Contacts of the helix formed by residues 112 - 126 (chain A) in PDB entry 1O4X
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 GLU 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A SER 3.8 4.6 + - - +
111A ILE* 1.3 76.4 - - - +
113A THR* 1.3 81.0 + - - +
114A ASN* 2.9 25.9 - - - +
115A ILE* 3.1 30.8 + - + +
116A ARG* 3.0 24.5 + - - +
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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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111A ILE 3.7 1.4 + - - -
112A GLU* 1.3 83.9 + - - +
114A ASN* 1.3 62.7 + - - +
116A ARG* 3.4 33.7 + - - +
117A VAL* 3.4 15.5 + - + +
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Residues in contact with ASN 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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112A GLU* 2.9 23.7 - - - +
113A THR* 1.3 73.5 - - - +
115A ILE* 1.3 84.1 + - - +
117A VAL* 2.4 32.3 - - + +
118A ALA* 3.3 8.3 + - - +
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Residues in contact with ILE 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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111A ILE* 3.8 2.2 - - + -
112A GLU* 3.2 34.3 - - + +
114A ASN* 1.3 86.9 - - - +
116A ARG* 1.3 57.6 + - - +
118A ALA* 3.3 6.3 + - - +
119A LEU* 2.8 43.2 + - + +
141A LEU* 3.9 33.7 - - + +
143A MET* 3.2 48.2 - - + -
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Residues in contact with ARG 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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110A SER* 4.5 9.3 + - - +
111A ILE* 3.2 38.6 + - + +
112A GLU 3.0 16.3 + - - +
113A THR* 3.4 22.7 + - - +
115A ILE* 1.3 75.3 - - - +
117A VAL* 1.3 54.5 + - + +
119A LEU* 2.9 13.2 + - - +
120A GLU* 2.7 40.3 + - + +
151A TRP* 4.4 18.3 - - + -
315C T 4.1 41.3 + - - -
316C A 5.8 0.4 - - - -
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Residues in contact with VAL 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* 3.9 9.6 - - + +
114A ASN* 2.4 47.3 - - + +
116A ARG* 1.3 75.2 - - + +
118A ALA* 1.3 59.0 + - + +
120A GLU* 3.1 11.4 + - - +
121A LYS* 2.9 27.6 + - - +
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Residues in contact with ALA 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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114A ASN 3.3 8.3 + - - +
115A ILE* 3.6 7.9 - - - +
116A ARG 3.2 0.6 - - - -
117A VAL* 1.3 78.9 - - + +
119A LEU* 1.3 67.7 + - - +
121A LYS* 3.0 9.7 + - - +
122A SER* 2.8 23.6 + - - -
141A LEU* 4.5 21.5 - - + -
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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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111A ILE* 4.3 13.9 - - + -
115A ILE* 2.8 38.9 + - + +
116A ARG* 3.1 10.5 - - - +
118A ALA* 1.3 76.6 - - - +
120A GLU* 1.3 57.0 + - - +
122A SER* 3.1 6.6 + - - -
123A PHE* 2.9 28.2 + - - +
137A ILE* 4.6 5.2 - - + -
141A LEU* 3.9 20.9 - - + -
148A ILE* 4.0 17.5 - - + -
151A TRP* 3.4 51.5 + - + +
152A PHE* 4.2 15.2 - - + -
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Residues in contact with GLU 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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116A ARG* 2.7 25.2 + - + +
117A VAL* 3.3 11.4 - - - +
119A LEU* 1.3 69.5 - - - +
121A LYS* 1.3 66.2 + - - +
123A PHE* 3.2 8.2 + - - +
124A LEU* 3.0 31.4 + - + +
151A TRP* 3.6 24.7 - - + -
155A ARG* 3.4 34.0 + - - -
158A LYS* 6.0 0.3 + - - -
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Residues in contact with LYS 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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117A VAL 2.9 12.3 + - - +
118A ALA* 3.2 13.5 - - - +
120A GLU* 1.3 75.1 - - - +
122A SER* 1.3 64.7 + - - +
124A LEU* 3.0 30.9 - - - +
125A GLU* 3.2 16.1 + - - +
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Residues in contact with SER 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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118A ALA 2.8 11.6 + - - -
119A LEU* 3.3 11.4 - - - -
121A LYS* 1.3 77.5 - - - +
123A PHE* 1.3 64.9 + - - +
125A GLU* 2.7 26.4 + - - +
126A ASN* 2.9 14.8 + - - +
129A PRO* 5.5 0.7 - - - +
137A ILE* 4.2 19.0 - - - +
152A PHE* 3.4 21.0 - - - -
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Residues in contact with PHE 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 LEU 2.9 16.4 + - - +
120A GLU* 3.4 13.5 - - - +
122A SER* 1.3 71.9 + - - +
124A LEU* 1.3 69.8 + - + +
126A ASN 3.2 21.3 - - - -
127A GLN* 3.2 69.1 + - + +
151A TRP* 5.4 1.1 - - - +
152A PHE* 3.8 15.1 - + + -
155A ARG* 3.3 66.9 - - + -
156A ARG* 3.9 11.7 - - + -
159A GLU* 4.4 10.1 - - + -
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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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120A GLU* 3.0 21.9 + - + +
121A LYS* 3.0 20.0 - - - +
123A PHE* 1.3 85.6 - - + +
125A GLU* 1.3 62.0 + - + +
127A GLN* 5.8 0.3 - - - +
155A ARG* 6.4 0.4 - - - +
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Residues in contact with GLU 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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121A LYS* 3.2 16.7 + - - +
122A SER* 2.7 20.7 + - - +
124A LEU* 1.3 77.4 - - + +
126A ASN* 1.3 61.6 + - + +
127A GLN 4.3 0.4 + - - -
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Residues in contact with ASN 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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122A SER* 2.9 16.3 + - - +
123A PHE* 3.2 13.1 - - - +
125A GLU* 1.3 78.2 - - + +
127A GLN* 1.3 66.5 + - - +
128A LYS* 2.9 26.2 + - - +
129A PRO* 3.7 5.1 - - + +
130A THR* 6.0 0.2 - - - +
133A GLU* 3.1 33.0 + - - +
152A PHE* 3.6 9.4 - - - -
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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