Contacts of the helix formed by residues 57 - 71 (chain C) in PDB entry 3ZXT
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 SER 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C ARG* 3.4 42.0 - - - +
56C VAL* 1.3 82.9 - - - +
58C ARG* 1.3 61.9 + - - +
59C GLU* 3.4 8.7 + - - +
60C ASP* 3.1 31.2 + - - -
61C ILE* 3.2 20.1 + - - +
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Residues in contact with ARG 58 (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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46C LYS* 4.6 12.3 - - + +
47C ARG* 4.9 2.2 - - - +
57C SER* 1.3 71.7 - - - +
59C GLU* 1.3 64.4 + - - +
61C ILE* 3.5 11.1 + - + +
62C GLU* 2.8 55.2 + - + +
84C GLU* 2.6 38.2 + - - -
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Residues in contact with GLU 59 (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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57C SER* 3.3 7.9 + - - +
58C ARG* 1.3 77.1 - - - +
60C ASP* 1.3 64.5 + - - +
62C GLU* 3.2 9.7 + - - +
63C ARG* 2.9 43.7 + - + +
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Residues in contact with ASP 60 (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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56C VAL* 3.6 23.5 - - + +
57C SER* 3.1 20.1 + - - +
59C GLU* 1.3 83.7 - - - +
61C ILE* 1.3 56.7 + - - +
63C ARG* 3.0 36.6 + - - +
64C GLU* 3.0 29.5 + - - +
163C GLY 5.1 5.3 - - - +
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Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 4.1 33.2 - - + +
46C LYS* 4.5 16.8 - - + -
56C VAL* 3.8 21.1 - - + +
57C SER 3.2 19.0 + - - +
58C ARG* 3.8 10.3 - - + +
59C GLU 3.3 0.6 - - - -
60C ASP* 1.3 75.9 - - - +
62C GLU* 1.3 55.8 + - + +
64C GLU* 3.5 7.9 + - - +
65C VAL* 2.7 49.4 + - + +
82C VAL* 6.4 0.2 - - + -
89C VAL* 3.8 31.6 - - + -
91C LEU* 5.2 0.7 - - + -
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Residues in contact with GLU 62 (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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58C ARG* 2.8 62.9 + - + +
59C GLU* 3.7 7.0 - - - +
61C ILE* 1.3 75.3 - - + +
63C ARG* 1.3 61.1 + - - +
65C VAL* 3.8 7.5 - - + +
66C SER* 2.9 32.7 + - - -
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Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 2.9 22.5 + - + +
60C ASP* 3.0 50.5 + - - +
61C ILE 3.2 0.2 - - - -
62C GLU* 1.3 73.6 - - - +
64C GLU* 1.3 66.4 + - - +
65C VAL 3.2 0.2 + - - -
66C SER* 3.3 5.5 + - - -
67C ILE* 2.9 36.7 + - + +
163C GLY 3.6 22.2 + - - -
164C LEU* 4.6 2.0 - - - +
165C ALA 3.5 16.2 + - - +
166C HIS* 3.4 45.4 + - - +
167C LYS 5.9 0.4 - - - +
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Residues in contact with GLU 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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42C LYS* 2.7 27.9 + - - +
44C ILE* 4.0 10.7 - - + +
60C ASP 3.0 16.7 + - - +
61C ILE* 3.8 6.0 - - - +
63C ARG* 1.3 74.6 - - - +
65C VAL* 1.3 58.9 + - + +
67C ILE* 3.8 4.9 - - - +
68C LEU* 2.9 47.6 + - + +
91C LEU* 4.0 16.7 - - + +
93C LEU* 6.0 0.3 - - - +
161C ASP* 5.1 0.2 - - - -
162C PHE* 3.7 30.2 + - + +
163C GLY* 3.5 23.6 - - - -
165C ALA 5.6 0.2 - - - -
1278C ACP 3.5 10.9 + - - -
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Residues in contact with VAL 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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61C ILE* 2.7 33.3 + - + +
62C GLU* 3.8 7.6 - - - +
63C ARG 3.2 0.2 - - - -
64C GLU* 1.3 73.0 - - - +
66C SER* 1.3 57.5 + - - +
68C LEU* 2.9 10.5 + - - +
69C LYS* 2.8 36.4 + - + +
79C LEU* 4.3 6.2 - - + +
82C VAL* 3.8 30.1 - - + -
91C LEU* 4.1 25.1 - - + -
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Residues in contact with SER 66 (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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62C GLU 2.9 20.3 + - - -
63C ARG* 3.6 5.2 - - - -
65C VAL* 1.3 77.7 - - - +
67C ILE* 1.3 67.4 + - - +
69C LYS* 3.4 11.9 + - - +
70C GLU* 3.6 13.7 + - - +
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Residues in contact with ILE 67 (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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63C ARG* 2.9 25.6 + - + +
64C GLU* 3.8 4.5 - - - +
66C SER* 1.3 79.6 - - - +
68C LEU* 1.3 63.4 + - - +
70C GLU* 3.3 23.4 + - - +
71C ILE* 3.6 11.4 - - + +
135C ILE* 4.6 19.9 - - + +
162C PHE* 4.0 28.5 - - + +
165C ALA* 3.0 42.4 - - + +
166C HIS* 3.5 16.6 - - - +
167C LYS* 4.0 14.8 - - + +
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Residues in contact with LEU 68 (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 GLU* 2.9 39.0 + - + +
65C VAL* 2.9 6.8 + - - +
67C ILE* 1.3 75.2 - - - +
69C LYS* 1.3 65.7 + - - +
70C GLU 3.3 0.3 + - - -
71C ILE* 3.4 41.2 + - + +
77C ILE* 4.1 18.8 - - + +
79C LEU* 4.1 26.2 + - + +
91C LEU* 4.2 13.7 - - + -
93C LEU* 4.1 23.6 - - + -
162C PHE* 3.9 23.3 - - + +
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Residues in contact with LYS 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 VAL* 2.8 21.8 + - + +
66C SER* 3.9 7.4 - - - +
67C ILE 3.3 0.6 - - - -
68C LEU* 1.3 74.2 - - - +
70C GLU* 1.3 59.8 + - - +
71C ILE 3.6 2.6 + - - +
72C GLN* 5.5 2.9 - - - +
79C LEU* 4.1 15.2 - - + +
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Residues in contact with GLU 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 SER* 3.6 10.0 + - - +
67C ILE* 3.3 14.3 + - - +
68C LEU 3.2 0.6 - - - -
69C LYS* 1.3 79.7 - - - +
71C ILE* 1.3 59.3 + - + +
72C GLN* 3.7 4.4 + - - +
129C TYR* 3.6 7.8 + - - -
133C LEU* 4.2 23.3 - - + +
135C ILE* 4.2 9.3 - - + +
167C LYS* 2.8 42.4 + - - -
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Residues in contact with ILE 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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67C ILE* 3.6 12.8 - - + +
68C LEU* 3.4 40.6 + - + +
69C LYS 4.6 1.2 - - - +
70C GLU* 1.3 76.0 - - + +
72C GLN* 1.3 69.6 + - - +
73C HIS 4.1 0.7 - - - -
76C VAL* 4.0 17.4 - - + +
77C ILE 4.1 12.4 - - - +
78C THR* 5.1 6.1 - - - -
79C LEU 5.5 0.5 + - - -
129C TYR* 3.5 10.3 - - + -
130C LEU* 4.1 18.4 - - + -
133C LEU* 5.0 0.9 - - + -
135C ILE* 4.1 16.8 - - + -
162C PHE* 3.7 35.9 - - + -
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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