Contacts of the helix formed by residues 65 - 82 (chain C) in PDB entry 1ZS4
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 65 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 5.2 10.9 + - - +
19C ASN* 6.1 1.2 - - - +
20C LYS* 2.7 40.6 + - - +
23C MET* 6.1 2.2 - - + +
63C VAL 3.4 4.3 + - - +
64C ASP* 1.3 75.3 + - - +
66C ASP* 1.3 64.9 + - - +
68C ALA* 3.4 5.8 + - - +
69C ARG* 3.0 20.6 + - - +
63D VAL* 3.9 20.8 - - - +
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Residues in contact with ASP 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE 5.3 0.2 - - - +
22B ALA* 4.1 18.9 - - + +
25B GLY* 5.2 0.3 - - - -
26B THR* 3.4 26.9 + - - -
40B ILE* 5.6 1.4 - - - +
41B SER* 5.5 2.6 + - - -
44B LYS* 2.9 30.5 + - - +
64C ASP* 3.0 17.1 + - - +
65C ASP* 1.3 76.9 - - - +
67C MET* 1.3 72.4 + - + +
69C ARG* 2.9 24.4 + - - +
70C LEU* 3.0 15.1 + - - +
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Residues in contact with MET 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.0 20.0 - - + -
73A GLN* 4.2 26.5 - - + +
74A VAL* 4.5 6.6 - - + +
77A ILE* 3.5 23.3 - - + +
22B ALA 3.5 25.1 - - - +
25B GLY* 5.8 2.7 - - - -
63C VAL* 4.8 0.7 - - + -
64C ASP* 3.0 32.4 + - + +
66C ASP* 1.3 80.1 - - + +
68C ALA* 1.3 57.6 + - - +
70C LEU* 3.2 20.0 + - + +
71C ALA* 2.8 28.2 + - - +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 4.3 0.6 - - - +
63C VAL* 4.2 8.7 - - + -
64C ASP 2.9 18.0 + - - +
65C ASP* 3.6 7.0 - - - +
67C MET* 1.3 76.8 - - - +
69C ARG* 1.3 63.7 + - - +
71C ALA* 3.2 3.0 + - - +
72C ARG* 2.9 33.6 + - - +
63D VAL* 3.6 30.3 - - + -
67D MET* 3.9 16.7 - - + +
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 3.2 31.1 + - - +
18B LEU* 3.5 43.4 - - - +
19B ASN* 2.6 28.3 + - - +
22B ALA* 4.5 7.6 - - - -
65C ASP 3.0 12.1 + - - +
66C ASP* 2.9 13.7 + - - +
68C ALA* 1.3 78.4 - - - +
70C LEU* 1.3 63.7 + - - +
72C ARG* 3.1 15.0 + - + +
73C GLN* 3.0 39.3 + - + +
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.2 8.3 - - + -
74A VAL* 4.0 12.6 - - + -
19B ASN* 3.9 19.3 - - - +
22B ALA* 3.8 33.4 - - + +
23B MET* 4.0 20.4 - - + -
67B MET* 3.9 24.0 - - - -
70B LEU* 4.2 10.1 - - + -
66C ASP 3.0 4.2 + - - +
67C MET* 3.5 30.1 - - + +
69C ARG* 1.3 80.4 - - - +
71C ALA* 1.3 57.7 + - - +
73C GLN* 3.3 3.8 + - - +
74C VAL* 2.8 36.4 + - - +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.6 21.3 - - + +
77A ILE* 3.7 28.5 - - + -
78A LEU* 3.8 11.6 - - + +
67C MET 2.8 16.5 + - - +
68C ALA 3.5 5.4 - - - +
69C ARG 3.2 0.2 - - - -
70C LEU* 1.3 76.1 - - - +
72C ARG* 1.3 58.0 + - - +
74C VAL* 3.5 1.3 + - - +
75C ALA* 2.9 30.8 + - - +
67D MET* 3.9 7.2 - - - -
70D LEU* 4.5 2.7 - - - -
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Residues in contact with ARG 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA* 2.9 24.2 + - - +
69C ARG* 3.1 14.5 + - - +
71C ALA* 1.3 77.7 - - - +
73C GLN* 1.3 62.6 + - + +
75C ALA* 3.4 2.6 + - - +
76C ALA* 3.0 23.0 + - - +
63D VAL* 4.8 8.7 - - - +
66D ASP* 3.3 33.9 + - - +
67D MET* 3.7 22.6 - - + +
70D LEU* 3.9 18.5 - - + +
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Residues in contact with GLN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 4.0 8.6 + - - -
19B ASN* 3.0 40.9 - - - +
67B MET* 3.9 16.0 - - + +
69C ARG* 3.0 36.9 + - + +
70C LEU* 3.6 8.1 - - - +
72C ARG* 1.3 76.4 - - + +
74C VAL* 1.3 64.0 + - - +
76C ALA* 3.2 8.9 + - - +
77C ILE* 3.1 30.2 + - + +
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 4.1 10.5 - - + -
78A LEU* 3.9 7.6 - - + -
67B MET* 3.9 17.3 - - + -
70B LEU* 3.9 23.1 - - + -
71B ALA* 4.0 13.9 - - - -
74B VAL* 3.9 30.1 - - + -
70C LEU 2.8 20.2 + - - +
71C ALA 3.8 3.1 - - - +
73C GLN* 1.3 74.5 - - - +
75C ALA* 1.3 62.1 + - - +
77C ILE* 3.0 10.0 + - - +
78C LEU* 2.8 36.3 + - + +
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.4 4.9 - - + +
71C ALA 2.9 18.6 + - - +
72C ARG 3.7 4.3 - - - +
73C GLN 3.3 0.2 - - - -
74C VAL* 1.3 77.5 - - - +
76C ALA* 1.3 57.9 + - - +
78C LEU* 3.3 3.0 + - - +
79C THR* 2.8 36.3 + - - +
70D LEU* 3.9 25.4 - - + -
74D VAL* 3.6 28.5 - - + -
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ARG 3.0 13.3 + - - +
73C GLN* 3.4 11.9 - - - +
74C VAL 3.2 0.2 - - - -
75C ALA* 1.3 78.0 - - - +
77C ILE* 1.3 57.1 + - + +
79C THR* 3.3 4.3 + - - -
80C ASN* 2.8 40.2 + - + +
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B MET* 3.8 37.5 - - + +
68B ALA* 4.9 4.0 - - - +
71B ALA* 3.6 25.8 - - + -
73C GLN* 3.1 18.2 + - + +
74C VAL 3.0 6.9 + - - +
76C ALA* 1.3 75.0 - - + +
78C LEU* 1.3 62.8 + - + +
81C LYS* 2.8 65.8 + - + +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 5.2 0.4 - - + -
71B ALA* 3.9 17.5 - - + +
74B VAL* 4.7 0.2 - - + -
75B ALA* 3.8 31.0 - - + +
78B LEU* 4.3 13.7 - - + -
74C VAL* 2.8 38.0 + - + +
75C ALA* 3.8 4.9 - - - +
77C ILE* 1.3 77.6 - - + +
79C THR* 1.3 61.7 - - - +
81C LYS 4.7 5.8 - - - +
74D VAL* 3.9 30.1 - - + -
77D ILE* 3.8 16.6 - - + +
78D LEU* 4.4 13.7 - - + +
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ALA* 2.8 21.9 + - - +
76C ALA* 3.8 4.9 - - - -
78C LEU* 1.3 79.5 - - - +
80C ASN* 1.3 76.0 + - - +
81C LYS 5.3 0.4 - - - +
73D GLN* 5.5 3.1 - - - +
74D VAL* 4.7 9.4 + - - +
77D ILE* 4.1 32.3 - - + +
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Residues in contact with ASN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ALA* 2.8 24.0 + - - +
79C THR* 1.3 96.9 + - - +
81C LYS* 1.3 59.1 + - - +
82C LYS* 3.6 16.1 + - - +
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Residues in contact with LYS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ALA* 5.7 10.5 - - + +
76C ALA 4.1 0.2 + - - -
77C ILE* 2.8 52.1 + - + +
78C LEU 4.7 5.2 - - - +
79C THR 5.3 0.3 - - - +
80C ASN* 1.3 72.9 - - - +
82C LYS* 1.3 69.1 + - - +
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Residues in contact with LYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 4.4 12.0 + - - +
81C LYS* 1.3 87.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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