Contacts of the helix formed by residues 74 - 83 (chain A) in PDB entry 1Z0F
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 ARG 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLN* 2.8 24.4 + - + +
71A GLU 4.3 0.2 - - - +
73A PHE* 1.3 73.7 - - + +
75A ALA* 1.3 60.0 + - - +
76A VAL* 4.6 2.7 - - + +
77A THR* 3.3 20.1 + - - +
78A ARG* 2.9 31.2 + - - +
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Residues in contact with ALA 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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73A PHE 4.0 2.4 + - - -
74A ARG* 1.3 72.1 - - - +
76A VAL* 1.3 64.8 + - + +
78A ARG* 3.3 26.5 - - - +
79A SER* 3.3 21.3 + - - -
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Residues in contact with VAL 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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65A TRP* 5.2 10.8 - - + -
74A ARG* 3.3 2.6 - - + +
75A ALA* 1.3 76.9 - - + +
77A THR* 1.3 65.6 + - - +
79A SER* 3.3 8.8 + - - +
80A TYR* 3.0 23.5 + - + +
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Residues in contact with THR 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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65A TRP* 3.2 34.0 - - + -
67A THR* 3.4 25.4 - - - +
70A GLN* 3.7 20.0 + - + +
71A GLU* 3.5 22.4 - - + +
74A ARG* 3.3 20.6 + - - +
76A VAL* 1.3 78.6 - - - +
78A ARG* 1.3 62.3 + - - +
80A TYR* 3.5 1.6 + - + +
81A TYR* 3.1 23.8 + - + +
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Residues in contact with ARG 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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71A GLU* 3.2 26.9 + - + +
72A ARG* 3.7 12.7 + - - +
73A PHE* 3.5 31.9 + - - +
74A ARG 2.9 10.6 + - - +
75A ALA* 3.3 33.5 - - - +
77A THR* 1.3 76.5 - - - +
79A SER* 1.3 56.8 + - - +
81A TYR* 3.4 5.9 - - - +
82A ARG* 3.3 32.4 + - + +
112A LEU* 4.8 6.2 - - + +
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Residues in contact with SER 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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13A LYS* 5.1 1.9 + - - -
75A ALA 3.3 10.0 + - - -
76A VAL* 3.3 13.0 + - - +
78A ARG* 1.3 75.8 - - - +
80A TYR* 1.3 67.1 + - - +
81A TYR 3.3 1.3 - - - -
82A ARG* 3.3 10.0 + - - +
83A GLY* 3.1 18.7 + - - -
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Residues in contact with TYR 80 (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 LYS* 3.5 49.2 - - + +
14A TYR 2.8 32.7 + - - -
15A ILE* 3.7 18.2 - - + -
48A PHE* 4.1 10.5 - + - -
63A GLN* 3.1 32.2 + - - +
64A ILE 3.8 1.2 + - - -
65A TRP* 3.5 41.2 + + + +
67A THR* 5.6 1.1 - - - -
76A VAL* 3.0 18.1 + - + +
77A THR 3.8 4.7 - - - +
79A SER* 1.3 75.9 + - - +
81A TYR* 1.3 64.1 + + - +
83A GLY 3.0 12.8 + - - -
84A ALA* 3.1 10.8 + - + -
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Residues in contact with TYR 81 (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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15A ILE* 3.4 31.4 - - + +
17A ILE* 3.8 19.4 - - - +
67A THR* 3.5 35.2 - - + +
69A GLY* 6.3 0.4 - - - -
71A GLU* 3.9 21.3 - - + -
77A THR 3.1 15.4 + - - +
78A ARG* 3.4 9.0 - - - +
80A TYR* 1.3 80.8 - + - +
82A ARG* 1.3 60.3 + - - +
84A ALA* 3.3 22.1 + - - +
105A TRP* 5.8 0.7 - - - -
108A ASP* 4.2 12.0 - - - +
109A ALA* 4.4 6.3 + - - -
112A LEU* 3.3 50.2 - - + +
113A THR* 3.3 26.3 - - + +
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Residues in contact with ARG 82 (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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78A ARG* 3.3 19.8 + - + +
79A SER* 3.3 13.4 + - - +
80A TYR 3.3 0.4 - - - -
81A TYR* 1.3 77.9 - - - +
83A GLY* 1.3 56.2 + - - +
84A ALA 3.4 0.4 - - - -
110A ARG 5.1 0.4 + - - -
111A ASN* 3.2 26.8 + - - +
112A LEU* 3.4 23.5 + - - +
113A THR* 2.9 24.9 + - - +
114A ASN* 3.0 25.8 + - - +
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Residues in contact with GLY 83 (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 LYS* 4.0 18.5 + - - +
79A SER 3.1 9.4 + - - -
80A TYR 3.0 10.5 + - - -
82A ARG* 1.3 77.6 - - - +
84A ALA* 1.3 64.9 + - - +
85A ALA* 3.3 4.3 + - - +
114A ASN* 3.8 4.9 + - - -
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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