Contacts of the helix formed by residues 58 - 74 (chain C) in PDB entry 1ZVM
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 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C THR 3.3 0.4 + - - -
57C LYS* 1.3 102.3 - - + +
59C PHE* 1.3 65.2 + - - +
60C PRO* 3.2 5.2 - - - -
61C GLU* 3.0 40.2 + - + +
62C THR* 2.8 28.4 + - - +
170C TYR* 4.1 6.4 - - - -
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Residues in contact with PHE 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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55C THR* 3.4 14.8 - - + -
56C THR* 3.1 22.0 + - - +
57C LYS 3.2 0.6 - - - -
58C ARG* 1.3 75.0 - - - +
60C PRO* 1.3 70.0 - - + +
62C THR* 3.2 6.7 + - - -
63C VAL* 3.0 44.2 + - + +
86C TRP* 3.5 32.3 - + - -
89C PHE* 4.0 12.3 - + - -
93C PHE* 4.0 12.6 - + - -
154C ALA* 5.9 0.2 - - - -
157C LEU* 4.0 20.0 - - + -
158C THR 4.1 10.3 - - - -
159C TRP* 3.5 50.5 - + + -
168C ILE* 4.7 3.1 - - + -
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Residues in contact with PRO 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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58C ARG* 3.3 4.7 - - - -
59C PHE* 1.3 96.3 - - + +
61C GLU* 1.3 70.5 + - - +
63C VAL* 4.1 1.9 - - - +
64C LEU* 3.2 22.6 + - - +
86C TRP* 3.8 33.9 - - + +
168C ILE* 3.8 18.6 - - + -
170C TYR* 3.5 20.9 - - - +
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Residues in contact with GLU 61 (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* 3.0 60.9 + - + +
60C PRO* 1.3 85.4 - - + +
62C THR* 1.3 57.7 + - - +
64C LEU* 3.9 5.6 - - - +
65C ALA* 2.9 32.6 + - - +
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Residues in contact with THR 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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56C THR* 5.2 2.8 - - - +
57C LYS 4.6 2.1 + - - -
58C ARG* 2.8 28.4 + - - +
59C PHE* 3.2 8.2 + - - -
61C GLU* 1.3 74.3 - - - +
63C VAL* 1.3 61.2 + - - +
65C ALA* 4.0 3.9 - - - +
66C ARG* 3.0 66.8 + - + +
157C LEU* 3.9 18.8 - - + -
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Residues in contact with VAL 63 (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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59C PHE* 3.0 49.4 + - + +
60C PRO 4.1 0.2 - - - +
62C THR* 1.3 71.9 - - - +
64C LEU* 1.3 67.9 + - - +
66C ARG* 4.6 3.4 - - - -
67C CYS* 3.0 23.1 + - + +
85C VAL* 5.0 2.9 - - + -
86C TRP* 4.1 23.8 - - + -
89C PHE* 3.8 27.4 - - + -
153C LEU* 3.4 31.8 - - + +
157C LEU* 4.4 1.8 - - + -
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Residues in contact with LEU 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 PRO 3.2 16.4 + - - +
61C GLU* 3.9 5.6 - - - +
63C VAL* 1.3 79.8 - - - +
65C ALA* 1.3 63.3 + - - +
67C CYS* 3.3 5.9 + - - +
68C VAL* 3.0 34.4 + - + +
82C CYS* 3.8 35.0 - - + +
83C GLN* 4.0 25.6 - - + +
86C TRP* 4.7 12.3 - - + +
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Residues in contact with ALA 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 GLU 2.9 20.5 + - - +
62C THR* 4.0 4.3 - - - +
64C LEU* 1.3 78.3 - - - +
66C ARG* 1.3 58.0 + - + +
68C VAL* 3.3 7.9 + - - +
69C LYS* 2.8 31.2 + - - +
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Residues in contact with ARG 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 THR* 3.0 40.2 + - + +
63C VAL 3.9 3.4 - - - +
65C ALA* 1.3 72.3 - - + +
67C CYS* 1.3 57.1 + - - +
69C LYS* 3.5 3.8 - - - +
70C TYR* 2.6 37.9 + - - +
152C TYR* 3.3 49.5 + - + +
153C LEU* 3.0 31.6 + - + -
155C ASP* 2.9 30.8 + - - +
156C ASP* 5.0 3.6 + - - +
157C LEU* 3.1 17.2 - - - +
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Residues in contact with CYS 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 VAL* 3.0 18.8 + - + +
64C LEU* 3.3 5.4 + - - +
66C ARG* 1.3 75.6 - - - +
68C VAL* 1.3 54.7 + - - +
70C TYR* 3.7 0.5 - - - +
71C THR* 2.7 37.9 + - - +
80C VAL* 4.1 6.7 - - - -
82C CYS* 2.1 51.8 - - + +
85C VAL* 4.1 20.9 - - + -
149C LEU* 4.2 13.7 - - - -
153C LEU* 3.3 16.0 - - + +
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Residues in contact with VAL 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 LEU* 3.0 26.4 + - + +
65C ALA* 3.6 10.5 - - - +
67C CYS* 1.3 76.1 - - - +
69C LYS* 1.3 63.3 + - - +
71C THR* 2.9 19.2 + - - -
72C GLU* 3.1 20.5 + - + +
82C CYS* 3.9 16.2 - - + -
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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 ALA 2.8 21.3 + - - +
66C ARG* 3.5 8.1 - - - +
68C VAL* 1.3 75.2 - - - +
70C TYR* 1.3 63.4 + - - +
72C GLU* 3.0 44.7 + - - +
73C ILE* 3.2 36.4 + - + +
152C TYR* 4.5 15.3 - - - +
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Residues in contact with TYR 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 ARG 2.6 20.9 + - - +
67C CYS 3.7 3.1 - - - +
69C LYS* 1.3 71.4 - - - +
71C THR* 1.3 61.5 + - - +
73C ILE* 3.2 5.4 + - - -
74C HIS* 3.0 71.1 + + + +
77C MET* 4.1 11.7 - - + -
115C GLN* 2.9 23.8 + - - -
143C PHE* 5.3 1.9 - - - -
147C ASP* 2.6 31.3 + - - -
148C THR 3.7 8.3 - - - -
149C LEU* 3.3 40.5 + - + -
152C TYR* 3.6 32.7 - + + -
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Residues in contact with THR 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 CYS* 2.7 28.2 + - - +
68C VAL* 2.9 16.5 + - - -
70C TYR* 1.3 76.1 - - + +
72C GLU* 1.3 58.7 + - - +
74C HIS 3.3 20.0 - - - +
75C PRO* 4.3 2.3 - - - +
77C MET* 3.4 30.1 - - + +
78C ARG* 4.5 12.4 + - - +
80C VAL* 3.9 22.2 + - + +
82C CYS* 3.9 10.6 - - - -
149C LEU* 4.9 7.2 - - + -
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Residues in contact with GLU 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 VAL* 3.1 18.3 + - + +
69C LYS* 3.0 50.1 + - - +
70C TYR 3.1 0.4 - - - -
71C THR* 1.3 78.6 - - - +
73C ILE* 1.3 69.0 + - + +
74C HIS 3.7 0.2 + - - -
75C PRO* 4.7 8.0 - - - +
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Residues in contact with ILE 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 LYS* 3.3 42.4 - - + +
70C TYR* 3.2 5.2 + - - +
72C GLU* 1.3 88.2 - - + +
74C HIS* 1.3 82.2 + - + +
75C PRO* 3.3 9.7 - - - +
152C TYR* 5.9 3.4 - - + +
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Residues in contact with HIS 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 TYR* 3.0 66.4 + + + +
71C THR 3.3 13.0 - - - +
72C GLU 3.4 0.2 - - - -
73C ILE* 1.3 99.5 - - + +
75C PRO* 1.3 61.3 - - - +
76C GLU* 3.1 6.1 - - + +
77C MET* 2.9 26.2 + - + +
115C GLN* 5.4 2.2 - - - +
143C PHE* 5.5 10.1 - + - -
147C ASP 4.9 2.0 + - - -
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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