Contacts of the helix formed by residues 61 - 72 (chain C) in PDB entry 1NTZ
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 THR 61 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C THR* 3.2 35.7 + - + -
58C ASP* 2.7 19.5 + - + +
60C THR* 1.3 83.6 - - + +
62C ALA* 1.3 57.6 + - - +
63C PHE 3.5 2.0 - - - -
64C SER* 3.8 11.4 - - - -
65C SER* 2.7 34.6 + - - -
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Residues in contact with ALA 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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55C TYR* 4.0 0.6 - - - -
56C THR 3.5 18.6 - - - +
58C ASP 2.6 20.4 + - - +
59C THR* 4.0 4.8 + - - +
60C THR 3.8 0.8 - - - -
61C THR* 1.3 69.9 - - - +
63C PHE* 1.3 62.2 + - - +
65C SER* 2.6 19.9 + - - -
66C VAL* 3.1 12.5 + - - +
133C LEU 4.0 12.1 - - - +
134C PRO 4.2 2.0 - - - -
135C TRP* 4.1 9.6 - - + -
175C LEU* 3.8 23.8 - - + -
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Residues in contact with PHE 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 THR 5.2 2.3 + - - +
61C THR 3.5 0.2 - - - -
62C ALA* 1.3 77.9 - - - +
64C SER* 1.3 57.1 + - - +
66C VAL* 3.1 9.2 + - + +
67C THR* 2.9 44.4 + - + -
134C PRO* 3.4 24.1 + - + +
135C TRP* 4.0 8.4 - - + +
136C GLY* 4.4 0.9 - - - -
255C ASN 3.6 18.2 - - - -
256C TYR* 2.9 43.1 - + + -
257C THR 4.3 0.2 - - - -
258C PRO* 3.7 34.8 - - + -
45D TYR* 3.9 23.1 - + - +
115D TYR* 5.3 5.8 - + + -
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Residues in contact with SER 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 THR 4.9 3.4 - - - -
61C THR* 3.3 19.6 + - - -
62C ALA 3.3 0.2 - - - -
63C PHE* 1.3 80.2 - - - +
65C SER* 1.3 51.7 + - - +
67C THR* 3.1 5.3 + - - -
68C HIS* 2.6 37.2 + - - +
45D TYR* 3.5 30.7 + - - -
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C HIS 3.8 10.5 - - - +
55C TYR* 3.4 7.3 - - - -
56C THR* 3.1 39.1 + - - -
61C THR* 2.7 20.7 + - - -
62C ALA 2.6 20.3 + - - -
64C SER* 1.3 69.3 - - - +
66C VAL* 1.3 65.0 + - - +
68C HIS* 3.3 10.2 + - - +
69C ILE* 3.0 30.3 + - - +
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 4.0 17.5 - - + -
62C ALA 3.3 13.2 - - - +
63C PHE* 3.1 10.4 + - + +
65C SER* 1.3 82.3 + - - +
67C THR* 1.3 60.4 + - - +
69C ILE* 3.3 24.4 + - + +
70C CYS* 3.4 10.8 + - - -
80C ARG* 3.5 42.8 - - + +
134C PRO* 3.9 26.0 - - + -
381C HEM 4.4 15.3 - - + +
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Residues in contact with THR 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 PHE* 2.9 35.7 + - + -
64C SER* 3.1 7.8 + - - -
66C VAL* 1.3 74.0 - - - +
68C HIS* 1.3 68.2 + - - +
70C CYS* 3.1 14.8 + - + +
71C ARG* 3.2 52.8 - - + +
45D TYR* 3.6 31.8 - - + -
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Residues in contact with HIS 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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54C HIS* 4.4 20.7 + - + +
64C SER 2.6 21.4 + - - +
65C SER* 3.4 13.5 + - - +
67C THR* 1.3 72.2 - - - +
69C ILE* 1.3 57.1 + - - +
71C ARG* 5.2 0.9 - - - -
72C ASP* 3.0 49.1 + - + +
73C VAL* 3.2 29.4 + - + +
90D TYR* 5.6 1.1 - - - -
65E SER* 3.8 22.5 + - - -
66E ALA* 4.8 7.4 + - + +
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Residues in contact with ILE 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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51C LEU* 3.8 33.9 - - + +
54C HIS* 3.7 34.8 - - + -
55C TYR* 4.0 18.6 - - + +
65C SER 3.0 22.7 + - - +
66C VAL* 3.4 14.8 - - + +
67C THR 3.1 0.2 - - - -
68C HIS* 1.3 77.2 - - - +
70C CYS* 1.3 61.4 + - - +
71C ARG 3.4 0.2 + - - -
73C VAL* 3.3 20.4 - - + +
76C GLY* 3.3 41.0 - - - +
80C ARG* 4.3 8.3 - - + -
381C HEM 5.4 2.5 - - + -
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Residues in contact with CYS 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 VAL 3.5 14.6 - - - +
67C THR* 3.1 9.3 + - + +
69C ILE* 1.3 77.3 - - - +
71C ARG* 1.3 64.1 + - + +
73C VAL 5.1 0.6 - - - +
77C TRP* 3.8 35.5 - - + +
80C ARG* 3.8 43.3 - - - -
81C TYR* 4.2 13.2 - - - +
118D ARG* 5.6 1.8 - - - +
196D PRO* 5.4 2.3 - - + +
197D GLU* 4.2 13.0 - - - +
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Residues in contact with ARG 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 THR* 3.2 35.9 + - + +
68C HIS* 5.2 0.4 - - - -
70C CYS* 1.3 81.8 - - + +
72C ASP* 1.3 78.2 + - - +
73C VAL 4.8 2.0 - - - +
45D TYR* 3.4 35.9 + - - +
46D VAL* 3.8 21.4 - - - +
50D HIS* 3.9 20.0 + - + +
114D SER* 3.5 15.8 + - - -
115D TYR* 5.2 3.6 - - - +
193D ALA* 2.5 31.9 + - - +
194D ALA 4.7 6.4 + - - -
196D PRO* 3.8 27.3 - - + +
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Residues in contact with ASP 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 HIS* 3.0 33.9 + - + +
71C ARG* 1.3 83.1 - - - +
73C VAL* 1.3 63.7 + - - +
74C ASN* 3.3 8.8 + - - -
49D ARG* 3.2 23.2 + - - -
50D HIS* 2.9 30.1 + - - -
90D TYR* 3.2 16.3 + - - -
65E SER* 3.5 31.8 + - - +
66E ALA* 3.7 8.4 - - - +
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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