Contacts of the helix formed by residues 113 - 120 (chain F) in PDB entry 1ZUM
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 PRO 113 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111F GLY 3.7 1.3 - - - +
112F LYS* 1.3 86.9 - - + +
114F TYR* 1.3 66.3 + - - +
115F VAL* 4.4 4.7 - - + +
116F ILE* 3.1 29.9 + - + +
117F SER* 3.0 18.4 + - - -
297F ASN* 5.9 2.0 - - - -
298F GLN* 3.5 15.0 - - - +
334F PRO* 3.5 14.6 - - + +
336F ASP 5.8 0.2 - - - +
339F THR* 3.9 17.3 - - + +
340F GLU 3.5 31.0 - - - +
341F GLN 4.6 0.4 - - - -
342F GLY* 4.2 5.6 - - - +
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Residues in contact with TYR 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 3.3 18.8 - - + -
9F PRO 2.8 28.6 + - - -
11F PRO* 3.4 37.2 - - + +
100F THR* 3.4 23.9 - - - +
103F ALA* 3.6 22.7 - - + -
104F ALA* 3.7 23.6 - - - -
107F THR* 3.1 16.7 + - - +
112F LYS 3.4 0.4 + - - -
113F PRO* 1.3 72.3 - - - +
115F VAL* 1.3 70.1 + - + +
117F SER* 4.2 0.7 - - - -
118F TYR* 2.9 37.1 + + - +
334F PRO 3.0 17.1 + - - +
335F PHE* 3.9 18.4 - + + -
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 4.7 16.4 - - + -
113F PRO* 3.2 4.6 - - + +
114F TYR* 1.3 85.2 - - + +
116F ILE* 1.3 67.6 + - + +
118F TYR* 3.9 3.0 - - - +
119F LEU* 2.9 50.1 + - + +
334F PRO 4.8 0.6 + - - -
336F ASP 5.6 0.4 - - - +
337F SER* 4.4 31.9 - - - +
339F THR 5.9 1.8 - - - +
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Residues in contact with ILE 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F LYS* 5.1 5.8 - - + +
113F PRO* 3.1 34.6 + - + +
115F VAL* 1.3 85.5 - - + +
117F SER* 1.3 60.2 + - - +
119F LEU* 6.2 0.2 - - + -
120F VAL* 2.7 55.8 + - + +
121F ASP* 3.2 15.9 + - - +
296F PHE* 3.9 25.6 - - + -
297F ASN* 6.0 1.3 - - - +
340F GLU 5.6 0.9 - - - +
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Residues in contact with SER 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ALA* 3.3 29.2 + - - -
106F GLU* 3.9 9.0 - - - +
107F THR* 3.0 18.9 + - - -
112F LYS* 3.1 21.8 - - - +
113F PRO 3.0 6.7 + - - -
114F TYR 3.2 6.0 + - - -
116F ILE* 1.3 74.9 - - - +
118F TYR* 1.3 59.2 + - - +
121F ASP* 3.5 12.1 - - - +
122F LEU* 2.9 35.9 + - - +
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Residues in contact with TYR 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ALA 4.4 6.1 - - - -
8F VAL* 3.7 20.4 - - + -
9F PRO* 3.4 30.6 - - + +
99F ARG* 2.9 75.3 + - + +
100F THR* 3.7 17.3 + - - -
103F ALA* 3.6 17.7 - - + +
114F TYR* 2.9 32.2 + - + +
115F VAL 3.9 2.2 - - - +
117F SER* 1.3 82.0 - - - +
119F LEU* 1.3 77.7 + - + +
122F LEU* 3.8 5.7 - - - +
123F ASP 3.9 0.5 + - - -
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Residues in contact with LEU 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ALA 4.4 12.1 - - - +
8F VAL* 3.7 25.4 - - + -
99F ARG* 4.1 5.6 + - - +
115F VAL* 2.9 35.4 + - + +
116F ILE* 6.2 0.2 - - + -
118F TYR* 1.3 94.4 - - + +
120F VAL* 1.3 66.2 + - + +
123F ASP* 3.3 20.9 - - - +
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Residues in contact with VAL 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE* 2.7 42.0 + - + +
119F LEU* 1.3 80.7 - - + +
121F ASP* 1.3 70.9 + - - +
122F LEU 3.4 0.9 - - - -
123F ASP* 3.2 2.1 + - - +
124F MET* 2.8 55.5 + - + +
296F PHE* 4.3 19.5 - - + -
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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