Contacts of the helix formed by residues 100 - 112 (chain F) in PDB entry 2ZJR
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 ASN 100 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F LEU* 1.3 81.7 - - - +
101F TRP* 1.3 104.3 + - - +
102F ASP* 2.3 45.7 + - + +
103F GLN* 2.3 47.6 + - - +
139F GLU* 2.8 27.5 + - - +
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Residues in contact with TRP 101 (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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100F ASN* 1.3 110.6 + - - +
102F ASP* 1.3 80.8 + - - -
104F VAL* 2.8 41.7 + - + +
105F LEU* 3.1 22.6 + - + +
138F VAL* 6.3 0.8 - - - +
139F GLU* 3.9 38.0 + - + +
140F GLY* 4.4 10.8 - - - -
141F GLY* 4.8 4.5 - - - -
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Residues in contact with ASP 102 (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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100F ASN* 2.3 36.0 + - + +
101F TRP* 1.3 79.7 + - - +
103F GLN* 1.3 65.1 + - + +
105F LEU* 2.9 41.7 - - - +
106F GLU* 3.8 3.5 + - - +
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Residues in contact with GLN 103 (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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81F ALA* 4.7 18.4 + - + +
99F LEU* 2.8 41.6 - - + +
100F ASN* 2.3 51.0 + - - +
102F ASP* 1.3 73.0 - - + +
104F VAL* 1.3 56.4 + - - +
105F LEU 2.6 16.1 + - - -
106F GLU* 2.8 42.4 - - - +
107F ILE* 3.2 9.8 - - + +
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Residues in contact with VAL 104 (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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99F LEU* 3.9 13.5 - - + -
100F ASN 3.6 4.7 - - - +
101F TRP* 2.8 33.3 + - + +
103F GLN* 1.3 70.3 - - - +
105F LEU* 1.3 65.1 + - + +
107F ILE* 3.2 14.5 - - + +
108F ALA* 3.3 19.8 + - + +
123F ALA 4.8 3.8 - - - +
124F ALA* 4.2 22.0 - - + +
127F VAL* 4.1 29.2 - - + -
138F VAL* 6.4 2.9 - - + -
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Residues in contact with LEU 105 (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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101F TRP* 3.3 24.0 - - + +
102F ASP* 2.9 42.4 - - - +
103F GLN 2.6 5.1 + - - -
104F VAL* 1.3 72.0 - - + +
106F GLU* 1.3 64.4 + - - +
107F ILE 3.1 1.6 + - - -
108F ALA* 3.1 7.9 + - - +
109F LYS* 2.9 22.5 + - - +
120F VAL* 6.5 0.9 - - + -
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Residues in contact with GLU 106 (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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102F ASP 3.8 2.0 + - - +
103F GLN* 2.8 44.0 - - - +
105F LEU* 1.3 77.8 - - - +
107F ILE* 1.3 75.7 + - + +
109F LYS* 3.0 27.4 + - - +
110F THR* 3.4 9.2 + - - -
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Residues in contact with ILE 107 (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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74F MET* 4.4 16.6 - - + -
77F LEU* 5.2 20.6 - - + +
78F ILE* 5.3 13.0 - - + -
99F LEU* 5.6 5.6 - - + -
103F GLN* 3.2 14.4 - - + +
104F VAL* 3.2 38.4 - - + +
106F GLU* 1.3 81.3 - - + +
108F ALA* 1.3 60.6 + - - +
110F THR* 3.1 6.8 + - - -
111F LYS* 2.9 41.5 + - + +
127F VAL* 4.6 21.3 - - + -
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Residues in contact with ALA 108 (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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104F VAL* 3.3 9.1 + - + +
105F LEU* 3.1 9.4 + - - +
107F ILE* 1.3 75.8 - - + +
109F LYS* 1.3 56.5 + - - +
110F THR 2.9 10.9 + - - -
111F LYS* 4.6 0.2 - - - -
112F MET* 3.0 23.6 + - - +
115F LEU* 3.1 28.2 - - + +
123F ALA* 4.5 15.9 - - + +
124F ALA* 6.1 0.9 - - - -
127F VAL* 6.1 2.5 - - + -
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Residues in contact with LYS 109 (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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105F LEU 2.9 13.4 + - - +
106F GLU* 3.0 16.7 + - - +
108F ALA* 1.3 74.7 - - - +
110F THR* 1.3 62.1 + - - +
112F MET* 3.4 27.1 - - - +
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Residues in contact with THR 110 (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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77F LEU* 5.6 10.5 - - + -
106F GLU 3.4 8.3 + - - -
107F ILE* 3.6 7.9 - - - -
108F ALA 2.9 1.4 + - - -
109F LYS* 1.3 82.5 + - - +
111F LYS* 1.3 59.2 + - + +
112F MET* 3.0 8.3 - - - +
113F PRO* 2.8 25.1 - - - +
114F ASP* 4.2 3.1 - - - +
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Residues in contact with LYS 111 (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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74F MET* 3.2 42.0 - - + +
77F LEU* 5.6 5.8 - - + -
107F ILE* 2.9 25.4 + - + +
108F ALA* 4.6 0.2 - - - -
110F THR* 1.3 80.9 + - + +
112F MET* 1.3 51.5 + - - +
113F PRO* 3.2 1.6 - - - -
114F ASP* 2.6 58.3 + - - -
115F LEU* 2.8 33.1 + - + +
1070X G 4.5 5.2 - - - +
1071X U 3.7 21.5 + - - +
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Residues in contact with MET 112 (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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108F ALA 3.0 17.7 + - - +
109F LYS* 3.4 39.7 - - - +
110F THR* 3.3 9.4 - - - +
111F LYS* 1.3 71.4 - - - +
113F PRO* 1.4 79.2 - - + +
114F ASP 2.8 10.7 + - - -
115F LEU* 2.9 31.9 + - + +
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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