Contacts of the helix formed by residues 63 - 77 (chain C) in PDB entry 2HR3
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 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C MSE 1.3 74.4 - - - +
64C SER* 1.3 69.7 + - - +
65C SER* 2.7 10.5 + - - +
66C ASN* 2.9 21.5 + - + +
67C LEU* 3.2 9.5 + - - +
31D ASP* 4.8 0.8 + - - -
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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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57C ALA* 5.0 6.8 - - - +
62C MSE 3.6 2.2 + - - -
63C ARG* 1.3 70.4 - - - +
65C SER* 1.3 65.8 + - - +
67C LEU* 3.7 5.6 + - - +
68C ALA* 3.1 26.2 + - - +
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Residues in contact with SER 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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63C ARG* 2.7 10.9 + - - +
64C SER* 1.3 78.7 + - - +
66C ASN* 1.3 66.1 + - - -
67C LEU 3.1 1.8 - - - -
68C ALA* 3.1 17.9 + - - +
69C ALA* 3.2 13.2 + - - +
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Residues in contact with ASN 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 MSE 3.3 15.3 - - + +
63C ARG* 2.9 22.9 + - + +
65C SER* 1.3 73.9 - - - +
67C LEU* 1.3 58.9 + - - +
69C ALA* 3.7 16.4 - - - +
70C LEU* 3.7 9.4 - - - +
31D ASP* 4.0 10.5 - - - +
33D VAL* 3.5 30.6 - - + +
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Residues in contact with LEU 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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40C VAL* 4.2 21.1 - - + -
53C PRO* 3.0 38.6 - - + +
56C LEU* 3.4 19.5 - - + -
57C ALA* 3.7 10.1 - - + +
60C GLU* 6.3 0.4 - - + -
62C MSE 3.4 25.1 - - + +
63C ARG 3.2 8.6 + - - +
64C SER* 4.0 7.9 - - - +
65C SER 3.1 0.6 - - - -
66C ASN* 1.3 74.2 - - - +
68C ALA* 1.3 62.0 + - - +
69C ALA 3.2 2.0 - - - -
70C LEU* 3.3 3.6 + - + +
71C LEU* 2.9 53.0 + - + +
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Residues in contact with ALA 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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64C SER 3.1 15.2 + - - +
65C SER* 3.1 14.0 + - - +
67C LEU* 1.3 76.9 - - - +
69C ALA* 1.3 56.4 + - - +
71C LEU* 4.0 8.2 - - - +
72C ARG* 3.0 30.7 + - - +
82C ARG* 6.1 0.4 - - - +
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Residues in contact with ALA 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 SER 3.2 7.9 + - - +
66C ASN* 3.7 13.0 - - - +
68C ALA* 1.3 78.1 - - - +
70C LEU* 1.3 60.3 + - + +
72C ARG* 3.2 7.9 - - - +
73C GLU* 3.0 29.5 + - - +
33D VAL* 6.3 0.2 - - + -
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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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33C VAL* 4.9 2.7 - - + +
36C SER* 3.2 30.7 - - - +
37C GLN* 3.8 32.8 - - + +
40C VAL* 4.3 19.7 - - + -
62C MSE 3.8 18.4 - - + -
66C ASN 3.7 16.6 + - - +
67C LEU* 3.3 6.5 + - + +
69C ALA* 1.3 76.8 - - + +
71C LEU* 1.3 59.9 + - - +
72C ARG 3.2 0.2 - - - -
73C GLU* 3.5 6.5 - - - +
74C LEU* 2.7 43.1 + - + +
33D VAL* 4.2 7.9 - - + -
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Residues in contact with LEU 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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40C VAL* 4.0 17.5 - - + -
53C PRO* 3.7 32.1 - - + -
56C LEU* 4.2 9.2 - - + -
67C LEU* 2.9 51.1 + - + +
68C ALA* 4.0 7.2 - - - +
70C LEU* 1.3 75.0 - - - +
72C ARG* 1.3 62.5 + - - +
74C LEU* 4.7 0.9 - - + -
75C GLU* 3.0 26.4 + - - +
80C ILE* 3.6 25.8 - - + +
82C ARG* 3.5 23.7 + - - +
94C VAL* 4.4 6.3 - - + -
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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 ALA 3.0 20.9 + - - +
69C ALA* 3.2 8.3 - - - +
71C LEU* 1.3 76.5 - - - +
73C GLU* 1.3 62.7 + - - +
75C GLU* 3.3 6.3 + - - +
76C ARG* 3.2 20.7 + - - +
82C ARG* 4.7 2.7 - - - +
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Residues in contact with GLU 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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33C VAL* 4.7 9.4 - - - +
37C GLN* 2.5 36.8 + - - +
69C ALA 3.0 14.3 + - - +
70C LEU* 3.2 13.6 + - - +
72C ARG* 1.3 78.9 - - - +
74C LEU* 1.3 58.4 + - - +
76C ARG* 3.1 21.4 + - + +
77C GLY* 3.2 10.4 + - - -
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Residues in contact with LEU 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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37C GLN* 3.8 39.9 - - + +
40C VAL* 3.8 29.8 - - + -
41C LEU* 3.8 22.4 - - + -
70C LEU* 2.7 25.3 + - + +
71C LEU* 4.0 0.9 - - + +
73C GLU* 1.3 72.1 - - - +
75C GLU* 1.3 56.1 + - - +
77C GLY 3.7 1.6 + - - +
78C GLY 3.2 4.7 + - - -
79C LEU* 2.8 60.5 + - + +
80C ILE* 3.5 25.4 + - + -
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Residues in contact with GLU 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 LEU 3.0 18.3 + - - +
72C ARG* 3.6 6.3 - - - +
73C GLU 3.3 0.2 - - - -
74C LEU* 1.3 74.1 - - - +
76C ARG* 1.3 65.1 + - - +
78C GLY* 3.2 10.7 + - - -
80C ILE* 3.8 22.2 - - + +
82C ARG* 5.2 11.9 - - + -
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Residues in contact with ARG 76 (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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72C ARG 3.2 10.9 + - - +
73C GLU* 3.1 14.6 + - + +
75C GLU* 1.3 80.0 - - - +
77C GLY* 1.3 59.8 + - - +
78C GLY* 3.0 1.8 + - - -
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Residues in contact with GLY 77 (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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73C GLU 3.2 9.7 + - - -
74C LEU 3.7 3.3 + - - -
75C GLU 3.4 0.2 - - - -
76C ARG* 1.3 77.7 - - - +
78C GLY* 1.3 60.3 + - - +
79C LEU* 3.4 20.5 + - - +
99C GLU* 5.6 1.4 - - - +
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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