Contacts of the helix formed by residues 61 - 72 (chain A) in PDB entry 1ZIO
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 ASP 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A VAL 4.7 0.9 - - - +
60A PRO* 1.3 69.4 - - - +
62A GLU* 1.3 62.7 + - + +
64A THR* 3.3 0.9 + - - -
65A ILE* 2.8 44.8 + - + +
89A THR* 3.0 27.7 + - - +
91A ALA* 4.4 13.7 - - + +
92A GLN* 2.7 37.5 + - + +
178A GLN* 5.2 3.1 + - - -
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Residues in contact with GLU 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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60A PRO* 3.5 3.4 + - + +
61A ASP* 1.3 80.0 - - + +
63A VAL* 1.3 64.5 + - + +
65A ILE* 3.6 15.1 + - - +
66A GLY* 3.1 19.9 + - - -
69A ARG* 5.4 4.5 + - - -
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Residues in contact with VAL 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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35A PHE* 4.5 0.7 - - + -
45A LEU* 3.2 35.0 - - + -
48A GLN* 4.4 18.6 - - + +
59A VAL* 3.9 16.4 - - + -
60A PRO* 3.4 21.0 + - + +
61A ASP 3.3 0.4 - - - -
62A GLU* 1.3 77.8 - - + +
64A THR* 1.3 64.3 + - - +
66A GLY* 3.4 2.6 + - - -
67A ILE* 3.3 22.7 + - - +
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Residues in contact with THR 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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31A THR* 4.0 7.9 - - + -
35A PHE* 3.5 23.8 - - + -
59A VAL* 3.5 12.6 + - - +
60A PRO 3.1 12.6 + - - -
61A ASP 3.3 6.2 + - - -
63A VAL* 1.3 74.9 - - - +
65A ILE* 1.3 66.5 + - - +
67A ILE* 3.1 23.2 - - - +
68A VAL* 3.3 8.1 + - - +
86A PHE* 3.8 22.2 - - + -
92A GLN* 4.0 8.1 - - - +
218A AP5 3.7 25.0 - - + +
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Residues in contact with ILE 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 ASP* 2.8 34.0 + - + +
62A GLU* 4.0 15.0 - - - +
64A THR* 1.3 71.6 - - - +
66A GLY* 1.3 56.5 + - - +
68A VAL* 3.3 2.6 + - - +
69A ARG* 3.0 52.7 + - - +
86A PHE* 4.2 12.3 - - + -
91A ALA* 4.0 11.2 - - + +
92A GLN* 4.1 17.3 - - + -
95A ALA* 3.3 29.2 - - + -
99A MET* 3.7 17.9 - - + +
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Residues in contact with GLY 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 GLU 3.1 14.4 + - - -
63A VAL* 3.8 4.0 - - - -
64A THR 3.1 0.4 - - - -
65A ILE* 1.3 77.9 - - - +
67A ILE* 1.3 60.8 + - - +
69A ARG* 3.4 20.7 + - - +
70A GLU* 3.2 30.5 + - - +
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Residues in contact with ILE 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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31A THR* 4.3 14.4 - - + +
34A MET* 4.4 26.1 - - + +
35A PHE* 3.5 35.0 - - + -
45A LEU* 3.5 29.8 - - + -
63A VAL 3.3 10.0 + - - +
64A THR 3.1 16.8 - - - +
66A GLY* 1.3 76.2 - - - +
68A VAL* 1.3 60.8 + - + +
70A GLU* 3.6 16.6 + - - +
71A ARG* 3.1 27.7 + - - +
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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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29A ILE* 5.7 1.6 - - + -
31A THR* 3.6 29.4 - - + -
34A MET* 4.5 5.8 - - + -
64A THR 3.3 13.8 + - - +
65A ILE 3.7 6.7 - - - +
66A GLY 3.2 0.6 - - - -
67A ILE* 1.3 77.4 - - + +
69A ARG* 1.3 58.9 + - - +
71A ARG* 3.3 4.6 + - - +
72A LEU* 2.9 43.7 + - + +
83A LEU* 4.4 10.1 - - + -
86A PHE* 3.7 37.7 - - + -
99A MET* 3.9 12.1 - - - -
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Residues in contact with ARG 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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62A GLU* 5.4 4.8 + - - -
65A ILE* 3.0 42.7 + - - +
66A GLY* 3.4 18.6 + - - +
68A VAL* 1.3 76.5 - - - +
70A GLU* 1.3 62.5 + - + +
72A LEU* 3.6 1.9 + - - +
73A SER* 3.4 21.7 + - - -
99A MET* 3.6 29.8 - - + +
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Residues in contact with GLU 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 GLY 3.2 16.1 + - - +
67A ILE* 3.6 19.9 - - - +
68A VAL 3.2 0.4 - - - -
69A ARG* 1.3 79.1 - - + +
71A ARG* 1.3 61.1 + - - +
73A SER* 2.7 23.3 + - - -
74A LYS* 3.9 9.2 - - - +
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Residues in contact with ARG 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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27A PRO* 3.6 19.4 - - - +
28A HIS 5.3 3.0 + - - -
29A ILE* 3.8 36.5 - - + +
34A MET* 4.4 16.1 - - - -
67A ILE 3.1 14.5 + - - +
68A VAL* 3.8 5.6 - - - +
70A GLU* 1.3 80.8 - - - +
72A LEU* 1.3 61.1 + - - +
73A SER 3.3 1.0 + - - -
74A LYS* 3.5 23.3 + - - +
76A ASP* 2.8 44.0 + - - -
77A CYS* 3.6 7.8 - - - -
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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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29A ILE* 3.7 27.6 - - + -
68A VAL* 2.9 24.6 + - + +
69A ARG* 4.1 4.3 - - - +
70A GLU 3.4 0.4 - - - -
71A ARG* 1.3 75.8 - - + +
73A SER* 1.3 59.9 + - - +
74A LYS 3.3 1.7 + - - +
77A CYS* 4.0 16.5 - - - +
81A PHE* 4.1 30.1 - - + -
83A LEU* 4.7 5.2 - - + -
96A LEU* 4.0 10.3 - - + -
99A MET* 4.0 28.0 - - + -
100A LEU* 4.0 24.0 - - + -
103A ILE* 3.6 24.2 - - + +
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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