Contacts of the helix formed by residues 76 - 81 (chain C) in PDB entry 1NQI
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 76 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LEU* 6.0 1.9 - - - +
287B VAL* 6.3 3.1 - - - -
61C CYS* 4.3 0.2 - - - -
62C LYS* 3.6 13.6 + - - +
64C SER* 5.0 3.8 - - - -
75C ILE* 1.3 82.1 - - - +
77C CYS* 1.3 67.4 + - - +
78C ASP* 3.2 22.9 + - - +
79C LYS* 2.9 32.2 + - - +
80C LEU* 4.0 3.1 + - - +
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Residues in contact with CYS 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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50C TYR* 3.5 35.4 - - + +
57C ASP* 3.6 12.3 - - - -
61C CYS* 2.0 64.2 - - - -
62C LYS 2.8 23.2 + - - +
63C SER* 3.5 5.6 - - - -
64C SER 5.5 0.2 - - - +
75C ILE 3.5 0.4 + - - -
76C SER* 1.3 72.4 + - - +
78C ASP* 1.3 62.6 + - - +
80C LEU* 3.0 22.3 + - - +
81C LEU 3.9 1.0 + - - -
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Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 6.1 0.9 - - - +
284B LEU* 5.6 9.4 - - + +
334B ARG* 5.6 1.0 - - - +
335B PRO 4.5 1.2 - - - +
336B ASN* 3.3 14.9 - - - +
337B ALA* 3.1 42.4 + - + +
50C TYR* 4.6 2.6 - - - -
64C SER* 2.6 34.2 + - - -
76C SER* 3.0 10.5 + - - +
77C CYS* 1.3 81.3 - - - +
79C LYS* 1.3 57.7 + - + +
80C LEU 3.1 0.4 - - - -
81C LEU* 3.1 28.8 + - - +
82C ASP* 4.4 1.7 + - - +
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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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5A LYS* 4.7 18.8 - - - +
117A GLN 5.9 0.7 - - - -
283B SER* 4.0 25.1 + - - -
284B LEU* 4.7 13.6 + - - +
75C ILE* 3.9 17.3 - - + -
76C SER* 2.9 23.1 + - - +
78C ASP* 1.3 77.7 - - + +
80C LEU* 1.3 51.4 + - - +
81C LEU 3.2 2.2 - - - -
82C ASP* 3.4 19.3 + - - +
87C ASP* 3.4 21.9 - - - +
526C CA 2.3 31.9 - - - -
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Residues in contact with LEU 80 (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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38C THR 3.3 3.6 - - - +
50C TYR* 4.1 15.3 - - + +
51C GLY* 3.2 23.0 - - - -
52C LEU 4.4 0.2 + - - -
55C ILE* 3.7 41.7 - - + -
61C CYS* 3.9 23.3 - - + -
75C ILE* 4.5 15.0 - - + -
76C SER 4.0 5.2 - - - +
77C CYS 3.0 10.8 + - - +
79C LYS* 1.3 81.7 - - - +
81C LEU* 1.3 60.0 + - - +
82C ASP 3.5 3.0 - - - +
87C ASP* 4.3 5.8 - - - +
88C ASP* 3.4 50.8 - - + +
91C CYS* 5.0 0.2 - - + -
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Residues in contact with LEU 81 (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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336B ASN* 4.0 16.2 - - + +
337B ALA* 4.3 8.0 - - + +
338B VAL* 4.0 18.1 - - + +
38C THR 3.5 6.3 - - - -
39C GLN* 3.2 53.3 + - - +
40C ALA 3.6 15.3 - - - +
41C VAL* 3.8 14.6 - - + -
50C TYR* 3.7 28.5 - - + -
51C GLY 3.7 13.0 - - - +
77C CYS 4.1 3.1 - - - +
78C ASP* 3.1 17.9 + - - +
80C LEU* 1.3 80.5 - - - +
82C ASP* 1.3 58.8 + - - +
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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