Contacts of the helix formed by residues 112 - 120 (chain A) in PDB entry 2F4N
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 PHE 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.6 19.1 - - + -
71A ILE* 5.2 1.6 - - + -
79A HIS 4.0 4.7 - - - -
81A ALA* 3.5 26.9 - - + -
94A ILE* 5.0 4.3 - - + -
96A ILE* 4.1 24.2 - - + -
104A LEU* 3.8 28.5 - - + -
105A VAL 3.0 49.4 - - - -
106A GLY* 3.3 13.0 - - - -
107A PRO* 4.6 11.0 + - + -
110A GLY 3.3 0.6 - - - -
111A LEU* 1.3 78.8 - - + +
113A THR* 1.3 59.7 + - - +
114A TYR 3.6 1.1 - - - -
115A VAL* 3.8 15.5 - - + -
116A ALA* 2.9 28.5 + - - +
165A MSE 5.3 4.0 - - - -
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Residues in contact with THR 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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110A GLY* 2.7 30.2 + - - -
111A LEU 3.2 1.6 + - - -
112A PHE* 1.3 76.2 - - - +
114A TYR* 1.3 70.6 + - + +
116A ALA* 3.9 2.4 - - - +
117A GLU* 2.9 47.6 + - - +
165A MSE 5.4 5.4 - - - -
166A VAL 3.9 1.0 + - - -
167A LYS* 3.4 16.3 - - + +
168A ILE* 3.0 45.6 + - + +
170A GLU* 4.5 0.9 - - - -
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Residues in contact with TYR 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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61A TYR* 4.7 7.7 + - - -
64A ALA* 3.6 35.6 + - + +
65A TYR* 4.0 13.2 - + + -
68A LEU* 3.8 31.9 - - + +
111A LEU 4.9 1.0 + - - -
112A PHE 3.6 0.2 - - - -
113A THR* 1.3 76.2 - - - +
115A VAL* 1.3 64.3 + - - +
117A GLU* 3.4 8.9 + - - +
118A LYS* 3.2 22.7 + - - +
168A ILE* 3.4 35.6 - - + +
170A GLU* 3.1 38.4 - - + +
176A ILE* 4.1 31.3 + - + +
187A ASN* 5.6 2.0 - - + +
239A PHE* 6.0 4.0 - + - -
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Residues in contact with VAL 115 (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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64A ALA 5.2 0.8 + - - +
67A LEU* 4.3 13.0 - - + +
68A LEU* 4.3 19.4 - - - +
71A ILE* 3.8 28.7 - - + -
72A PRO* 4.7 5.6 - - + -
104A LEU* 3.9 13.7 - - + -
111A LEU 5.2 0.2 - - - +
112A PHE* 3.4 31.6 - - + +
114A TYR* 1.3 76.9 - - - +
116A ALA* 1.3 64.2 + - - +
118A LYS* 3.3 3.3 + - - +
119A LEU* 3.0 50.1 + - + +
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Residues in contact with ALA 116 (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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96A ILE* 4.6 7.6 - - + -
98A THR* 5.3 1.8 - - - -
104A LEU* 4.3 15.7 - - + -
112A PHE* 2.9 26.2 + - + +
113A THR* 3.9 2.9 - - - +
115A VAL* 1.3 78.1 - - - +
117A GLU* 1.3 58.6 + - + +
119A LEU* 3.8 2.6 - - - -
120A GLY* 3.0 31.9 + - - -
121A ILE* 3.7 28.8 + - + +
165A MSE 4.7 3.8 - - - -
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Residues in contact with GLU 117 (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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113A THR* 2.9 27.2 + - - +
114A TYR* 3.7 7.7 - - - +
115A VAL 3.2 0.6 - - - -
116A ALA* 1.3 79.8 - - + +
118A LYS* 1.3 60.0 + - - +
119A LEU 3.4 0.7 + - - -
120A GLY* 3.4 9.9 + - - -
121A ILE* 5.5 3.6 - - + -
167A LYS* 3.6 32.8 + - - +
170A GLU* 2.8 41.3 - - - +
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Residues in contact with LYS 118 (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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68A LEU* 4.3 21.0 + - + +
72A PRO* 4.4 24.7 - - + +
73A TYR* 5.7 5.5 + - - -
114A TYR 3.2 14.0 + - - +
115A VAL* 3.3 4.7 + - - +
117A GLU* 1.3 79.5 - - - +
119A LEU* 1.3 66.6 + - + +
120A GLY 3.4 0.4 - - - -
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Residues in contact with LEU 119 (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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71A ILE* 4.0 7.0 - - + -
72A PRO* 4.5 23.3 - - + +
98A THR* 3.6 27.6 - - + +
99A LYS* 3.4 18.2 + - - +
100A SER* 4.6 2.8 + - - -
102A TYR* 3.9 39.3 - - + +
104A LEU* 4.9 2.2 - - + -
115A VAL* 3.0 38.3 + - + +
116A ALA 4.4 0.2 - - - +
118A LYS* 1.3 85.0 - - + +
120A GLY* 1.3 67.6 + - - +
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Residues in contact with GLY 120 (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 THR* 3.1 7.1 - - - -
99A LYS* 2.9 22.8 + - - -
116A ALA 3.0 11.0 + - - -
117A GLU* 3.4 10.0 + - - -
118A LYS 3.4 0.6 - - - -
119A LEU* 1.3 87.2 - - - +
121A ILE* 1.3 61.3 + - - -
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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