Contacts of the helix formed by residues 59 - 71 (chain A) in PDB entry 2HAN
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 CYS 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ALA 5.0 1.3 - - - -
43A CYS* 3.9 15.5 - - - -
44A ARG 4.8 2.5 - - - -
49A CYS* 3.8 17.9 - - + -
50A ILE 5.8 0.4 + - - +
51A ILE* 3.7 5.7 - - + +
55A GLN 4.6 0.6 + - - -
56A ARG 3.9 5.6 + - - -
57A ASN 3.4 1.0 - - - -
58A ARG* 1.3 80.5 - - + +
60A GLN* 1.3 64.2 + - - +
61A TYR* 3.8 4.7 - - - -
62A CYS* 3.4 15.3 - - + -
63A ARG* 2.9 28.8 + - - +
352A ZN 2.3 37.0 - - - -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 3.3 21.3 - - + -
41A TYR* 3.6 41.5 + - + -
56A ARG 5.5 0.4 - - - -
57A ASN* 5.2 8.5 - - - +
58A ARG 4.2 0.4 + - - -
59A CYS* 1.3 72.1 - - - +
61A TYR* 1.3 62.3 + - - +
63A ARG* 3.3 2.5 + - - +
64A TYR* 3.0 22.3 + - - +
11D T 3.5 20.2 + - - -
12D T 3.0 30.3 + - - +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 6.0 2.2 - - + -
41A TYR* 3.3 37.7 - - + +
42A ALA* 3.8 6.2 + - - -
43A CYS* 3.5 38.1 - - + +
47A ARG* 3.8 46.6 + - + +
59A CYS* 3.3 1.4 - - - -
60A GLN* 1.3 77.7 - - - +
62A CYS* 1.3 65.0 + - - +
64A TYR* 3.4 3.9 + + - +
65A GLN* 2.9 69.2 + - + +
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Residues in contact with CYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A CYS* 3.8 0.7 - - - -
47A ARG* 3.6 24.5 - - - -
48A ASN* 4.4 0.2 - - - -
49A CYS* 3.3 32.1 - - + +
51A ILE* 3.8 13.8 - - + +
59A CYS* 3.3 6.4 + - - -
61A TYR* 1.3 85.1 - - - +
63A ARG* 1.3 56.9 + - - +
65A GLN* 3.4 4.9 + - - +
66A LYS* 3.0 29.3 + - - +
352A ZN 2.1 36.3 - - - -
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.5 2.9 - - + +
26A GLY* 3.2 22.0 - - - -
27A CYS* 3.2 21.6 - - - +
30A PHE* 3.5 46.0 - - + +
51A ILE* 3.5 25.9 - - + +
56A ARG* 3.5 34.7 - - - +
57A ASN* 3.2 17.8 + - - +
59A CYS 2.9 16.8 + - - +
60A GLN* 3.7 5.4 - - - +
62A CYS* 1.3 77.4 - - - +
64A TYR* 1.3 57.3 + - - +
66A LYS* 3.2 3.9 + - - +
67A CYS* 2.9 33.5 + - - -
12D T 4.5 3.2 + - - -
13D G 2.8 29.5 + - - -
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Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 3.5 12.5 - + + -
31A PHE* 3.6 32.3 - + - -
34A THR* 3.5 31.6 - - + -
35A VAL* 4.5 0.9 - - + -
39A LEU 5.4 4.0 - - - -
40A THR* 6.5 0.4 - - - -
41A TYR* 4.0 12.1 - + + -
60A GLN 3.0 17.3 + - - +
61A TYR* 3.8 5.2 - + - +
63A ARG* 1.3 71.5 - - - +
65A GLN* 1.3 79.8 + - - +
67A CYS* 3.0 15.1 + - - +
68A LEU* 3.1 36.7 + - + +
74A ARG* 2.6 41.8 + - - -
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 2.9 60.7 + - + +
62A CYS* 3.9 5.6 - - - +
64A TYR* 1.3 90.6 - - + +
66A LYS* 1.3 56.9 + - - +
68A LEU* 3.3 23.9 + - - +
69A THR* 3.0 39.7 + - + +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER 4.7 4.0 - - - -
9A ILE* 3.0 33.4 + - + +
51A ILE* 2.9 43.2 + - + +
62A CYS 3.0 17.7 + - - +
63A ARG* 3.6 5.2 - - - +
64A TYR 3.2 0.2 - - - -
65A GLN* 1.3 75.2 - - - +
67A CYS* 1.3 66.0 + - - +
69A THR* 3.3 10.5 + - - +
70A CYS* 3.0 32.2 + - - -
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Residues in contact with CYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.7 23.3 - - - +
27A CYS* 4.4 9.4 - - - -
30A PHE* 4.3 16.2 - - - -
31A PHE* 3.7 27.4 - - + -
63A ARG* 2.9 24.1 + - - -
64A TYR* 3.0 7.4 + - - +
66A LYS* 1.3 76.9 - - - +
68A LEU* 1.3 59.5 + - - +
70A CYS* 3.4 1.9 + - - +
71A GLY 3.3 4.9 + - - -
72A MET* 3.0 45.7 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.6 28.3 - - + -
64A TYR* 3.1 42.5 + - + +
65A GLN* 3.4 31.0 - - - +
66A LYS 3.2 0.2 - - - -
67A CYS* 1.3 77.5 - - - +
69A THR* 1.3 63.1 + - + +
71A GLY* 3.1 14.9 + - - -
72A MET 4.0 13.8 + - - +
74A ARG* 4.8 5.8 - - + -
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLN* 3.0 23.9 + - + +
66A LYS* 3.3 18.8 + - - +
68A LEU* 1.3 78.3 - - + +
70A CYS* 1.3 65.5 + - - +
71A GLY* 3.5 0.3 + - - -
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Residues in contact with CYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 3.4 46.8 + - - +
9A ILE* 3.8 13.9 - - + -
21A VAL* 3.4 14.4 - - + +
66A LYS* 3.0 30.6 + - - +
67A CYS 3.8 4.9 - - - +
68A LEU 3.2 0.4 - - - -
69A THR* 1.3 79.1 + - - +
71A GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR 3.8 0.9 - - - +
20A GLY* 4.5 2.6 - - - -
21A VAL* 3.2 12.2 - - - +
68A LEU 3.1 11.0 + - - -
69A THR 3.3 1.5 - - - -
70A CYS* 1.3 79.4 - - - +
72A MET* 1.3 66.6 + - - +
73A LYS* 3.4 25.4 - - - +
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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