3.1 11.0 + - - +
64C SER* 3.7 10.3 - - - +
65C ASN 3.3 0.2 - - - -
66C GLY* 1.3 76.7 - - - +
68C TRP* 1.3 63.0 + - - +
70C ARG* 3.5 21.2 + - - +
71C GLN* 3.0 24.5 + - - +
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Residues in contact with TRP 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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11C VAL* 3.6 37.2 - - + -
34C GLN* 4.0 17.5 - - + -
35C ASP* 3.9 29.6 - - - -
36C ILE* 3.7 22.0 - - + -
64C SER 3.0 13.3 + - - +
65C ASN* 3.4 13.5 - - - +
67C ALA* 1.3 74.6 - - - +
69C ILE* 1.3 65.2 + - - +
71C GLN* 3.1 16.4 + - - +
72C GLN* 2.9 44.6 + - + +
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Residues in contact with ILE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 3.3 40.2 - - + +
10C THR* 3.8 28.0 - - - +
11C VAL* 4.0 9.4 - - + -
36C ILE* 3.9 25.7 - - + +
60C THR* 3.8 15.5 - - + -
65C ASN 2.8 23.6 + - - +
66C GLY* 3.6 5.8 - - - +
68C TRP* 1.3 74.6 - - - +
70C ARG* 1.3 59.0 + - - +
72C GLN* 3.2 2.0 + - - +
73C ILE* 2.9 31.2 + - + +
80C LEU* 5.2 0.7 - - + -
90C SER* 4.1 20.9 - - - +
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Residues in contact with ARG 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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60C THR* 3.0 35.8 + - + +
61C GLY 3.0 22.6 + - - -
62C ASN* 5.2 2.2 - - - +
63C ASP 4.9 1.4 + - - -
66C GLY 3.0 25.7 + - - +
67C ALA* 3.6 25.7 - - - +
69C ILE* 1.3 75.9 - - - +
71C GLN* 1.3 60.1 + - - +
73C ILE* 3.7 6.0 + - - +
74C LYS* 3.2 24.9 + - - +
80C LEU* 4.6 11.9 - - + -
83C ASP 4.3 17.3 - - - -
84C GLY 5.3 0.4 - - - -
85C HIS* 3.4 29.2 + - - +
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Residues in contact with GLN 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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67C ALA 3.0 18.8 + - - +
68C TRP* 3.4 17.3 - - - +
70C ARG* 1.3 74.9 - - - +
72C GLN* 1.3 74.0 + - - +
74C LYS* 3.3 21.9 + - - +
75C ASN* 3.7 11.6 + - - +
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Residues in contact with GLN 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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35C ASP* 5.5 2.8 + - - -
36C ILE* 3.6 22.8 - - + +
68C TRP* 2.9 40.7 + - + +
69C ILE 3.6 6.7 - - - +
71C GLN* 1.3 85.4 + - - +
73C ILE* 1.3 63.1 + - + +
75C ASN* 2.9 33.9 + - - +
76C GLU* 3.9 7.7 + - - +
271C LEU* 4.2 21.4 - - + +
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Residues in contact with ILE 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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9C ILE* 3.6 28.9 - - + -
36C ILE* 5.2 3.8 - - + -
45C ILE* 3.6 36.3 - - + -
56C LEU* 4.9 2.2 - - + -
69C ILE* 2.9 22.5 + - + +
70C ARG 4.0 3.8 - - - +
72C GLN* 1.3 77.9 - - + +
74C LYS* 1.3 58.6 + - - +
76C GLU* 2.9 30.7 + - + +
78C LEU* 4.7 21.7 - - + +
80C LEU* 3.8 34.1 - - + +
271C LEU* 6.0 0.7 - - + -
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Residues in contact with LYS 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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70C ARG 3.2 13.0 + - - +
71C GLN* 3.3 15.5 - - - +
72C GLN 3.1 1.0 - - - -
73C ILE* 1.3 81.0 - - - +
75C ASN* 1.3 62.6 + - - +
76C GLU 3.4 6.2 + - - +
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Residues in contact with ASN 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 GLN* 3.7 18.5 + - - +
72C GLN* 2.9 25.9 + - - +
74C LYS* 1.3 79.6 - - - +
76C GLU* 1.3 66.3 + - - +
77C PRO* 4.4 2.3 - - - +
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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