Contacts of the helix formed by residues 67 - 81 (chain A) in PDB entry 1ZG3
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 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 4.3 21.1 - - + +
64A HIS* 2.8 25.8 + - + +
66A SER* 1.3 89.9 - - - +
68A VAL* 1.3 66.6 + - - +
69A ASN 3.3 2.5 - - - -
70A ILE* 2.9 39.8 + - + +
71A LEU* 2.9 12.6 + - - +
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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
----------------------------------------------------------
54A LEU* 3.2 32.4 - - + +
55A SER* 5.9 0.7 - - - -
58A ALA* 3.8 25.1 - - + -
63A LEU* 4.5 7.0 - - + +
64A HIS 3.7 3.3 + - - +
65A PRO* 3.6 26.2 - - + +
66A SER 3.4 0.6 - - - -
67A LYS* 1.3 77.6 - - - +
69A ASN* 1.3 64.2 + - - +
71A LEU* 3.0 11.9 + - - +
72A HIS* 2.9 19.8 + - - +
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO 4.8 0.6 + - - -
66A SER 3.3 25.1 + - - -
67A LYS 3.3 0.4 - - - -
68A VAL* 1.3 80.9 - - - +
70A ILE* 1.3 71.4 + - - +
72A HIS* 3.4 11.1 + - + +
73A ARG* 3.1 33.6 + - - +
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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
----------------------------------------------------------
66A SER 4.5 2.2 - - - +
67A LYS* 2.9 41.8 + - + +
69A ASN* 1.3 90.8 - - - +
71A LEU* 1.3 66.3 + - - +
73A ARG* 3.1 7.4 + - + +
74A PHE* 3.1 45.5 + - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.2 14.6 - - + -
41A ILE* 4.0 26.0 - - + -
54A LEU* 3.6 30.1 - - + +
57A LEU* 4.0 23.8 - - + -
58A ALA* 4.3 4.7 - - + +
61A LEU* 4.5 5.8 - - + -
63A LEU* 3.8 25.8 - - + -
67A LYS 2.9 10.5 + - - +
68A VAL 3.2 8.7 - - - +
70A ILE* 1.3 77.0 - - - +
72A HIS* 1.3 56.4 + - - +
74A PHE* 3.4 4.3 + - + +
75A LEU* 3.0 37.0 + - + +
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Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.1 24.4 - - + +
68A VAL 2.9 11.9 + - - +
69A ASN* 3.5 15.5 - - - +
71A LEU* 1.3 78.6 - - - +
73A ARG* 1.3 65.1 + - - +
75A LEU* 3.2 6.6 + - - +
76A ARG* 2.9 42.6 + - + +
100A ILE* 4.4 13.5 - - + -
102A TYR* 3.8 21.2 + - - -
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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 ASN* 3.1 25.4 + - - +
70A ILE* 3.1 10.0 + - + +
72A HIS* 1.3 82.8 - - + +
74A PHE* 1.3 68.1 + - + +
76A ARG* 3.3 44.6 + - - +
77A LEU* 3.3 13.5 + - - +
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A MET* 4.6 1.8 - - + -
32A ALA* 4.1 24.0 - - + -
35A SER* 3.1 40.6 - - - -
39A LEU* 5.2 10.1 - - + -
70A ILE* 3.1 36.9 + - + +
71A LEU* 3.8 9.9 - - + +
73A ARG* 1.3 80.8 - - + +
75A LEU* 1.3 57.5 - - + +
77A LEU* 3.4 6.0 + - - +
78A LEU* 2.9 41.3 + - + +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.9 29.6 - - + -
54A LEU* 4.1 13.9 - - + -
57A LEU* 3.8 23.8 - - + -
71A LEU* 3.0 25.8 + - + +
72A HIS* 3.4 6.3 - - - +
74A PHE* 1.3 75.1 - - - +
76A ARG* 1.3 60.0 + - - +
78A LEU* 3.9 2.4 - - + +
79A THR* 2.8 36.9 + - - -
84A PHE* 4.1 22.7 - - + -
102A TYR* 3.7 44.4 - - + +
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Residues in contact with ARG 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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72A HIS* 2.9 27.4 + - + +
73A ARG* 3.3 44.6 + - - +
75A LEU* 1.3 75.3 - - - +
77A LEU* 1.3 63.7 + - - +
79A THR* 3.4 5.0 + - - -
80A HIS* 3.0 22.5 + - + +
86A LYS* 4.3 22.2 + - - +
102A TYR* 5.2 2.0 + - - +
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Residues in contact with LEU 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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28A VAL* 5.3 9.0 - - + +
29A SER* 4.8 6.7 - - - -
32A ALA* 3.5 30.3 - - + -
73A ARG 3.3 9.3 + - - +
74A PHE* 3.8 7.2 - - - +
75A LEU 3.3 0.4 - - - -
76A ARG* 1.3 80.2 - - - +
78A LEU* 1.3 64.3 + - + +
80A HIS* 3.1 10.2 + - + +
81A ASN* 2.9 53.4 + - - +
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Residues in contact with LEU 78 (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 SER 5.4 0.9 - - - +
32A ALA* 3.9 35.2 - - + +
33A LEU* 3.9 11.0 - - + +
36A ALA* 3.7 26.5 - - + +
39A LEU* 6.2 0.2 - - + -
41A ILE* 4.8 5.8 - - + -
74A PHE* 2.9 32.7 + - + +
75A LEU* 3.9 3.8 - - - +
77A LEU* 1.3 78.6 - - + +
79A THR* 1.3 61.6 + - - +
81A ASN* 3.1 6.3 + - + +
82A GLY 3.1 5.5 + - - -
83A PHE* 2.9 47.9 + - + +
84A PHE* 3.8 23.6 - - + -
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Residues in contact with THR 79 (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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75A LEU 2.8 23.1 + - - -
76A ARG 3.7 4.0 - - - -
78A LEU* 1.3 73.3 - - - +
80A HIS* 1.3 68.8 + - - +
82A GLY* 3.0 13.5 + - - -
84A PHE* 3.5 38.3 - - - +
85A ALA* 4.7 0.2 - - - -
86A LYS* 3.4 41.7 - - + +
102A TYR* 3.7 14.9 - - - -
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Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 3.0 16.0 + - + +
77A LEU* 3.1 14.4 + - + +
79A THR* 1.3 77.8 - - - +
81A ASN* 1.3 72.0 + - - +
82A GLY* 3.1 4.0 + - - -
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Residues in contact with ASN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 4.0 19.0 - - - +
77A LEU* 2.9 43.9 + - - +
78A LEU* 3.1 7.1 + - + +
80A HIS* 1.3 90.7 + - - +
82A GLY* 1.3 60.3 + - - +
83A PHE* 3.5 26.8 - - + -
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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