Contacts of the helix formed by residues 62 - 72 (chain C) in PDB entry 4ICX
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 ARG 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ASP* 3.3 42.9 + - - +
8C LEU* 3.6 26.9 - - + +
60C ILE 3.9 0.6 + - - -
61C ASP* 1.3 77.7 + - - +
63C LYS* 1.3 60.8 + - - +
65C LEU* 3.3 15.6 - - + +
66C HIS* 3.3 19.2 + - - +
104C GLU* 3.4 22.6 + - - -
134C THR* 3.4 29.7 - - - +
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Residues in contact with LYS 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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61C ASP* 3.3 11.2 + - - +
62C ARG* 1.3 75.2 - - - +
64C ALA* 1.3 65.2 + - - +
66C HIS* 3.4 17.6 + - + +
67C GLN* 3.4 12.6 + - - +
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Residues in contact with ALA 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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35C ASP* 5.8 0.2 - - - +
60C ILE* 4.0 12.6 - - + -
61C ASP* 3.4 18.3 + - + +
62C ARG 3.4 0.4 - - - -
63C LYS* 1.3 75.0 - - - +
65C LEU* 1.3 57.8 - - - +
67C GLN* 3.3 6.6 + - - +
68C HIS* 2.7 51.0 + - + -
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Residues in contact with LEU 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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8C LEU* 3.6 28.7 - - + -
10C ILE* 4.6 0.9 - - + -
60C ILE* 3.8 22.8 - - + +
61C ASP 3.1 13.5 + - - +
62C ARG* 3.3 18.2 - - + +
63C LYS 3.2 0.2 - - - -
64C ALA* 1.3 74.7 - - - +
66C HIS* 1.3 59.3 + - - +
68C HIS* 3.3 3.2 + - - +
69C ARG* 2.9 59.5 + - - +
99C LEU* 4.2 23.7 - - + +
132C LEU* 3.8 24.5 - - + -
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Residues in contact with HIS 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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62C ARG 3.3 9.3 + - - +
63C LYS* 3.6 13.8 + - + +
64C ALA 3.3 0.4 - - - -
65C LEU* 1.3 78.1 - - - +
67C GLN* 1.3 71.8 + - - +
69C ARG* 3.4 10.7 + - + +
70C LEU* 3.1 45.7 + - + +
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Residues in contact with GLN 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 LYS 3.4 8.8 + - - +
64C ALA* 3.3 10.4 + - - +
65C LEU 3.3 0.6 - - - -
66C HIS* 1.3 91.3 + - - +
68C HIS* 1.3 58.6 + - + +
70C LEU* 3.4 21.5 + - - +
71C GLN* 3.0 65.0 + - - +
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Residues in contact with HIS 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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34C PHE* 3.8 7.2 - + - -
35C ASP* 3.4 36.6 + - - -
60C ILE* 3.3 21.7 - - + +
64C ALA* 2.7 34.5 + - + +
65C LEU 3.3 4.5 + - - +
67C GLN* 1.3 73.5 - - + +
69C ARG* 1.3 66.0 + - - +
72C ARG* 3.1 4.5 + - - -
73C THR* 2.9 65.3 + - + +
99C LEU* 3.8 22.5 + - + +
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Residues in contact with ARG 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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65C LEU* 2.9 46.8 + - + +
66C HIS* 3.6 10.0 - - + +
67C GLN 3.3 0.2 - - - -
68C HIS* 1.3 74.1 - - - +
70C LEU* 1.3 63.1 + - - +
72C ARG* 3.3 7.2 + - - +
99C LEU* 3.1 39.9 + - + +
100C ARG* 2.9 46.1 + - + +
102C ALA 2.6 28.7 + - - -
103C GLN* 5.8 0.4 - - - +
104C GLU* 5.9 0.4 + - - -
132C LEU* 3.7 12.7 - - - +
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Residues in contact with LEU 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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66C HIS* 3.1 34.2 + - + +
67C GLN* 3.7 28.3 - - - +
69C ARG* 1.3 77.0 - - - +
71C GLN* 1.3 62.4 + - + +
72C ARG* 4.7 0.5 - - - +
100C ARG* 2.9 24.8 + - - +
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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 GLN* 3.0 55.4 + - - +
68C HIS* 6.5 0.2 - - - -
70C LEU* 1.3 80.7 - - + +
72C ARG* 1.3 69.3 + - - +
73C THR* 3.5 13.1 + - - +
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Residues in contact with ARG 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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68C HIS 3.1 7.8 + - - -
69C ARG 3.3 2.6 + - - -
70C LEU 3.3 1.8 - - - -
71C GLN* 1.3 80.3 - - - +
73C THR* 1.3 66.0 + - - +
74C PRO* 3.1 8.5 - - - +
98C ASP* 3.0 48.8 + - - +
99C LEU 5.9 0.7 - - - +
100C ARG* 3.5 51.9 - - - +
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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
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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