Contacts of the helix formed by residues 63 - 79 (chain C) in PDB entry 1TZY
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 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C LEU 4.0 1.9 + - - +
62C ILE* 1.3 78.8 - - - +
64C LYS* 1.3 65.9 + - - +
66C PRO* 3.3 32.3 - - + +
67C PHE* 3.1 19.5 + - - +
69C ARG* 5.0 4.4 - - - +
28D GLY* 2.8 32.1 + - - -
30D THR* 3.6 22.0 + - + +
33D ALA* 5.2 1.8 - - + +
1612D CL 3.8 22.9 - - + +
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Residues in contact with LYS 64 (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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60C LEU* 4.1 13.1 - - + +
62C ILE 3.4 2.5 + - - +
63C ARG* 1.3 72.2 - - - +
65C LEU* 1.3 76.3 + - + +
67C PHE* 3.3 2.4 + - - +
68C GLN* 3.0 23.2 + - - +
89C VAL* 5.4 0.7 - - - +
90C MET* 3.3 37.7 - - - +
93C GLN* 4.0 21.4 + - - +
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Residues in contact with LEU 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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64C LYS* 1.3 87.7 - - + +
66C PRO* 1.3 66.4 - - + +
68C GLN* 3.0 32.0 + - - +
69C ARG* 2.9 48.6 + - - +
72C ARG* 5.7 2.5 - - - +
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Residues in contact with PRO 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 5.3 0.9 - - + -
63C ARG* 3.3 53.4 - - + +
65C LEU* 1.3 93.5 - - + +
67C PHE* 1.3 65.7 + - - +
69C ARG* 3.3 25.4 + - + +
70C LEU* 3.0 23.4 + - - +
25D ASN* 4.9 3.5 - - - +
28D GLY* 3.5 26.2 - - - +
29D ILE* 4.7 4.7 - - + +
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Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 3.9 26.8 - - + +
63C ARG 3.1 16.5 + - - +
64C LYS 3.6 4.3 - - - +
65C LEU 3.3 0.2 - - - -
66C PRO* 1.3 77.8 - - - +
68C GLN* 1.3 58.1 + - - +
70C LEU* 3.0 15.7 + - + +
71C VAL* 2.9 42.2 + - + +
89C VAL* 3.8 14.4 - - + -
92C LEU 3.7 4.3 - - - -
93C GLN* 3.5 52.0 - - + +
96C SER* 3.6 31.4 - - - -
29D ILE* 4.6 2.7 - - + -
58D LEU* 4.9 1.6 - - + -
62D LEU* 3.9 26.0 - - + -
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Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LYS 3.0 16.5 + - - +
65C LEU* 3.0 33.1 + - - +
67C PHE* 1.3 73.8 - - - +
69C ARG* 1.3 62.9 + - - +
71C VAL* 3.3 3.5 + - - +
72C ARG* 2.9 57.6 + - - +
86C SER* 5.1 12.5 - - - +
89C VAL* 4.0 40.4 - - + +
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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
----------------------------------------------------------
63C ARG* 5.0 4.9 - - - +
65C LEU* 2.9 40.7 + - - +
66C PRO* 3.7 29.9 - - + +
67C PHE 3.3 0.2 - - - -
68C GLN* 1.3 77.0 - - - +
70C LEU* 1.3 63.1 + - - +
72C ARG* 3.9 22.0 - - - +
73C GLU 3.1 15.6 + - - -
25D ASN* 3.0 33.3 - - + +
28D GLY* 5.9 2.2 - - - -
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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
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66C PRO 3.0 12.1 + - - +
67C PHE* 3.0 13.1 + - + +
69C ARG* 1.3 74.7 - - - +
71C VAL* 1.3 67.0 + - - +
73C GLU* 3.2 4.7 + - - +
74C ILE* 3.1 40.0 + - + +
25D ASN* 3.8 15.2 - - + +
26D ILE* 3.7 49.4 - - + +
29D ILE* 3.9 20.2 - - + -
58D LEU* 4.3 3.1 - - + -
59D LYS* 4.7 4.9 - - - +
62D LEU* 3.4 28.7 - - + -
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE* 2.9 47.2 + - + +
68C GLN* 3.3 8.0 + - - +
70C LEU* 1.3 76.5 - - - +
72C ARG* 1.3 57.6 + - - +
74C ILE* 3.2 2.9 + - - +
75C ALA* 2.9 28.2 + - - +
84C PHE* 3.6 34.3 - - + -
89C VAL* 4.6 9.0 - - + -
92C LEU* 3.6 23.8 - - + -
62D LEU* 4.6 4.3 - - + -
66D ILE* 3.9 15.3 - - + +
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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
----------------------------------------------------------
65C LEU* 5.3 2.4 + - - +
68C GLN* 2.9 52.5 + - - +
69C ARG* 3.9 26.3 - - - +
71C VAL* 1.3 78.3 - - - +
73C GLU* 1.3 63.8 + - - +
75C ALA* 3.8 5.6 - - + +
76C GLN* 3.0 32.6 + - - +
82C LEU 5.3 7.4 - - - +
83C ARG* 6.1 2.7 - - - +
84C PHE* 4.8 17.7 - - + +
89C VAL* 6.6 0.2 - - - -
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Residues in contact with GLU 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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69C ARG 3.1 18.1 + - - +
70C LEU* 3.7 5.1 - - - +
72C ARG* 1.3 77.4 - - - +
74C ILE* 1.3 65.0 + - - +
76C GLN* 3.3 5.5 + - - -
77C ASP* 3.2 10.2 + - - +
23D ARG* 3.0 66.7 + - - +
24D ASP* 3.2 6.8 + - - -
25D ASN* 2.9 44.8 + - - +
26D ILE* 4.7 1.4 + - - +
59D LYS* 3.7 22.5 + - - -
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Residues in contact with ILE 74 (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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70C LEU* 3.1 34.4 + - + +
71C VAL 3.8 5.6 - - - +
73C GLU* 1.3 78.9 - - - +
75C ALA* 1.3 63.0 + - - +
76C GLN 3.2 0.5 + - - -
77C ASP* 3.3 21.2 + - + +
78C PHE* 3.5 27.6 - - + -
59D LYS* 4.1 29.2 - - + +
62D LEU* 3.7 28.7 - - + -
63D GLU* 4.0 21.3 - - + +
66D ILE* 3.8 17.5 - - + -
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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
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71C VAL 2.9 9.2 + - - +
72C ARG* 3.8 3.8 - - + +
74C ILE* 1.3 79.0 - - - +
76C GLN* 1.3 57.6 + - - +
78C PHE* 3.1 8.3 + - - +
79C LYS 3.0 28.3 + - - +
82C LEU* 4.3 10.7 - - + +
84C PHE* 3.2 42.2 - - + -
66D ILE* 4.0 12.1 - - + +
70D VAL* 4.7 6.3 - - + -
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Residues in contact with GLN 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 ARG* 3.0 27.1 + - - +
73C GLU* 4.6 0.4 - - - -
74C ILE 3.2 0.4 - - - -
75C ALA* 1.3 76.5 - - - +
77C ASP* 1.3 61.4 + - - +
78C PHE 3.4 0.3 + - - -
79C LYS* 3.6 15.7 + - - -
80C THR* 3.4 24.7 - - + +
81C ASP* 3.2 29.4 - - - +
82C LEU 5.1 5.9 + - - +
23D ARG* 3.6 18.8 - - - +
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Residues in contact with ASP 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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73C GLU* 3.2 14.4 + - - +
74C ILE* 3.3 13.2 + - + +
76C GLN* 1.3 77.4 - - - +
78C PHE* 1.3 70.1 + - + +
23D ARG* 2.5 32.6 + - - +
59D LYS* 5.9 0.5 + - - -
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Residues in contact with PHE 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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74C ILE* 3.5 33.0 + - + -
75C ALA* 3.1 6.7 + - - +
76C GLN 4.2 0.2 - - - -
77C ASP* 1.3 85.5 - - + +
79C LYS* 1.3 62.4 + - - +
63D GLU* 3.7 20.9 - - + -
66D ILE* 4.2 9.0 - - + -
67D ARG* 3.6 63.7 - - + -
70D VAL* 4.1 17.3 - - + -
74D GLU* 4.7 2.3 - - - +
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Residues in contact with LYS 79 (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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75C ALA 3.0 14.8 + - - +
76C GLN* 3.6 9.9 + - - +
78C PHE* 1.3 82.4 - - + +
80C THR* 1.3 78.0 + - - +
82C LEU* 3.2 39.1 + - + +
70D VAL* 5.4 0.2 - - + -
74D GLU* 3.5 23.3 - - + +
79D LYS* 6.5 1.1 - - + -
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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