Contacts of the helix formed by residues 81 - 86 (chain C) in PDB entry 4ZIN
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 ASP 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LYS 4.9 2.8 - - - +
73C VAL 3.4 0.5 - - - +
75C HIS* 2.8 44.0 + - + +
79C ILE 3.2 2.5 + - - +
80C PRO* 1.3 69.1 - - - +
82C TYR* 1.3 52.1 + - - +
83C LEU* 3.9 4.5 + - - +
84C LYS* 2.7 58.2 + - + +
85C LEU* 2.8 41.0 + - + +
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Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C HIS* 5.5 0.4 + - - -
80C PRO 3.2 5.2 + - - +
81C ASP* 1.3 73.6 + - - +
83C LEU* 1.3 85.1 + - + +
85C LEU* 3.3 7.9 + - - +
86C SER* 3.1 23.6 + - - -
155C GLY 3.7 15.6 + - - -
156C ALA* 4.2 0.2 - - - -
157C LEU* 3.9 22.4 - - + -
181C TYR 3.6 19.6 + - - -
182C LYS* 3.7 6.2 + - - +
183C ALA* 2.9 31.5 + - + +
186C PRO* 6.0 0.5 - - - +
187C VAL* 3.6 33.4 - - + +
188C GLN 3.3 29.4 - - - +
189C LEU* 3.4 23.3 - - + +
190C PRO* 4.1 14.4 - - + -
193C TYR* 5.9 0.4 + - - -
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS* 3.4 39.3 - - + +
71C ALA* 5.3 1.3 - - - -
81C ASP* 3.1 4.0 + - - +
82C TYR* 1.3 102.9 - - + +
84C LYS* 1.3 62.7 + - - +
86C SER* 2.9 23.8 + - - -
87C PHE* 3.1 15.5 - - - -
91C PHE* 3.8 34.8 - - + -
150C MET* 6.1 1.1 - - + -
157C LEU* 4.7 9.0 - - + -
181C TYR* 3.8 35.0 - - + -
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Residues in contact with LYS 84 (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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8C ILE* 3.7 30.2 - - + +
37C PRO* 3.2 29.6 + - - -
38C TYR* 3.9 32.3 - - + +
71C ALA* 2.9 32.4 + - - +
73C VAL 2.8 21.4 + - - +
75C HIS 5.2 0.2 - - - +
81C ASP* 2.7 46.4 + - + +
83C LEU* 1.3 75.2 - - - +
85C LEU* 1.3 63.9 + - + +
86C SER 3.3 0.3 + - - -
87C PHE* 3.5 10.9 + - - +
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Residues in contact with LEU 85 (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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80C PRO* 4.4 7.0 - - + -
81C ASP* 2.8 35.0 + - + +
82C TYR* 3.6 5.2 - - - +
83C LEU 3.3 0.4 - - - -
84C LYS* 1.3 76.9 - - + +
86C SER* 1.3 55.0 + - - +
87C PHE 3.0 7.6 + - - +
185C LYS* 2.8 25.8 + - - -
187C VAL* 3.9 13.6 - - + +
188C GLN* 4.0 33.2 - - + +
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Residues in contact with SER 86 (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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82C TYR 3.1 10.3 + - - -
83C LEU* 2.9 19.0 + - - -
84C LYS 3.2 0.4 - - - -
85C LEU* 1.3 77.1 - - - +
87C PHE* 1.3 58.4 + - - +
89C GLU* 3.6 0.2 - - - +
90C GLY* 3.0 44.4 + - - +
91C PHE* 3.5 8.5 - - - -
183C ALA* 3.7 21.3 - - - -
185C LYS* 3.0 27.5 - - - +
187C VAL* 4.0 5.4 - - - +
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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