Contacts of the helix formed by residues 64 - 78 (chain C) in PDB entry 1Z6T
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 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.7 14.7 - - - +
34C PHE* 4.0 10.2 - - - -
63C LYS* 1.3 77.0 - - - +
65C ASN* 1.3 63.8 + - - +
66C ASP* 3.0 33.6 + - - +
67C SER* 2.6 39.2 + - - -
68C TYR 3.4 8.7 + - - -
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Residues in contact with ASN 65 (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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1C MET* 3.2 10.1 - - - +
2C ASP* 2.8 51.9 + - - +
64C ASP* 1.3 75.8 - - - +
66C ASP* 1.3 64.9 + - - +
68C TYR* 3.3 19.0 - - - +
69C VAL* 3.5 11.8 + - - +
92C PRO* 3.2 21.9 - - + +
94C VAL* 5.8 4.8 - - - +
95C SER* 3.3 18.9 + - - +
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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
----------------------------------------------------------
34C PHE* 3.8 21.8 - - + -
64C ASP* 3.0 21.4 + - - +
65C ASN* 1.3 80.2 + - - +
67C SER* 1.3 58.6 + - - +
69C VAL* 3.3 4.8 + - - +
70C SER* 2.9 27.5 + - - -
94C VAL 5.3 0.2 - - - +
95C SER* 3.9 22.9 - - - +
98C SER* 5.5 8.9 - - - -
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Residues in contact with SER 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 3.7 4.9 - - - +
34C PHE* 3.2 25.6 - - - +
60C ILE* 4.8 3.6 - - - -
63C LYS* 3.7 29.4 - - - +
64C ASP* 2.6 31.0 + - - -
66C ASP* 1.3 75.0 - - - +
68C TYR* 1.3 59.5 + - - +
70C SER* 3.5 8.4 - - - -
71C PHE* 2.9 32.1 + - - +
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Residues in contact with TYR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.7 27.2 - - + +
5C ALA* 3.2 33.4 - - + -
8C CYS* 3.2 19.8 - - - -
9C LEU* 4.0 16.8 - - + -
60C ILE* 4.7 3.4 - - - -
64C ASP 3.4 4.0 + - - +
65C ASN* 3.3 12.9 + - - +
67C SER* 1.3 78.4 - - - +
69C VAL* 1.3 61.0 + - - +
71C PHE* 3.2 10.0 + + - +
72C TYR* 2.8 25.5 + - + +
87C LEU* 2.7 43.4 + - + +
90C GLY* 3.4 7.4 - - - -
91C ILE* 3.6 26.9 - - + -
92C PRO* 3.7 14.8 - - + -
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Residues in contact with VAL 69 (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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65C ASN 3.5 5.1 + - - +
66C ASP* 3.3 8.6 + - - +
68C TYR* 1.3 74.2 - - + +
70C SER* 1.3 55.5 + - - +
72C TYR* 3.1 14.3 + - + +
73C ASN* 2.8 51.2 + - - +
91C ILE* 4.0 22.9 - - + -
92C PRO* 4.1 7.6 - - + -
95C SER* 3.5 42.6 - - - +
96C SER 4.4 9.9 - - - +
98C SER* 5.4 9.6 - - - +
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C HIS* 5.6 0.3 - - - +
29C MET* 3.6 16.5 - - - +
32C ASP* 3.0 26.3 + - - +
34C PHE* 3.5 27.9 - - - -
66C ASP 2.9 17.5 + - - -
67C SER* 3.5 4.5 - - - -
69C VAL* 1.3 76.3 - - - +
71C PHE* 1.3 57.8 + - - +
73C ASN* 3.3 5.6 + - - +
74C ALA* 2.8 29.7 + - - +
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Residues in contact with PHE 71 (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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9C LEU* 4.2 17.9 - - + -
16C LEU* 4.3 9.2 - - + -
20C ILE* 4.6 5.6 - - + -
25C ILE* 3.9 26.7 - - + -
29C MET* 3.9 15.4 - - + +
56C LEU* 4.4 8.3 - - + -
57C ILE* 4.4 15.9 - - + -
60C ILE* 3.5 35.4 - - + -
67C SER 2.9 21.0 + - - +
68C TYR* 3.4 7.2 - + - +
70C SER* 1.3 71.0 + - - +
72C TYR* 1.3 63.1 + - - +
74C ALA* 3.6 1.3 - - - +
75C LEU* 3.0 49.9 + - + +
87C LEU* 3.8 27.4 - - + -
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Residues in contact with TYR 72 (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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68C TYR* 2.8 20.7 + - + +
69C VAL* 3.1 15.0 + - + +
71C PHE* 1.3 72.7 - - - +
73C ASN* 1.3 69.4 + - - +
75C LEU* 3.4 12.5 + - - +
76C LEU* 3.2 45.3 + - + +
84C ALA* 3.0 41.7 - - + +
85C ALA* 5.9 0.2 - - - -
87C LEU* 4.3 14.6 - - + -
88C HIS* 3.2 26.4 + - - +
91C ILE* 3.8 30.3 - - + -
108C SER* 3.5 27.3 - - - -
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Residues in contact with ASN 73 (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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32C ASP* 5.8 2.0 - - - +
69C VAL* 2.8 40.4 + - - +
70C SER* 3.8 5.6 - - - +
72C TYR* 1.3 77.5 - - - +
74C ALA* 1.3 60.3 + - - +
75C LEU 3.2 0.7 - - - -
76C LEU* 3.2 7.2 + - - +
77C HIS* 2.8 33.0 + - - +
96C SER 5.7 1.2 + - - -
98C SER* 5.4 2.8 + - - -
101C ASP* 4.7 6.7 + - - -
108C SER* 3.4 18.3 + - - -
111C ARG* 3.0 44.6 + - - +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 3.8 27.4 - - + +
28C HIS* 3.9 32.5 - - + +
29C MET* 4.2 3.1 - - + -
70C SER 2.8 20.2 + - - +
71C PHE* 3.6 7.4 - - - +
73C ASN* 1.3 73.2 - - - +
75C LEU* 1.3 57.6 + - - +
77C HIS* 3.4 2.1 + - - +
78C GLU* 3.0 34.7 + - - +
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 4.1 13.0 - - + -
20C ILE* 4.2 16.2 - - + -
25C ILE* 3.7 25.3 - - + +
71C PHE* 3.0 34.4 + - + +
72C TYR* 3.4 9.9 - - - +
74C ALA* 1.3 76.0 - - - +
76C LEU* 1.3 59.2 + - - +
78C GLU 3.4 1.6 + - - -
79C GLY 3.3 3.8 + - - -
80C TYR* 2.9 51.6 + - + +
83C LEU* 5.2 0.2 - - + -
84C ALA* 4.3 17.3 - - + +
87C LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 76 (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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72C TYR* 3.2 37.6 + - + +
73C ASN* 3.2 11.2 + - - +
75C LEU* 1.3 71.6 - - - +
77C HIS* 1.3 68.0 + - - +
78C GLU 3.0 1.6 - - - -
79C GLY* 2.9 15.0 + - - +
80C TYR 4.6 0.9 - - - +
81C LYS* 4.6 16.2 - - + +
84C ALA* 3.4 24.9 - - + -
108C SER* 3.6 41.3 - - - +
111C ARG* 4.0 24.0 - - + +
112C THR* 3.8 17.6 - - - +
115C CYS* 4.2 2.8 - - - +
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Residues in contact with HIS 77 (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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28C HIS* 3.1 42.7 + + + +
73C ASN 2.8 21.8 + - - +
74C ALA* 3.5 5.4 - - - +
76C LEU* 1.3 73.4 - - - +
78C GLU* 1.3 59.1 + - - +
79C GLY 3.5 0.7 + - - -
111C ARG* 3.8 27.7 - - + +
115C CYS* 4.8 4.0 - - - +
121C GLN* 3.2 46.4 + - + +
122C ARG* 5.0 11.1 + - + +
428C ARG* 4.3 1.6 - - - -
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Residues in contact with GLU 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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24C TYR* 3.3 14.4 - - + +
25C ILE* 3.9 18.8 - - + +
28C HIS* 2.5 28.5 + - - +
74C ALA 3.0 19.1 + - - +
75C LEU 3.4 3.6 + - - +
76C LEU 3.0 1.4 - - - -
77C HIS* 1.3 80.4 + - - +
79C GLY* 1.3 57.8 + - - +
80C TYR* 3.6 18.2 - - + -
121C GLN* 4.2 0.7 - - - +
428C ARG* 3.0 62.9 + - - +
430C GLY* 3.0 22.2 + - - +
433C PHE* 5.4 1.0 - - - -
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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