Contacts of the helix formed by residues 124 - 133 (chain F) in PDB entry 3KZ1
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 ASP 124 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120F ASP 4.2 5.0 + - - +
121F LEU* 3.4 32.7 - - + +
122F ARG 3.3 1.7 - - - +
123F ASN* 1.3 76.5 - - - +
125F GLU* 1.3 61.7 + - - +
126F HIS* 2.7 27.0 + - - +
127F THR* 2.8 33.1 + - - +
128F ARG* 3.5 14.8 + - - +
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Residues in contact with GLU 125 (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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123F ASN 3.6 4.0 + - - +
124F ASP* 1.3 70.0 + - - +
126F HIS* 1.3 67.4 + - - +
127F THR 3.1 1.0 + - - -
128F ARG* 3.3 21.5 + - + +
129F ARG* 3.4 19.1 + - + +
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Residues in contact with HIS 126 (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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124F ASP* 2.7 17.7 + - - +
125F GLU* 1.3 74.0 - - - +
127F THR* 1.3 64.0 + - - -
129F ARG* 4.0 4.0 + - - +
130F GLU* 3.4 39.1 + - + +
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Residues in contact with THR 127 (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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87F ASP* 3.8 33.2 - - + +
121F LEU* 3.4 28.7 - - + +
124F ASP* 2.8 26.4 + - - -
125F GLU 3.1 0.4 - - - -
126F HIS* 1.3 83.3 + - - +
128F ARG* 1.3 63.5 + - - +
129F ARG 3.2 1.3 + - - -
130F GLU* 3.4 13.7 + - - +
131F LEU* 3.4 23.8 + - + +
138F PRO* 5.9 0.4 - - + -
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Residues in contact with ARG 128 (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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121F LEU 5.5 0.2 + - - -
122F ARG 3.8 16.9 + - - -
123F ASN* 4.5 9.8 + - - +
124F ASP 3.5 12.2 + - - +
125F GLU* 3.3 14.2 + - + +
127F THR* 1.3 77.1 - - - +
129F ARG* 1.3 62.6 + - - +
130F GLU 3.4 0.2 - - - -
131F LEU* 3.5 11.3 - - + +
132F ALA* 3.3 20.1 + - - +
136F GLN 4.7 0.3 - - - +
137F GLU* 5.5 3.4 - - + -
138F PRO* 3.5 35.8 - - + +
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Residues in contact with ARG 129 (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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125F GLU* 3.4 18.4 + - + +
126F HIS* 4.3 4.3 - - - +
127F THR 3.2 1.2 - - - -
128F ARG* 1.3 78.7 - - - +
130F GLU* 1.3 69.2 + - - +
132F ALA* 3.5 19.7 + - - +
133F LYS* 2.6 49.2 + - - +
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Residues in contact with GLU 130 (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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126F HIS* 3.4 34.9 + - + +
127F THR* 3.4 6.4 + - - +
128F ARG 3.4 0.2 - - - -
129F ARG* 1.3 92.1 + - - +
131F LEU* 1.3 65.2 + - - +
133F LYS* 3.4 36.0 + - - +
134F MET* 4.0 6.2 + - - +
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Residues in contact with LEU 131 (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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86F ILE 5.5 0.2 - - - +
87F ASP* 4.0 17.3 - - - +
89F PRO* 3.6 31.6 - - + -
127F THR* 3.4 28.4 + - + +
128F ARG* 3.5 11.7 - - - +
130F GLU* 1.3 76.7 - - - +
132F ALA* 1.3 62.3 + - - +
134F MET* 3.0 12.6 + - - +
136F GLN* 2.9 43.2 + - + +
137F GLU* 4.1 9.9 - - - -
138F PRO* 3.5 35.9 - - + -
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Residues in contact with ALA 132 (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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128F ARG 3.3 10.3 + - - +
129F ARG* 3.5 16.4 - - - +
130F GLU 3.3 0.2 - - - -
131F LEU* 1.3 77.8 - - - +
133F LYS* 1.3 57.4 + - + +
134F MET 3.0 0.2 - - - -
135F LYS* 2.8 24.7 + - - +
136F GLN 3.4 7.8 + - - +
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Residues in contact with LYS 133 (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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129F ARG* 2.6 61.7 + - - +
130F GLU* 3.4 33.3 + - - +
131F LEU 3.2 0.6 - - - -
132F ALA* 1.3 78.4 - - + +
134F MET* 1.3 62.2 + - + +
135F LYS 3.4 0.7 - - - -
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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