Contacts of the helix formed by residues 101 - 112 (chain F) in PDB entry 3HR4
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 SER 101 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F TYR 3.1 3.8 + - - -
100F ILE* 1.3 76.2 - - - +
102F ALA* 1.3 64.9 + - - +
103F ALA* 3.4 9.6 + - - +
104F GLU* 2.9 36.7 + - - +
105F LEU* 3.1 22.0 + - - +
125F ILE* 4.6 2.5 - - - -
135F GLN* 3.8 27.6 - - - -
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Residues in contact with ALA 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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101F SER* 1.3 74.5 - - - +
103F ALA* 1.3 57.1 + - - +
105F LEU* 3.2 5.4 + - - +
106F ARG* 3.0 47.9 + - - +
121F VAL* 4.2 8.3 - - + +
125F ILE* 3.7 27.8 - - + +
134F GLY 4.7 5.0 + - - +
135F GLN* 5.0 0.6 - - - +
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Residues in contact with ALA 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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101F SER* 3.1 10.8 + - - +
102F ALA* 1.3 76.4 - - - +
104F GLU* 1.3 66.0 + - + +
106F ARG* 3.2 29.9 + - - +
107F HIS* 3.1 22.3 + - - +
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Residues in contact with GLU 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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92F PHE* 3.2 24.4 - - - +
93F ASP* 3.7 1.2 - - - +
94F LYS* 3.3 21.7 + - + +
95F ASP* 3.2 19.4 + - - +
99F TYR 2.8 12.3 - - - +
100F ILE* 3.2 8.6 - - + -
101F SER* 2.9 26.8 + - - +
103F ALA* 1.3 77.3 - - + +
105F LEU* 1.3 59.9 + - - +
107F HIS* 3.6 8.4 - - - +
108F VAL* 3.3 28.2 + - - +
203F CA 2.4 30.2 - - - -
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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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515E LEU* 4.2 18.4 - - + -
518E LEU* 4.7 3.6 - - + -
92F PHE* 3.6 31.6 - - + -
100F ILE* 4.6 9.1 - - + +
101F SER 3.1 12.1 + - - +
102F ALA* 3.4 13.2 - - - +
103F ALA 3.1 0.6 - - - -
104F GLU* 1.3 76.5 - - - +
106F ARG* 1.3 65.8 + - - +
108F VAL* 3.4 1.3 + - - -
109F MET* 3.0 25.2 + - + +
121F VAL* 4.1 11.9 - - + -
124F MET* 3.3 39.0 - - + -
125F ILE* 5.1 10.3 - - + -
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Residues in contact with ARG 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 ALA* 3.0 30.3 + - - +
103F ALA* 3.2 34.8 + - - +
105F LEU* 1.3 75.1 - - - +
107F HIS* 1.3 65.2 + - - +
109F MET* 2.7 11.7 + - - +
110F THR* 2.7 29.5 + - + +
116F LEU* 3.9 27.6 - - + -
118F ASP* 4.3 15.9 + - - -
121F VAL* 3.9 23.1 - - + +
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Residues in contact with HIS 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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94F LYS* 3.9 25.0 + - + +
103F ALA 3.1 10.2 + - - +
104F GLU* 3.6 14.0 - - - +
106F ARG* 1.3 78.1 - - - +
108F VAL* 1.3 58.2 + - - +
110F THR* 3.0 10.7 + - - -
111F ASN* 2.8 60.9 + - - -
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Residues in contact with VAL 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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518E LEU* 4.7 4.7 - - + -
522E VAL* 5.6 0.7 - - + -
39F LEU* 4.4 13.2 - - + -
91F VAL* 3.9 23.6 - - + +
92F PHE* 3.6 40.8 - - + -
94F LYS* 4.2 9.6 - - - +
104F GLU 3.3 16.6 + - - +
105F LEU* 4.0 2.7 - - + +
106F ARG 3.2 0.8 - - - -
107F HIS* 1.3 79.4 - - - +
109F MET* 1.3 61.8 + - - +
111F ASN* 3.4 8.4 + - + +
112F LEU* 3.2 39.3 + - + +
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Residues in contact with MET 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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513E ILE* 4.3 11.7 - - + +
518E LEU* 3.7 29.2 - - + -
105F LEU* 3.0 34.6 + - + +
106F ARG* 2.7 17.9 + - - +
108F VAL* 1.3 71.1 - - - +
110F THR* 1.3 62.1 + - - +
112F LEU* 3.2 9.0 + - - +
113F GLY 3.1 4.3 + - - -
114F GLU* 3.1 48.2 + - + +
115F LYS 4.9 0.7 - - - -
116F LEU* 4.6 14.1 - - + +
120F GLU* 3.0 28.7 - - - +
121F VAL* 5.2 0.2 - - + -
124F MET* 3.7 22.7 - - + +
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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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106F ARG* 2.7 23.1 + - + +
107F HIS* 3.0 19.4 + - - -
109F MET* 1.3 70.5 - - - +
111F ASN* 1.3 63.2 + - - +
113F GLY* 2.9 19.5 + - - +
114F GLU 4.6 0.9 - - - +
115F LYS* 4.0 22.7 + - - +
116F LEU* 3.5 34.8 - - + +
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Residues in contact with ASN 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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38F SER* 3.3 40.5 + - - +
94F LYS* 3.8 15.8 - - - +
107F HIS* 2.8 55.1 + - - +
108F VAL* 3.8 8.6 - - - +
109F MET 3.3 0.2 - - - -
110F THR* 1.3 75.5 + - - +
112F LEU* 1.3 58.7 + - - +
113F GLY 3.2 0.6 + - - -
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Residues in contact with LEU 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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518E LEU* 3.7 30.7 - - + -
18F LEU* 4.5 15.0 - - + -
21F LYS* 4.6 16.1 + - - +
35F VAL* 4.2 22.4 - - + -
38F SER* 4.1 10.3 - - - -
39F LEU* 3.6 26.0 - - + -
108F VAL* 3.2 29.3 + - + +
109F MET* 3.6 8.7 - - - +
110F THR 3.1 0.8 - - - -
111F ASN* 1.3 76.7 - - - +
113F GLY* 1.3 62.3 + - - +
114F GLU* 4.0 18.5 - - - +
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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