Contacts of the helix formed by residues 104 - 114 (chain A) in PDB entry 5FN2
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 THR 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LYS 5.2 2.5 - - - -
102A HIS 3.1 15.9 + - - +
103A PHE* 1.3 79.3 - - - +
105A ARG* 1.3 67.7 + - - +
106A ASP* 4.3 4.4 + - + +
107A LEU* 3.8 21.2 - - + +
108A MET* 3.2 25.8 + - - +
134A PHE* 5.8 2.1 - - - +
169A ASN* 3.3 18.9 + - - +
171A LEU* 4.0 8.2 - - - +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR* 1.3 80.2 + - - +
106A ASP* 1.3 69.4 + - - +
108A MET* 3.2 4.3 + - - +
109A GLU* 2.8 66.5 + - + +
169A ASN* 3.1 39.4 + - + +
170A GLY* 3.0 26.3 + - - -
171A LEU* 3.7 20.4 - - - -
174A GLU* 3.3 18.9 + - - +
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR* 4.3 4.4 - - + +
105A ARG* 1.3 89.4 - - - +
107A LEU* 1.3 57.9 + - - +
109A GLU* 3.2 8.9 + - - +
110A LYS* 2.9 33.0 + - - +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 6.2 2.0 - - + -
79A GLU* 4.2 16.8 - - - +
82A LEU* 3.5 35.2 - - + -
98A LEU* 4.2 26.2 - - + -
102A HIS* 3.1 34.8 - - + +
103A PHE* 4.3 3.8 - - + -
104A THR* 3.8 16.6 - - + +
105A ARG 3.2 0.2 - - - -
106A ASP* 1.3 77.3 - - - +
108A MET* 1.3 61.1 + - - +
110A LYS* 3.2 12.8 + - - +
111A LEU* 2.9 34.8 + - + +
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Residues in contact with MET 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 6.3 0.2 - - - -
103A PHE* 3.6 34.5 - - + -
104A THR 3.2 18.0 + - - +
105A ARG 3.2 5.5 + - - +
107A LEU* 1.3 80.9 - - - +
109A GLU* 1.3 60.5 + - - +
111A LEU* 3.2 10.6 + - - +
112A LYS* 2.9 29.0 + - - +
121A LEU* 4.0 13.0 - - + -
171A LEU* 3.8 13.5 - - + -
174A GLU* 5.9 0.4 - - + -
176A PHE* 3.2 49.8 - - + -
178A PHE* 4.9 4.7 - - + -
180A ILE* 3.8 22.9 - - + -
287A PHE* 4.0 4.5 - - + -
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 2.8 42.4 + - - +
106A ASP* 3.2 12.5 + - - +
108A MET* 1.3 79.0 - - - +
110A LYS* 1.3 56.1 + - - +
112A LYS* 3.2 20.0 + - - +
113A GLY* 2.9 26.0 + - - -
174A GLU* 4.5 17.7 - - - +
176A PHE* 6.1 0.3 - - - -
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLU* 4.2 22.2 + - - +
82A LEU* 3.4 26.0 - - + +
86A LEU* 5.3 6.3 - - + +
106A ASP* 2.9 14.0 + - - +
107A LEU* 3.3 15.7 - - - +
109A GLU* 1.3 76.1 - - - +
111A LEU* 1.3 63.1 + - - +
113A GLY* 3.2 15.1 + - - -
114A ARG* 3.6 6.9 + - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LEU* 4.2 20.1 - - + +
86A LEU* 4.9 4.0 - - - +
96A VAL* 4.6 5.8 - - + -
98A LEU* 5.6 7.4 - - + -
107A LEU* 2.9 21.4 + - + +
108A MET* 3.3 14.4 - - - +
110A LYS* 1.3 77.4 - - - +
112A LYS* 1.3 61.9 + - - +
114A ARG* 3.3 23.9 + - - +
115A THR* 4.2 0.5 - - - -
118A ILE* 3.3 53.7 - - + +
121A LEU* 3.5 28.7 - - + -
178A PHE* 3.4 28.7 - - + -
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A MET 2.9 12.6 + - - +
109A GLU* 3.2 26.4 + - - +
111A LEU* 1.3 76.1 - - - +
113A GLY* 1.3 58.8 + - - +
115A THR* 2.9 33.3 + - - +
174A GLU* 3.0 26.3 + - + +
175A ASP* 3.8 21.9 + - - +
176A PHE* 4.4 20.0 - - + -
177A SER 6.1 1.1 - - - +
178A PHE* 4.5 12.3 - - + -
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU 2.9 13.6 + - - -
110A LYS* 3.2 7.7 + - - -
112A LYS* 1.3 75.3 - - - +
114A ARG* 1.3 63.4 + - - +
115A THR 3.7 0.6 + - - -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.4 61.2 + - + +
87A THR* 4.5 14.3 + - - +
110A LYS 3.6 3.8 + - - +
111A LEU 3.3 12.3 + - - +
112A LYS 3.1 0.4 - - - -
113A GLY* 1.3 79.9 - - - +
115A THR* 1.3 63.1 + - - +
116A SER* 3.4 3.9 + - - +
117A ARG* 3.7 22.1 + - + +
118A ILE* 3.5 13.5 + - - +
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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