Contacts of the helix formed by residues 58 - 77 (chain A) in PDB entry 1NZ4
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 SER 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.8 1.4 - - - -
49A LEU* 4.0 20.7 - - - +
54A GLU 4.2 2.5 - - - -
55A MET 3.4 12.5 + - - +
56A LYS 3.3 5.1 - - - +
57A ALA* 1.4 80.4 - - - +
59A GLU* 1.3 65.2 + - - +
60A ASP* 3.5 10.9 + - - +
61A LEU* 3.1 32.1 + - - +
62A LYS* 3.3 12.8 + - - +
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Residues in contact with GLU 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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56A LYS 5.0 4.0 - - - +
57A ALA 4.2 3.1 + - - +
58A SER* 1.3 72.9 + - - +
60A ASP* 1.3 60.5 + - - +
62A LYS* 3.2 40.8 + - - +
63A GLU* 2.7 40.0 + - + +
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 6.1 0.5 - - - +
46A PHE* 3.8 20.5 - - + -
58A SER* 3.2 9.1 + - - +
59A GLU* 1.3 80.9 - - - +
61A LEU* 1.4 62.5 + - - +
63A GLU* 3.4 11.1 + - - +
64A HIS* 3.0 17.7 + - - +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN* 4.5 16.6 - - + +
29A LEU* 3.7 25.9 - - + +
30A ILE* 4.7 6.3 - - + -
33A PHE* 4.0 23.8 - - + -
40A LEU* 5.7 0.2 - - + -
46A PHE* 3.8 22.4 - - + -
49A LEU* 4.4 10.3 - - + -
55A MET* 4.0 37.2 - - + +
58A SER* 3.1 25.0 + - - +
59A GLU 3.2 0.2 - - - -
60A ASP* 1.4 76.3 - - - +
62A LYS* 1.3 62.4 + - + +
64A HIS* 3.1 6.4 + - - +
65A GLY 3.0 22.9 + - - -
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Residues in contact with LYS 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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22A ALA* 3.8 31.3 - - + +
23A GLY* 5.4 0.9 - - - +
26A GLN* 3.0 35.3 + - + +
56A LYS 4.9 9.8 + - - -
58A SER 3.3 7.5 + - - +
59A GLU* 3.2 42.7 + - - +
61A LEU* 1.3 81.8 - - + +
63A GLU* 1.3 64.8 + - + +
65A GLY* 3.2 3.4 + - - +
66A THR* 3.0 25.3 + - - -
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Residues in contact with GLU 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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59A GLU* 2.7 26.4 + - + +
60A ASP* 3.9 11.2 - - - +
62A LYS* 1.3 74.1 - - + +
64A HIS* 1.4 63.7 + - - +
66A THR* 3.2 12.7 + - + +
67A VAL* 3.0 27.0 + - + +
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Residues in contact with HIS 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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29A LEU* 4.1 11.7 - - + -
43A PHE* 3.6 27.2 - + - -
46A PHE* 3.8 24.2 - + + -
60A ASP 3.0 8.6 + - - +
61A LEU 3.1 7.6 + - - +
63A GLU* 1.4 77.5 - - - +
65A GLY* 1.3 55.6 + - - +
67A VAL* 3.1 14.4 + - + +
68A VAL* 3.0 49.3 + - + +
154A HEM 3.9 56.2 + + + -
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Residues in contact with GLY 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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25A GLY* 4.0 23.6 - - - -
26A GLN 4.6 0.2 - - - -
29A LEU* 3.6 19.6 - - - +
61A LEU 3.0 11.0 + - - -
62A LYS 3.2 4.7 + - - -
64A HIS* 1.3 73.9 - - - +
66A THR* 1.3 57.4 + - - +
68A VAL* 3.4 4.5 + - - +
69A LEU* 2.9 36.2 + - - +
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Residues in contact with THR 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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21A ILE* 4.3 18.5 - - + +
22A ALA* 3.2 26.5 - - + +
62A LYS 3.0 14.4 + - - -
63A GLU* 3.3 14.9 - - + +
64A HIS 3.1 0.4 - - - -
65A GLY* 1.3 75.2 - - - +
67A VAL* 1.3 56.1 + - + +
69A LEU* 3.4 1.0 + - - +
70A THR* 2.7 47.3 + - + +
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Residues in contact with VAL 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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63A GLU 3.0 17.4 + - - +
64A HIS* 3.1 19.7 + - + +
66A THR* 1.3 75.3 - - + +
68A VAL* 1.3 62.5 + - - +
70A THR* 3.2 12.6 - - + +
71A ALA* 3.1 23.2 + - - +
154A HEM 3.8 36.3 - - + -
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Residues in contact with VAL 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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28A VAL* 5.8 1.6 - - + -
29A LEU* 4.8 9.0 - - + -
64A HIS* 3.0 45.3 + - + +
65A GLY* 3.7 10.1 - - - +
66A THR 3.3 0.2 - - - -
67A VAL* 1.3 77.1 - - - +
69A LEU* 1.3 69.4 - - + +
71A ALA 3.4 0.5 + - - -
72A LEU* 3.1 22.5 + - - +
107A ILE* 4.5 13.9 - - + -
154A HEM 3.5 60.0 - - + +
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Residues in contact with LEU 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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14A TRP* 3.1 27.4 - - + -
17A VAL* 3.9 14.4 - - + -
21A ILE* 3.4 19.3 - - + +
24A HIS* 3.7 17.9 - - + +
25A GLY* 3.5 30.1 - - - +
28A VAL* 4.6 18.4 - - + -
65A GLY 2.9 16.4 + - - +
68A VAL* 1.3 84.2 - - + +
70A THR* 1.3 61.8 + - - +
72A LEU* 4.3 15.0 - - + -
73A GLY 2.9 24.1 + - - -
111A ILE* 4.9 8.7 - - + -
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Residues in contact with THR 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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14A TRP* 5.5 0.2 - - - -
21A ILE* 4.3 18.2 - - - +
66A THR* 2.7 37.6 + - + +
67A VAL* 3.2 20.6 - - + +
69A LEU* 1.3 76.4 - - - +
71A ALA* 1.3 61.0 + - - +
73A GLY* 3.5 0.8 + - - -
74A GLY* 3.1 19.8 + - - -
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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 VAL 3.1 16.0 + - - +
68A VAL 3.6 4.7 - - - +
70A THR* 1.3 74.7 - - - +
72A LEU* 1.3 64.8 + - - +
74A GLY* 3.3 3.5 + - - -
75A ILE* 3.1 32.8 + - + +
89A LEU* 5.3 5.6 - - + -
154A HEM 4.0 31.4 - - + -
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Residues in contact with LEU 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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14A TRP* 4.3 17.7 - - + -
68A VAL 3.1 17.0 + - - +
69A LEU* 3.8 11.0 - - + +
70A THR 3.3 0.2 - - - -
71A ALA* 1.3 75.5 - - - +
73A GLY* 1.3 54.8 + - - +
75A ILE* 2.9 7.8 + - + -
76A LEU* 2.8 60.7 + - + +
111A ILE* 4.0 28.7 - - + -
131A MET* 6.5 0.4 - - - -
135A LEU* 4.2 17.9 - - + -
138A PHE* 4.5 25.4 - - + -
154A HEM 4.2 20.8 - - + +
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Residues in contact with GLY 73 (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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14A TRP* 3.4 36.7 - - - -
69A LEU 2.9 12.2 + - - -
70A THR* 3.5 2.0 + - - -
71A ALA 3.3 0.2 - - - -
72A LEU* 1.3 75.3 - - - +
74A GLY* 1.3 56.3 + - - +
76A LEU* 3.2 4.2 + - - +
77A LYS* 3.0 39.7 + - - +
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Residues in contact with GLY 74 (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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70A THR 3.1 13.3 + - - -
71A ALA* 3.7 4.7 - - - -
72A LEU 3.2 0.2 - - - -
73A GLY* 1.3 76.0 - - - +
75A ILE* 1.3 63.0 + - - +
77A LYS* 3.7 11.6 + - - +
78A LYS* 3.6 17.7 + - - +
85A GLU* 5.0 5.2 - - - +
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Residues in contact with ILE 75 (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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71A ALA* 3.1 19.4 + - + +
72A LEU* 2.9 12.9 + - + +
74A GLY* 1.3 76.3 - - - +
76A LEU* 1.3 67.9 + - + +
78A LYS* 3.1 23.3 + - - +
79A LYS 4.0 1.7 + - - -
80A GLY 4.8 0.7 + - - -
82A HIS* 3.8 31.5 + - + +
85A GLU* 3.8 25.1 - - + -
86A LEU* 4.5 6.1 - - + -
89A LEU* 4.0 27.8 - - + -
138A PHE* 4.1 36.8 - - + -
154A HEM 5.4 1.6 - - + -
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Residues in contact with LEU 76 (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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7A TRP* 3.9 14.0 - - + -
10A VAL* 4.2 17.0 - - + -
11A LEU* 4.0 17.5 - - + +
14A TRP* 3.6 39.9 - - + -
72A LEU* 2.8 35.7 + - + +
73A GLY* 3.6 6.7 - - - +
75A ILE* 1.3 79.8 - - + +
77A LYS* 1.3 59.0 + - - +
79A LYS* 3.0 24.4 + - - +
131A MET* 4.5 7.4 - - - -
134A ALA* 4.1 31.0 - - + +
135A LEU* 5.0 3.6 - - + -
138A PHE* 5.8 2.5 - - + -
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Residues in contact with LYS 77 (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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11A LEU* 4.0 27.8 - - + +
14A TRP* 4.5 10.9 - - + +
18A GLU* 2.6 33.9 + - - -
73A GLY 3.0 19.4 + - - +
74A GLY* 3.9 9.0 - - - +
75A ILE 3.2 0.6 - - - -
76A LEU* 1.3 77.3 - - - +
78A LYS* 1.3 61.3 + - + +
79A LYS* 3.2 10.6 + - - +
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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