Contacts of the helix formed by residues 69 - 73 (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 SER 69 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLN* 2.8 40.6 + - - -
65C PHE 3.6 15.9 - - - -
66C CH6 1.3 84.4 + - - -
70C LYS* 1.3 57.3 + - - +
71C ALA 3.1 10.1 + - - -
72C TYR* 3.3 17.8 + - - -
73C VAL* 5.0 0.7 - - - +
120C TYR* 2.6 33.3 + - - -
215C GLU* 5.3 1.9 - - - +
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Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C CH6 3.4 43.1 + - + +
69C SER* 1.3 72.2 - - - +
71C ALA* 1.3 63.5 + - - +
72C TYR 3.1 2.8 + - - -
73C VAL* 3.4 29.7 + - + +
75C HIS* 5.3 0.9 - - - -
81C ASP* 4.9 4.5 - - - +
83C LEU* 3.4 32.8 - - + +
91C PHE* 4.3 12.8 - - + -
93C TRP* 5.2 0.7 - - - +
120C TYR* 4.8 0.2 + - - -
148C GLU* 2.6 25.9 + - - -
150C MET* 5.9 1.6 - - - -
181C TYR* 3.0 44.9 + - + -
195C VAL* 5.5 3.0 - - - +
197C ILE* 3.9 9.7 - - - +
215C GLU* 5.6 3.0 + - - +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 5.2 0.2 - - + -
37C PRO* 3.6 4.6 - - - +
69C SER 3.1 1.4 + - - -
70C LYS* 1.3 78.2 - - - +
72C TYR* 1.3 62.6 + - + +
73C VAL 3.4 0.4 - - - -
83C LEU* 5.3 0.4 - - - -
84C LYS* 2.9 40.8 + - + +
87C PHE* 4.1 20.4 - - + -
91C PHE* 4.7 4.2 - - + -
118C PHE* 3.8 35.0 - - + -
120C TYR* 4.3 7.2 + - + +
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Residues in contact with TYR 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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12C MET 2.8 26.4 + - - -
13C ARG 3.7 0.9 + - - -
14C PHE* 3.3 22.1 - + - -
34C GLU 4.2 0.7 - - - -
35C GLY* 3.5 40.4 - - - -
36C ARG 3.8 4.0 - - - -
37C PRO* 3.8 27.1 - - + -
40C GLY* 3.3 18.5 - - - +
41C THR 3.8 8.5 - - - +
42C GLN* 3.8 22.0 + - + +
69C SER* 3.3 28.8 + - - -
70C LYS 3.1 1.6 - - - -
71C ALA* 1.3 80.6 - - - +
73C VAL* 1.3 61.4 + - - +
118C PHE* 3.4 23.5 - + - -
120C TYR* 3.5 12.3 - - - -
217C ALA* 4.2 4.9 - - - +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PRO 3.7 2.2 - - - -
69C SER 5.0 0.9 - - - +
70C LYS* 3.4 36.7 + - + +
71C ALA 3.4 2.8 - - - -
72C TYR* 1.3 80.0 - - - +
74C LYS* 1.3 61.2 + - - +
75C HIS* 3.1 36.4 + - + +
84C LYS* 2.8 26.9 + - - -
195C VAL* 3.9 23.1 - - + -
215C GLU* 5.9 0.4 - - - +
217C ALA* 3.8 18.4 - - + +
219C GLY 3.7 20.0 - - - +
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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
------------------------------------------------------------
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