Contacts of the helix formed by residues 58 - 72 (chain A) in PDB entry 2MZD
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 PRO 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLY 3.3 11.6 - - - +
57A CYS* 1.4 80.6 - - - +
59A ILE* 1.2 59.5 + - - +
61A LYS* 3.4 40.8 - - + +
62A GLN* 3.4 27.0 + - + +
15B ASP* 3.8 18.2 - - - +
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Residues in contact with ILE 59 (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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42A VAL* 3.2 36.3 - - + -
45A HIS* 3.6 29.2 - - + +
46A THR* 3.8 5.6 - - - +
57A CYS* 2.7 10.9 + - - +
58A PRO* 1.2 75.1 - - - +
60A CYS* 1.4 74.2 - - - +
61A LYS 3.2 0.9 - - - -
62A GLN* 3.3 2.3 + - - -
63A LEU* 2.5 35.0 + - - +
15B ASP* 4.0 10.5 - - + +
16B ILE* 4.0 5.2 - - + +
19B TRP* 3.2 42.2 - - + +
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Residues in contact with CYS 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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45A HIS* 4.7 2.7 - - - -
46A THR* 3.0 41.2 + - + +
49A CYS* 4.8 1.3 - - - -
52A LYS* 3.1 48.0 - - + -
53A THR* 4.6 0.4 - - + -
57A CYS* 3.3 12.1 - - - -
59A ILE* 1.4 77.0 - - - +
61A LYS* 1.2 57.8 + - - +
63A LEU* 3.4 5.3 - - - +
64A ILE* 2.5 38.4 + - + +
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Residues in contact with LYS 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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52A LYS 4.2 4.0 - - - +
53A THR* 3.7 26.9 + - + -
56A GLY* 4.1 21.8 + - - -
58A PRO* 3.4 32.5 - - + +
59A ILE 3.2 0.8 - - - +
60A CYS* 1.2 82.2 - - - +
62A GLN* 1.3 65.6 + - + +
64A ILE* 3.7 3.6 - - + +
65A ALA* 2.8 26.9 + - - +
11B LEU* 4.7 10.9 - - + +
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Residues in contact with GLN 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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58A PRO* 3.4 27.3 + - + +
59A ILE 3.3 2.0 + - - -
61A LYS* 1.3 84.3 - - + +
63A LEU* 1.3 52.2 + - - +
65A ALA* 3.1 6.4 - - - +
66A LEU* 2.7 31.7 + - - +
11B LEU* 3.4 20.7 - - + +
12B SER* 3.4 35.2 + - - +
13B PRO* 5.8 0.3 - - - +
14B ASP* 4.0 10.7 + - - +
15B ASP* 3.7 28.8 + - + +
16B ILE* 3.0 17.2 - - + +
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Residues in contact with LEU 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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20A LEU* 3.2 39.5 - - + -
42A VAL* 3.5 21.1 - - + +
43A VAL* 3.6 15.9 - - - -
46A THR* 3.1 30.5 - - + +
59A ILE 2.5 22.1 + - - +
60A CYS* 3.4 4.7 - - - -
62A GLN* 1.3 71.0 - - - +
64A ILE* 1.3 56.3 + - + +
65A ALA 3.0 0.9 - - - -
66A LEU* 3.6 5.4 - - + -
67A ALA* 2.5 40.1 + - + +
82A PRO* 4.5 7.9 - - + -
83A PHE* 6.2 0.2 - - + -
16B ILE* 3.5 6.9 - - + +
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Residues in contact with ILE 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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46A THR* 5.4 0.2 - - + -
52A LYS* 5.6 2.7 - - - -
53A THR* 3.5 34.8 - - + +
60A CYS* 2.5 32.5 + - + +
61A LYS* 3.7 5.6 - - + +
63A LEU* 1.3 71.5 - - - +
65A ALA* 1.3 58.4 + - - +
67A ALA* 4.3 6.5 - - - -
68A ALA* 2.6 45.8 + - + +
83A PHE* 3.3 40.8 - - + -
87A ILE* 6.2 1.8 - - + -
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Residues in contact with ALA 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 LYS 2.8 19.1 + - - +
62A GLN* 3.1 9.6 - - + +
64A ILE* 1.3 79.4 - - - +
66A LEU* 1.3 58.0 + - - +
68A ALA* 4.9 0.2 - - - -
69A TYR* 2.8 52.2 + - + +
10B MET* 4.7 1.1 - - - -
11B LEU* 3.4 39.7 - - + +
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Residues in contact with LEU 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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13A ILE* 3.6 23.1 - - + -
16A ALA* 3.5 10.1 - - + +
17A ILE* 3.0 46.3 - - + +
20A LEU* 3.4 38.6 - - + -
62A GLN 2.7 21.8 + - - +
63A LEU* 3.2 4.0 - - + +
65A ALA* 1.3 73.4 - - - +
67A ALA* 1.3 55.9 + - - +
69A TYR 3.9 0.3 - - - -
70A HIS* 2.9 30.3 + - - +
10B MET* 4.0 7.1 - - - +
16B ILE* 3.2 27.1 - - + -
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Residues in contact with ALA 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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20A LEU* 4.1 6.3 - - - -
63A LEU* 2.5 31.6 + - + +
64A ILE* 4.1 2.9 - - - +
66A LEU* 1.3 73.8 - - - +
68A ALA* 1.3 50.8 + - - +
70A HIS* 3.0 10.0 + - - +
71A ALA* 2.6 31.0 + - - +
81A VAL* 3.7 9.9 - - + -
82A PRO* 3.0 31.4 - - + +
83A PHE 3.0 8.4 - - - +
84A CYS 4.2 0.3 + - - -
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Residues in contact with ALA 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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64A ILE* 2.6 33.3 + - + +
65A ALA* 4.3 1.1 - - - +
67A ALA* 1.3 68.5 - - - +
69A TYR* 1.3 62.6 + - + +
70A HIS 3.0 5.2 - - - -
71A ALA* 3.0 2.3 - - - +
72A LYS* 2.7 36.7 + - + +
83A PHE* 2.8 18.2 + - + +
87A ILE* 4.4 19.2 - - + +
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Residues in contact with TYR 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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64A ILE* 6.2 0.2 - - + -
65A ALA* 2.8 42.4 + - + +
68A ALA* 1.3 77.8 - - + +
70A HIS* 1.3 57.9 + - - +
72A LYS* 3.4 40.4 - - + +
73A HIS* 2.8 20.4 + - - -
9B LEU* 3.1 25.1 - - - +
10B MET* 3.3 33.2 - - + +
11B LEU* 3.3 32.2 - - + +
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Residues in contact with HIS 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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17A ILE* 3.3 27.4 - - + -
21A VAL* 3.3 25.5 - - + +
66A LEU 2.9 17.9 + - - +
67A ALA* 3.0 11.9 + - - +
69A TYR* 1.3 75.8 - - - +
71A ALA* 1.3 55.4 + - - +
72A LYS 3.0 1.6 - - - -
73A HIS* 2.7 24.2 + - - -
74A CYS* 2.7 60.6 + - + +
81A VAL* 4.5 4.9 - - + +
84A CYS* 3.8 19.2 - - - +
2B PRO 3.3 6.0 + - - -
3B SER* 3.3 26.5 + - - -
10B MET* 4.3 0.4 - - - +
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Residues in contact with ALA 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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67A ALA 2.6 17.1 + - - +
68A ALA 3.0 10.8 - - - +
70A HIS* 1.3 76.2 - - - +
72A LYS* 1.3 63.8 + - - +
73A HIS 2.9 2.1 + - - -
74A CYS 2.9 12.8 + - - +
83A PHE 3.2 14.4 - - - +
84A CYS* 3.4 19.1 - - - +
87A ILE* 3.6 13.9 - - + -
88A LYS* 2.9 27.8 - - + -
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Residues in contact with LYS 72 (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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68A ALA* 2.7 17.5 + - - +
69A TYR* 3.4 50.3 - - + +
71A ALA* 1.3 76.0 - - - +
73A HIS* 1.3 56.1 + - - +
75A GLN* 3.6 13.4 + - - -
87A ILE* 5.2 8.7 - - + +
88A LYS* 4.6 4.0 - - - +
9B LEU* 5.1 12.6 - - + -
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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