Contacts of the helix formed by residues 106 - 123 (chain D) in PDB entry 1CX2
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 PRO 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D ASN 5.6 0.9 - - - +
105D ILE* 1.3 96.9 - - + +
107D PHE* 1.3 62.3 + - + +
108D LEU 2.7 12.1 + - - -
109D ARG* 3.3 12.1 + - + +
110D SER* 2.8 20.4 + - - -
360D LYS* 5.3 0.7 + - - -
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Residues in contact with PHE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ILE* 3.3 37.5 - - + -
106D PRO* 1.3 85.0 - - + +
108D LEU* 1.3 61.1 + - + +
110D SER* 3.6 9.1 + - - -
111D LEU* 3.9 16.3 - - - +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 5.7 2.9 - - + -
103D VAL* 4.3 25.4 - - + +
105D ILE* 3.2 43.7 - - + +
106D PRO 2.7 6.9 + - - -
107D PHE* 1.3 80.0 - - + +
109D ARG* 1.3 68.1 + - - +
110D SER 3.1 1.1 - - - -
111D LEU* 3.1 23.5 + - + +
112D ILE* 2.9 33.8 + - + +
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Residues in contact with ARG 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D VAL* 4.1 12.7 + - + +
104D ASN* 4.5 14.2 + - - +
105D ILE 3.0 14.1 + - - +
106D PRO* 4.0 7.9 - - + +
108D LEU* 1.3 73.6 - - - +
110D SER* 1.3 53.1 + - - +
112D ILE* 2.9 8.5 + - - +
113D MET* 2.8 31.1 + - - -
346D GLU* 3.5 10.7 + - - -
357D PHE* 3.1 30.2 - - + -
358D LYS* 2.5 48.1 + - - +
359D LEU 2.5 24.7 + - - -
360D LYS* 3.0 38.7 - - + +
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Residues in contact with SER 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PRO 2.8 18.3 + - - -
107D PHE* 3.6 11.6 + - - -
109D ARG* 1.3 73.5 - - - +
111D LEU* 1.3 63.2 + - - +
113D MET* 3.7 6.4 - - - +
114D LYS* 2.7 37.7 + - - +
360D LYS* 3.5 28.0 - - - +
365D LEU* 4.0 13.1 - - - +
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE 3.9 18.6 - - - +
108D LEU* 3.1 23.7 + - + +
110D SER* 1.3 82.2 + - - +
112D ILE* 1.3 68.2 + - + +
114D LYS* 3.6 22.4 - - + +
115D TYR* 3.1 21.5 + - - +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 5.5 2.0 - - + -
100D TRP* 4.2 19.1 - - + -
103D VAL* 4.4 16.4 - - + -
108D LEU* 2.9 21.5 + - + +
109D ARG 3.1 9.9 - - - +
111D LEU* 1.3 77.5 - - + +
113D MET* 1.3 51.7 + - - +
115D TYR* 2.8 27.4 + - + +
116D VAL* 2.9 19.7 + - + +
357D PHE* 3.5 33.2 - - + -
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Residues in contact with MET 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ARG 2.8 16.3 + - - +
110D SER* 3.7 8.5 - - - +
112D ILE* 1.3 67.5 - - - +
114D LYS* 1.3 67.0 + - - +
116D VAL* 2.9 39.4 - - + +
117D LEU* 2.9 43.9 + - + +
345D ILE* 4.6 10.5 - - + -
357D PHE* 3.6 7.0 - - + -
359D LEU* 3.6 21.1 - - + -
360D LYS* 2.8 55.2 - - + +
365D LEU* 3.5 17.9 - - + -
531D LEU* 5.8 0.7 - - + -
701D S58 5.5 2.0 - - - -
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D SER 2.7 24.4 + - - +
111D LEU* 3.6 21.3 - - + +
113D MET* 1.3 72.6 - - - +
115D TYR* 1.3 58.5 + - - +
117D LEU* 3.3 5.4 - - - +
118D THR* 2.9 40.0 + - + +
365D LEU* 3.1 46.0 - - + +
366D LEU* 5.6 0.4 - - + -
368D ASN* 4.4 8.2 + - - +
369D GLN* 3.5 32.8 - - - +
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Residues in contact with TYR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU 3.1 12.9 + - - +
112D ILE* 2.8 16.5 + - + +
114D LYS* 1.3 77.7 - - - +
116D VAL* 1.3 69.7 + - + +
118D THR* 3.0 17.8 + - - -
119D SER* 2.7 54.1 + - - -
120D ARG* 6.2 2.0 - - - -
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 5.4 11.0 - - + -
112D ILE* 2.9 29.0 + - + +
113D MET* 2.9 50.7 - - + +
115D TYR* 1.3 79.9 - - + +
117D LEU* 1.3 69.8 + - + +
119D SER* 3.6 1.6 + - - -
120D ARG* 3.0 38.1 + - - +
355D TYR* 5.6 0.7 - - + -
357D PHE* 4.9 7.0 - - + -
359D LEU* 4.8 8.3 - - + -
531D LEU* 4.8 0.7 - - - -
701D S58 4.4 24.5 - - - -
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D MET* 2.9 48.2 + - + +
114D LYS* 3.3 9.0 - - - +
115D TYR 3.0 0.4 - - - -
116D VAL* 1.3 86.5 - - + +
118D THR* 1.3 67.8 + - - +
120D ARG* 3.5 5.7 + - - +
121D SER* 3.6 14.0 + - - -
345D ILE* 5.4 1.3 - - + -
360D LYS 4.9 0.4 - - - +
365D LEU* 4.5 12.3 - - + -
366D LEU* 4.2 27.8 - - + -
531D LEU* 3.9 27.1 - - + +
535D MET* 3.8 35.2 - - + -
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Residues in contact with THR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS* 2.9 24.9 + - + +
115D TYR* 3.0 23.6 + - - -
117D LEU* 1.3 78.4 - - - +
119D SER* 1.3 63.6 + - - +
121D SER* 3.6 7.6 + - - -
122D TYR* 3.8 8.3 + - - +
366D LEU* 3.7 20.2 - - + +
369D GLN* 3.7 36.1 - - + +
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Residues in contact with SER 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D TYR* 2.7 57.5 + - - -
116D VAL* 3.6 2.4 + - - -
118D THR* 1.3 76.0 + - - +
120D ARG* 1.3 75.0 + - - +
121D SER 3.0 1.6 + - - -
122D TYR* 3.0 34.4 + - - -
123D LEU* 3.9 0.5 - - - +
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Residues in contact with ARG 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D VAL* 4.7 16.8 - - - +
93D LEU* 5.4 2.6 - - - +
115D TYR* 6.2 1.4 - - - -
116D VAL* 3.0 29.8 + - - +
117D LEU 3.8 3.4 - - - +
118D THR 3.5 0.2 - - - -
119D SER* 1.3 84.3 + - - +
121D SER* 1.3 57.5 + - - +
123D LEU* 3.0 22.5 - - - +
355D TYR* 4.0 8.1 + - - -
524D GLU* 5.1 12.9 + - - -
527D ALA* 3.3 26.6 - - + +
528D PRO* 3.3 25.1 - - + +
531D LEU* 3.7 15.5 - - + -
701D S58 2.6 54.2 + - - +
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU 3.6 8.5 + - - -
118D THR 3.6 6.0 + - - -
119D SER 3.1 1.0 - - - -
120D ARG* 1.3 77.4 - - - +
122D TYR* 1.3 60.1 + - - +
123D LEU 2.9 6.1 + - - -
124D ILE* 3.2 27.7 + - - +
371D PHE* 5.6 4.7 - - - -
528D PRO* 3.3 18.5 + - - +
531D LEU* 3.8 16.5 - - - +
532D LYS* 3.6 23.0 - - - +
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Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D THR 3.8 6.1 + - - +
119D SER* 3.0 31.3 + - - +
121D SER* 1.3 77.3 - - - +
123D LEU* 1.3 86.2 + - + +
124D ILE 3.2 8.9 + - - +
471D SER* 2.7 30.1 + - - -
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ARG* 5.3 1.3 - - - +
119D SER 3.9 1.1 - - - +
120D ARG* 3.0 27.8 - - - +
121D SER 2.9 1.0 - - - -
122D TYR* 1.3 127.4 - - + +
124D ILE* 1.3 64.5 + - + +
469D ARG* 2.5 51.2 + - - +
470D PHE* 4.1 33.4 - - + +
471D SER* 3.8 10.1 - - - +
528D PRO* 4.3 4.5 - - + -
529D PHE* 4.8 0.7 - - - -
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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