Contacts of the helix formed by residues 32 - 37 (chain F) 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 MET 32 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F PHE* 4.0 3.1 - - - -
30F GLY 4.0 2.4 + - - +
31F LEU* 1.3 77.0 - - - +
33F ARG* 1.3 67.0 + - - +
34F ASP 3.3 1.3 - - - +
35F ASP* 2.9 35.5 + - - +
36F THR* 3.5 7.8 - - - +
61F ARG* 3.7 30.5 - - - +
81F THR* 4.5 9.2 - - - +
85F GLU 5.3 4.7 - - - +
86F ASP* 3.3 25.4 - - - +
87F LYS* 3.5 36.8 - - + +
89F TYR* 4.3 15.0 - - + -
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Residues in contact with ARG 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C LEU* 2.7 44.2 + - + -
378C LYS* 3.6 12.5 + - - +
379C TRP* 3.3 53.8 - - + +
21F TYR* 5.1 2.0 - - + -
26F PHE* 3.6 29.5 - - + -
32F MET* 1.3 71.8 - - - +
34F ASP* 1.3 79.4 + - - +
36F THR* 2.6 29.5 + - - +
86F ASP* 3.1 24.0 + - - +
88F SER* 3.6 21.3 - - - -
91F GLU* 3.4 21.0 + - - +
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Residues in contact with ASP 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C TRP* 3.8 12.2 + - - -
32F MET* 3.3 1.8 - - - +
33F ARG* 1.3 103.0 + - - +
35F ASP* 1.3 59.1 + - - +
36F THR 3.1 1.5 + - - -
37F ILE* 3.4 23.4 - - - +
58F ARG* 4.1 3.6 + - - -
86F ASP* 5.0 0.8 + - - -
87F LYS 5.1 0.8 + - - +
88F SER* 3.1 24.2 - - - +
89F TYR* 3.7 22.4 + - + -
90F LEU* 3.0 45.8 + - + +
91F GLU* 3.5 4.4 + - - +
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Residues in contact with ASP 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ILE* 3.3 20.0 - - - +
31F LEU* 3.7 10.3 - - + -
32F MET* 2.9 30.9 + - - +
34F ASP* 1.3 76.0 - - - +
36F THR* 1.3 59.4 + - - +
37F ILE 3.5 0.7 - - - +
58F ARG* 4.1 10.1 + - - +
61F ARG* 2.7 42.8 + - - +
62F ILE* 3.4 26.4 - - + +
89F TYR* 2.3 35.5 + - - -
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Residues in contact with THR 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C THR 5.5 0.7 - - - +
210C GLY 5.3 1.9 - - - +
211C ILE* 3.8 12.6 - - - +
312C GLN* 3.4 34.5 + - - +
313C ARG 4.8 1.6 + - - -
317C PHE* 4.0 11.2 - - + -
379C TRP* 3.5 6.2 - - - -
26F PHE* 3.8 32.8 - - + -
31F LEU* 3.8 12.8 - - + -
32F MET 3.5 15.5 - - - +
33F ARG* 2.6 18.6 + - - +
35F ASP* 1.3 79.6 - - - +
37F ILE* 1.3 67.0 + - - +
38F HIS* 3.4 2.1 + - - -
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Residues in contact with ILE 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C GLY 5.4 1.6 - - - +
211C ILE* 5.3 5.0 - - - +
311C LYS* 3.6 35.0 - - + +
379C TRP* 3.6 29.4 - - + +
33F ARG 3.7 1.4 + - - -
34F ASP* 3.4 18.3 + - - +
35F ASP 3.5 2.3 - - - +
36F THR* 1.3 81.8 + - - +
38F HIS* 1.3 82.0 + - + +
39F GLU* 3.6 6.4 + - - +
40F ASN* 5.6 2.0 - - - +
43F VAL* 3.6 38.1 - - + -
58F ARG* 4.5 9.7 + - - +
90F LEU* 4.0 12.6 - - + -
94F LEU* 5.0 4.7 - - + -
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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