Contacts of the helix formed by residues 56 - 75 (chain A) in PDB entry 1NZ0
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 LYS 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLY* 1.3 74.1 - - - -
57A ALA* 1.3 67.9 + - - +
58A THR* 3.2 4.0 - - - +
59A ARG* 3.1 7.1 + - - +
60A ARG* 3.0 23.9 + - - +
62D LYS* 4.9 12.9 - - - +
5001D SO4 5.0 4.4 + - - -
5007D SO4 5.6 3.2 + - - -
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Residues in contact with ALA 57 (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* 1.3 77.4 - - - +
58A THR* 1.3 65.3 + - - +
60A ARG* 3.6 13.6 - - - +
61A ASN* 2.8 42.8 + - - +
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Residues in contact with THR 58 (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* 3.1 2.5 + - - +
57A ALA* 1.3 79.0 - - - +
59A ARG* 1.3 63.8 - - - +
61A ASN* 3.9 3.9 - - - +
62A LYS* 3.1 24.6 + - + +
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Residues in contact with ARG 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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54A PHE* 2.8 53.0 + - + +
55A GLY* 4.5 3.4 - - - -
56A LYS* 3.1 11.8 + - + +
58A THR* 1.3 81.9 - - + +
60A ARG* 1.3 62.1 + - - +
62A LYS* 3.4 7.2 + - - +
63A LEU 3.2 17.2 + - - -
93A SER* 2.8 48.3 + - - +
96A PHE* 3.6 21.4 - - + +
97A GLU* 2.8 41.6 + - - +
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Residues in contact with ARG 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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50A VAL* 2.9 38.7 + - + +
51A LYS 3.2 20.0 + - - -
52A ARG* 3.4 25.5 + - - +
54A PHE* 4.0 12.7 - - + -
55A GLY 3.0 24.6 + - - +
56A LYS* 3.0 23.8 + - - +
57A ALA* 3.3 11.7 - - - +
59A ARG* 1.3 74.8 - - - +
61A ASN* 1.3 73.4 + - - +
63A LEU* 3.3 3.9 + - - +
64A LYS* 3.0 29.4 + - - +
5009A SO4 2.5 46.8 + - - +
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Residues in contact with ASN 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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57A ALA* 2.8 36.6 + - - +
58A THR* 4.0 4.0 - - - +
60A ARG* 1.3 85.6 - - - +
62A LYS* 1.3 55.1 + - - +
64A LYS* 3.5 23.6 - - - +
65A ARG* 2.9 30.8 + - - +
68A ARG* 5.1 1.9 + - - -
5009A SO4 5.1 2.1 + - - -
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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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58A THR* 3.1 17.5 + - + +
59A ARG* 3.6 7.6 - - - +
60A ARG 3.3 0.2 - - - -
61A ASN* 1.3 70.5 - - - +
63A LEU* 1.3 68.4 + - - +
65A ARG* 3.3 18.7 + - - +
66A TRP* 3.1 63.9 + - - +
96A PHE* 4.0 18.7 - - + -
97A GLU* 6.2 1.6 - - - +
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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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32A PHE* 4.6 4.0 - - + -
48A ILE* 5.8 1.1 - - + -
50A VAL* 4.7 7.6 - - + -
54A PHE* 3.3 39.5 - - + -
59A ARG 3.2 4.2 + - - -
60A ARG* 3.3 7.4 + - - +
62A LYS* 1.3 80.2 - - - +
64A LYS* 1.3 61.9 + - + +
66A TRP* 3.2 5.2 + - + +
67A VAL* 3.0 37.9 + - + +
88A PRO* 3.4 35.4 - - + -
92A LEU* 4.1 18.6 - - + -
96A PHE* 3.9 19.7 - - + -
104A VAL* 5.0 6.1 - - + -
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Residues in contact with LYS 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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48A ILE* 3.8 26.6 - - + +
50A VAL* 3.8 25.4 - - + -
60A ARG* 3.0 19.1 + - - +
61A ASN* 3.5 27.4 - - - +
63A LEU* 1.3 76.0 - - - +
65A ARG* 1.3 58.2 + - - +
67A VAL* 3.3 2.5 + - - +
68A ARG* 2.9 54.2 + - - +
5009A SO4 4.1 24.7 - - - +
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Residues in contact with ARG 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 ASN 2.9 17.8 + - - +
62A LYS* 3.8 18.9 + - - +
63A LEU 3.3 0.4 - - - -
64A LYS* 1.3 74.0 - - - +
66A TRP* 1.3 88.4 - - - +
68A ARG* 3.3 22.4 + - - +
69A GLU* 3.0 71.9 + - + +
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Residues in contact with TRP 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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62A LYS* 3.1 46.2 + - + +
63A LEU* 3.2 8.5 + - - +
65A ARG* 1.3 111.0 - - - +
67A VAL* 1.3 64.5 - - + +
69A GLU* 3.3 9.9 + - - +
70A ILE* 3.0 34.2 + - + +
96A PHE* 4.0 19.1 - + - -
99A VAL 3.9 12.6 - - - -
100A ASP* 4.7 0.4 - - - -
101A PHE* 3.6 55.1 - + + -
104A VAL* 3.8 35.4 - - + -
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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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32A PHE* 4.2 20.6 - - + -
46A LEU* 4.3 6.1 - - + -
48A ILE* 3.7 30.7 - - + -
63A LEU* 3.0 37.2 + - + +
64A LYS* 3.8 3.1 - - - +
66A TRP* 1.3 77.8 - - + +
68A ARG* 1.3 61.5 + - - +
70A ILE* 3.3 2.5 + - - +
71A PHE* 3.0 23.4 + - + +
86A VAL* 4.1 18.4 - - + -
88A PRO* 6.5 0.2 - - + -
104A VAL* 5.3 2.0 - - + -
108A LEU* 3.9 24.0 - - + +
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Residues in contact with ARG 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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46A LEU* 4.2 13.9 - - + +
48A ILE* 3.9 14.5 - - + +
61A ASN 5.1 1.4 + - - -
64A LYS* 2.9 51.1 + - - +
65A ARG* 3.3 26.5 + - - +
67A VAL* 1.3 77.0 - - - +
69A GLU* 1.3 57.9 + - + +
71A PHE* 3.5 2.4 + - - +
72A ARG* 2.9 40.8 + - - +
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Residues in contact with GLU 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 ARG* 3.0 67.3 + - + +
66A TRP* 3.6 13.0 - - - +
68A ARG* 1.3 76.0 - - + +
70A ILE* 1.3 65.9 + - - +
72A ARG* 4.4 19.7 - - - +
73A ARG* 3.0 68.3 + - - +
101A PHE* 4.3 5.2 - - + -
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Residues in contact with ILE 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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66A TRP 3.0 26.9 + - - +
67A VAL* 3.7 3.8 - - - +
69A GLU* 1.3 73.8 - - - +
71A PHE* 1.3 68.5 + - - +
73A ARG* 5.1 0.7 - - - +
74A ASN* 2.9 34.7 + - - +
101A PHE* 3.9 25.8 - - + -
104A VAL* 4.1 14.1 - - + -
105A ARG* 3.6 33.4 - - + +
108A LEU* 3.9 25.1 - - + -
109A LEU* 3.7 30.7 - - + -
112A LEU* 4.9 1.1 - - + -
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Residues in contact with PHE 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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9A GLU* 4.9 7.9 - - + -
44A SER* 4.2 30.5 - - - -
46A LEU* 3.7 49.4 - - + -
67A VAL* 3.0 17.7 + - + +
68A ARG 3.8 2.5 - - - +
70A ILE* 1.3 81.6 - - - +
72A ARG* 1.3 65.0 + - + +
74A ASN 3.6 0.7 - - - -
75A LYS* 3.0 48.0 + - + -
78A ILE* 3.9 26.6 - - + +
84A ILE* 3.9 24.0 - - + -
108A LEU* 5.9 0.2 - - + -
112A LEU* 4.2 11.9 - - + -
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Residues in contact with ARG 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 ARG* 2.9 36.4 + - - +
69A GLU* 3.9 21.1 + - - +
70A ILE 3.3 0.2 - - - -
71A PHE* 1.3 78.6 - - + +
73A ARG* 1.3 72.3 + - + +
74A ASN 3.4 0.3 + - - -
75A LYS* 3.6 19.9 + - + +
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Residues in contact with ARG 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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69A GLU* 3.0 57.8 + - - +
70A ILE* 5.1 0.9 - - - +
72A ARG* 1.3 86.0 - - + +
74A ASN* 1.3 70.3 + - - +
75A LYS 3.5 1.0 + - - -
76A GLY 5.1 0.7 + - - -
101A PHE* 4.0 23.8 - - - -
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Residues in contact with ASN 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 ILE* 2.9 32.2 + - - +
71A PHE 3.6 2.7 - - - -
73A ARG* 1.3 87.4 - - - +
75A LYS* 1.3 63.0 + - - +
76A GLY 3.1 3.4 - - - -
77A VAL* 3.0 27.7 + - + +
78A ILE* 3.1 15.1 + - + +
105A ARG* 3.2 29.9 + - - +
109A LEU* 3.7 36.4 - - + +
113A LYS* 5.2 1.2 + - - -
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Residues in contact with LYS 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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43A TYR* 6.5 1.8 - - + -
44A SER* 5.4 8.5 - - - +
71A PHE* 3.0 40.5 + - + +
72A ARG* 3.7 15.5 - - + +
73A ARG 3.5 2.6 - - - -
74A ASN* 1.3 75.9 - - - +
76A GLY* 1.3 63.7 + - - +
77A VAL 3.2 0.5 + - - -
78A ILE* 3.3 24.2 - - + +
80A LYS* 3.4 14.0 + - + +
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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