Contacts of the helix formed by residues 114 - 126 (chain A) in PDB entry 3F9C
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 HIS 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A SER* 2.5 24.4 + - - -
113A THR* 1.3 95.2 - - + +
115A TRP* 1.3 77.6 + + + +
116A LEU* 3.2 32.1 + - + +
117A MET* 3.2 37.5 + - + -
118A GLY* 3.3 7.8 + - - -
120A ILE* 6.1 0.4 - - + -
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Residues in contact with TRP 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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105A TRP* 5.5 3.9 - - - -
114A HIS* 1.3 83.9 - + + +
116A LEU* 1.3 105.8 + - + +
118A GLY* 3.5 2.8 + - - +
119A ASN* 3.0 44.2 + - + +
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Residues in contact with LEU 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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114A HIS* 3.2 23.8 + - + +
115A TRP* 1.3 115.8 - - + +
117A MET* 1.3 61.5 + - - +
119A ASN* 3.3 6.1 + - + +
120A ILE* 2.9 49.1 + - + +
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Residues in contact with MET 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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108A SER* 4.1 2.0 - - - +
111A LEU* 4.2 19.1 - - + -
113A THR* 3.3 33.7 - - + +
114A HIS* 3.2 20.2 + - + +
116A LEU* 1.3 71.9 - - - +
118A GLY* 1.3 61.0 + - - +
120A ILE* 3.1 23.1 + - + +
121A LEU* 2.8 60.2 + - + +
124A LEU* 6.5 0.2 - - + -
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Residues in contact with GLY 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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104A PHE* 3.5 33.4 - - - +
105A TRP* 4.6 10.7 - - - -
108A SER* 3.6 5.9 - - - -
114A HIS 3.3 8.6 + - - -
115A TRP* 3.8 4.9 - - - -
116A LEU 3.3 0.8 - - - -
117A MET* 1.3 78.4 - - - +
119A ASN* 1.3 60.9 + - - +
121A LEU* 3.6 1.3 + - - -
122A ARG* 3.2 23.4 + - - +
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Residues in contact with ASN 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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105A TRP* 4.6 12.5 + - - +
115A TRP* 3.0 39.7 + - + +
116A LEU* 3.9 7.2 - - + +
117A MET 3.2 0.6 - - - -
118A GLY* 1.3 76.2 - - - +
120A ILE* 1.3 63.4 + - - +
122A ARG* 3.5 22.9 + - - +
123A LEU* 3.2 29.6 + - + +
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Residues in contact with ILE 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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114A HIS* 6.1 0.2 - - + -
116A LEU* 2.9 45.1 + - + +
117A MET* 3.1 25.3 + - + +
119A ASN* 1.3 74.1 - - - +
121A LEU* 1.3 59.9 + - + +
123A LEU* 3.1 10.2 + - + +
124A LEU* 3.0 44.3 + - + +
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Residues in contact with LEU 121 (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 PHE* 3.5 24.5 - - + +
107A LEU* 4.2 29.2 - - + -
108A SER 4.4 5.6 - - - +
111A LEU* 4.5 10.8 - - + -
117A MET* 2.8 51.7 + - + +
118A GLY 3.9 2.9 - - - +
120A ILE* 1.3 71.8 - - - +
122A ARG* 1.3 53.1 + - - +
124A LEU* 3.4 6.9 + - + -
125A PHE* 2.8 64.4 + - + +
357A PHE* 5.3 5.6 - - + -
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Residues in contact with ARG 122 (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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101A LYS* 3.5 42.1 - - + +
104A PHE* 3.7 30.7 - - + -
105A TRP* 5.6 3.8 - - - +
118A GLY 3.2 15.2 + - - +
119A ASN* 3.7 22.5 + - - +
120A ILE 3.3 0.2 - - - -
121A LEU* 1.3 78.1 - - - +
123A LEU* 1.3 57.8 + - - +
126A GLY* 2.7 32.5 + - - -
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Residues in contact with LEU 123 (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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119A ASN* 3.2 18.9 + - + +
120A ILE* 3.1 11.7 + - + +
122A ARG* 1.3 75.9 - - - +
124A LEU* 1.3 66.3 + - + +
125A PHE 3.4 0.3 + - - -
126A GLY 4.4 1.2 + - - -
127A SER* 5.0 5.4 + - - -
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Residues in contact with LEU 124 (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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117A MET* 6.5 0.2 - - + -
120A ILE* 3.0 37.5 + - + +
121A LEU* 4.7 4.5 - - + -
123A LEU* 1.3 80.0 - - + +
125A PHE* 1.3 98.4 + - + +
127A SER* 5.4 1.7 + - - -
128A MET* 4.7 6.6 + - - +
361A THR* 6.4 0.7 - - + -
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Residues in contact with PHE 125 (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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97A TRP* 4.2 24.8 - + + -
98A ILE* 5.2 3.5 + - - +
104A PHE* 3.8 15.8 - + + -
121A LEU* 2.8 52.2 + - + +
124A LEU* 1.3 108.0 - - + +
126A GLY* 1.3 52.0 + - - +
127A SER* 2.8 16.8 + - - -
128A MET* 3.0 34.9 + - + +
357A PHE* 4.0 18.2 - + - -
360A ALA* 3.5 38.1 - - + -
361A THR* 4.5 12.8 - - + -
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Residues in contact with GLY 126 (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 LEU* 3.9 20.4 - - - +
98A ILE 4.4 5.5 - - - +
104A PHE* 3.9 18.3 - - - -
122A ARG* 2.7 30.0 + - - -
123A LEU 4.4 1.0 + - - -
124A LEU 3.9 0.6 - - - -
125A PHE* 1.3 69.4 - - - +
127A SER* 1.3 57.5 + - - +
128A MET 5.1 0.2 - - - -
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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