Contacts of the strand formed by residues 74 - 80 (chain C) in PDB entry 1ZM9
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 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C SER* 4.6 0.4 + - - -
73C THR* 1.3 81.3 - - - +
75C ILE* 1.3 66.8 + - - +
101C ASN* 5.6 4.0 - - + +
102C LEU 3.4 12.3 - - - +
103C ILE* 4.4 8.1 - - + -
104C ASP 4.6 0.2 - - - +
397C PHE* 3.9 25.8 - - + -
437C MET* 3.0 13.8 + - + +
439C GLY* 2.9 29.0 + - - -
453C ILE* 4.5 7.2 - - + -
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Residues in contact with ILE 75 (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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36C THR* 6.4 0.9 - - - -
40C VAL* 3.6 39.0 - - + -
44C GLY* 5.0 2.7 - - - -
45C ILE 5.3 0.9 - - - +
72C SER* 4.5 14.6 - - - +
74C ALA* 1.3 79.6 - - - +
76C SER* 1.3 66.6 + - - +
77C LEU* 3.5 22.6 + - + -
100C ILE 3.6 1.2 - - - +
101C ASN* 3.7 3.3 - - - -
102C LEU* 2.9 49.0 + - + +
438C MET 5.5 0.2 - - - -
439C GLY* 4.8 5.8 - - - +
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Residues in contact with SER 76 (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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9C MET* 4.0 19.0 - - - +
44C GLY* 3.7 0.9 - - - -
45C ILE* 2.8 56.0 + - - -
74C ALA 4.3 0.2 + - - -
75C ILE* 1.3 77.0 - - - +
77C LEU* 1.3 62.0 + - - +
99C LEU* 4.5 7.4 - - - +
100C ILE 3.7 4.3 - - - -
101C ASN* 5.0 8.6 + - - +
437C MET 4.9 6.1 + - - -
438C MET* 4.0 15.3 - - - +
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Residues in contact with LEU 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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22C MET* 5.9 0.2 - - - -
39C LEU* 3.5 56.3 - - + +
40C VAL* 5.0 0.7 - - - -
43C ALA* 3.2 11.2 - - + +
44C GLY* 4.6 1.8 - - - -
45C ILE* 3.7 2.7 - - - -
75C ILE* 3.5 26.7 - - + +
76C SER* 1.3 82.2 - - - +
78C TYR* 1.3 60.5 + - - +
98C PHE 3.5 2.8 - - - +
99C LEU* 3.5 5.6 - - - +
100C ILE* 2.8 64.3 + - + +
102C LEU* 4.4 14.4 - - + -
335C LEU* 4.0 10.1 - - + -
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Residues in contact with TYR 78 (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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2C VAL* 4.8 5.8 - - + -
4C PHE* 3.7 31.2 - + + -
12C LEU* 3.9 16.4 - - + -
43C ALA* 2.9 31.0 + - - +
45C ILE* 3.0 22.8 - - + +
77C LEU* 1.3 74.0 - - - +
79C SER* 1.3 73.1 + - - +
80C GLU* 3.2 29.7 + - + +
97C SER* 2.9 41.7 + - - -
98C PHE 3.4 8.3 - - - -
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Residues in contact with SER 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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78C TYR* 1.3 84.6 - - - +
80C GLU* 1.3 63.2 + - - +
81C MET* 3.8 22.7 - - - +
96C ASN 3.8 0.2 - - - +
97C SER* 3.7 1.0 - - - -
98C PHE* 2.9 36.9 + - - +
100C ILE* 4.8 9.4 - - - -
335C LEU* 4.4 20.4 - - - +
339C VAL* 4.3 15.9 - - - +
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Residues in contact with GLU 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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78C TYR* 3.2 25.6 + - + +
79C SER* 1.3 79.0 + - - +
81C MET* 1.3 77.6 + - - +
96C ASN* 3.0 37.4 + - + +
97C SER* 4.7 1.8 - - - -
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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