Contacts of the helix formed by residues 57 - 65 (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 ALA 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C PHE* 1.3 87.1 - - - +
58C TRP* 1.3 64.6 + - - +
59C ASP* 3.2 5.0 + - + +
60C ILE* 3.5 12.5 + - + +
134C PRO 4.3 3.4 - - - +
135C VAL* 2.9 32.9 + - + +
138C LYS* 4.1 13.2 - - - +
140C THR* 3.3 26.9 - - + +
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Residues in contact with TRP 58 (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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29C ILE* 3.8 31.6 - - + -
46C LEU* 3.9 22.9 - - + -
48C VAL* 4.3 9.2 - - + -
54C LEU* 4.5 6.5 - - + -
56C PHE* 3.4 5.1 + - - -
57C ALA* 1.3 71.9 - - - +
59C ASP* 1.3 66.6 + - - +
61C LEU* 2.8 31.7 + - + +
62C SER* 3.3 9.8 + - - -
65C PHE* 3.8 17.7 - + - -
201C ILE* 3.6 22.6 - - + +
208C TYR* 3.8 42.4 - + + -
211C VAL* 3.6 34.9 - - + +
213C GLN* 2.8 27.3 + - - -
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Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA* 3.2 2.4 - - + -
58C TRP* 1.3 80.7 - - - +
60C ILE* 1.3 63.6 + - - +
61C LEU 3.1 0.5 + - - -
62C SER* 3.2 21.3 + - - -
63C PRO* 3.3 0.3 - - - +
140C THR* 2.7 30.6 + - - +
141C MET* 3.4 2.3 + - - -
142C GLY* 2.9 38.4 + - - -
143C 4OO 3.0 19.0 + - + -
165C LEU* 3.9 20.6 - - + -
201C ILE* 4.3 16.3 - - - +
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Residues in contact with ILE 60 (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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22C VAL* 4.0 30.3 - - + -
56C PHE* 4.1 5.6 - - + -
57C ALA* 3.5 15.0 + - + +
58C TRP 2.9 0.6 + - - -
59C ASP* 1.3 78.7 - - - +
61C LEU* 1.3 70.5 + - + +
63C PRO* 3.9 2.1 - - - +
64C GLN* 3.2 21.7 + - - -
97C MET* 4.6 4.0 - - - +
99C PHE* 3.9 26.2 - - + -
105C VAL* 4.4 9.6 - - + +
124C LEU* 4.6 2.4 - - + +
129C PHE* 4.2 11.0 - - + -
135C VAL* 3.7 43.7 - - + -
143C 4OO 4.2 5.6 - - - -
165C LEU* 4.6 6.3 - - + -
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Residues in contact with LEU 61 (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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18C MET* 4.3 3.1 - - + -
22C VAL* 4.7 0.2 - - + -
27C PHE* 3.8 23.3 - - + -
29C ILE* 3.7 26.5 - - + -
54C LEU* 3.8 22.7 - - + -
56C PHE* 4.0 15.0 - - + -
58C TRP* 2.8 21.5 + - + +
60C ILE* 1.3 90.2 - - + +
62C SER* 1.3 64.5 + - - +
63C PRO* 3.4 2.7 - - - -
64C GLN* 2.9 22.4 + - - +
65C PHE* 3.2 25.2 - - + -
124C LEU* 3.8 23.1 - - + -
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Residues in contact with SER 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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58C TRP* 3.3 17.3 + - - +
59C ASP* 3.2 13.5 + - - -
61C LEU* 1.3 79.4 - - - +
63C PRO* 1.4 68.3 - - - +
64C GLN 3.2 4.2 + - - -
65C PHE* 3.6 9.1 + - - -
66C CH6 3.7 4.0 - - - +
143C 4OO 3.3 14.9 - - - -
199C LEU* 3.6 16.1 - - - +
201C ILE* 4.4 3.4 - - - -
213C GLN* 3.0 44.9 + - - -
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Residues in contact with PRO 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 ASP 3.3 9.2 - - - +
60C ILE 3.9 4.7 - - - +
61C LEU 3.4 4.7 - - - -
62C SER* 1.4 95.5 - - - +
64C GLN* 1.3 66.6 + - - +
65C PHE 3.3 1.1 - - - -
66C CH6 2.9 59.3 + - + +
95C ARG* 3.1 11.9 + - - +
97C MET* 4.6 5.6 - - + -
143C 4OO 3.5 28.5 - - + +
163C GLN* 4.9 4.3 - - - +
199C LEU* 3.9 4.0 - - + -
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Residues in contact with GLN 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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18C MET* 3.6 15.9 - - + -
60C ILE 3.2 20.4 + - - -
61C LEU 2.9 15.7 + - - +
63C PRO* 1.3 85.8 - - - +
65C PHE* 1.3 62.8 + - - +
66C CH6 3.3 3.3 - - - +
93C TRP* 3.7 23.7 - - + -
95C ARG* 2.9 32.9 + - - +
97C MET* 3.4 24.7 - - - +
107C VAL* 3.7 13.7 - - + +
109C GLN* 4.9 0.5 + - - +
122C VAL* 3.9 22.0 - - + +
124C LEU* 3.8 22.9 - - + +
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Residues in contact with PHE 65 (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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14C PHE* 3.9 11.1 - - - -
16C VAL* 4.0 25.4 - - + -
18C MET* 3.5 35.0 - - + -
29C ILE* 3.8 39.5 - - + -
44C ALA* 5.4 0.9 - - + -
46C LEU* 3.8 27.4 - - + -
58C TRP* 3.8 20.4 - + - -
61C LEU* 3.2 29.8 - - + -
62C SER* 3.6 12.5 + - - +
63C PRO 3.3 0.4 - - - -
64C GLN* 1.3 81.3 - - - +
66C CH6 1.3 77.6 + - + +
69C SER* 3.6 11.3 - - - -
120C TYR* 4.4 6.0 - - - -
122C VAL* 5.3 0.2 - - + -
213C GLN* 4.3 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