Contacts of the helix formed by residues 107 - 122 (chain A) in PDB entry 1DIY
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A PHE* 6.3 0.7 - + - -
106A THR* 1.3 81.3 + - - +
108A ILE* 1.3 73.6 + - + +
109A ARG 2.7 14.1 + - - -
110A ASP* 2.9 27.4 + - + +
111A THR* 2.7 30.7 + - + -
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Residues in contact with ILE 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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102A PHE* 4.1 28.3 - - + -
103A VAL* 3.2 32.1 - - + -
106A THR* 2.7 23.2 + - + +
107A PHE* 1.3 105.0 - - + +
109A ARG* 1.3 57.7 + - - +
111A THR* 3.4 11.0 - - - -
112A LEU* 3.0 32.4 + - + +
753A BOG 4.2 8.3 - - + -
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Residues in contact with ARG 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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103A VAL* 3.5 12.0 + - - +
104A ASN* 3.6 23.9 + - - +
106A THR 2.8 15.4 + - - +
107A PHE 2.7 0.6 + - - -
108A ILE* 1.3 74.1 - - - +
110A ASP* 1.3 63.9 + - - +
111A THR 3.0 1.1 - - - -
112A LEU* 2.9 10.8 + - - +
113A MET* 2.7 37.0 + - + +
346A GLU* 4.7 7.9 + - - -
357A LEU* 4.5 10.8 - - + +
358A GLN* 3.0 59.4 + - - +
359A LEU 3.5 5.5 + - - -
360A LYS* 3.4 32.2 - - + +
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Residues in contact with ASP 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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107A PHE* 2.9 18.9 + - + +
109A ARG* 1.3 80.6 - - - +
111A THR* 1.3 57.1 + - - +
113A MET* 3.8 7.4 - - - +
114A ARG* 2.8 41.7 + - - +
360A LYS* 2.7 37.8 + - - +
365A LEU* 3.9 17.2 - - + +
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Residues in contact with THR 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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107A PHE* 2.7 28.0 + - + -
108A ILE* 3.4 15.3 - - - -
110A ASP* 1.3 78.6 - - - +
112A LEU* 1.3 59.5 + - + +
114A ARG* 3.7 11.2 - - - +
115A LEU* 2.9 28.4 + - + +
752A BOG 6.4 1.8 - - + -
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Residues in contact with LEU 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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100A TRP* 3.7 16.8 - - + -
103A VAL* 3.2 27.6 - - + -
108A ILE* 3.0 28.0 - - + +
109A ARG 2.9 4.3 + - - +
111A THR* 1.3 78.6 - - + +
113A MET* 1.3 56.7 + - - +
115A LEU* 2.8 12.8 + - + +
116A VAL* 2.6 40.4 + - + +
357A LEU* 3.8 19.7 - - + -
751A BOG 4.3 31.9 - - + -
753A BOG 4.5 11.2 - - + -
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Residues in contact with MET 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 ARG* 2.7 22.5 + - + +
110A ASP* 3.8 3.4 - - - +
112A LEU* 1.3 73.7 - - - +
114A ARG* 1.3 63.3 + - - +
116A VAL* 3.1 24.2 + - + +
117A LEU* 3.0 52.5 + - + +
345A ILE* 5.5 2.9 - - + -
357A LEU* 4.7 4.5 - - + +
358A GLN 6.1 0.2 - - - +
359A LEU* 3.8 21.8 - - + -
360A LYS* 3.2 50.9 - - + +
365A LEU* 3.5 22.2 - - + -
531A LEU* 5.0 4.0 - - + -
700A ACD 5.5 0.2 - - - +
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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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110A ASP* 2.8 33.2 + - - +
111A THR* 3.7 9.8 - - - +
113A MET* 1.3 73.3 - - - +
115A LEU* 1.3 59.2 + - - +
117A LEU* 4.0 4.3 - - - +
118A THR* 2.7 37.1 + - + +
364A GLU 4.5 3.2 + - - -
365A LEU* 3.0 60.9 + - + +
366A LEU* 5.0 0.4 - - + +
368A GLY* 5.7 2.6 - - - +
369A ALA* 6.4 1.3 - - - -
752A BOG 6.5 1.6 - - + -
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Residues in contact with LEU 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 THR 2.9 14.6 + - - +
112A LEU* 2.8 16.9 + - + +
114A ARG* 1.3 75.3 - - - +
116A VAL* 1.3 67.5 + - - +
118A THR* 2.6 21.1 + - - +
119A VAL* 3.2 29.3 - - + +
751A BOG 3.3 34.8 - - + -
752A BOG 3.5 58.6 - - + +
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Residues in contact with VAL 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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93A LEU* 6.3 1.8 - - + -
112A LEU* 2.6 27.1 + - + +
113A MET* 3.2 25.8 - - + +
115A LEU* 1.3 73.8 - - - +
117A LEU* 1.3 69.3 + - - +
119A VAL* 4.3 0.9 - - - +
120A ARG* 3.2 25.8 + - - +
355A TYR* 6.1 2.7 - - + -
357A LEU* 4.3 17.0 - - + -
359A LEU* 4.9 3.4 - - + -
531A LEU* 4.1 5.8 - - + -
700A ACD 3.5 32.3 - - - +
751A BOG 4.5 26.4 - - + +
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Residues in contact with LEU 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 MET* 3.0 39.4 + - + +
114A ARG* 4.0 2.9 - - - +
116A VAL* 1.3 82.2 - - - +
118A THR* 1.3 69.4 + - - +
120A ARG* 3.5 0.3 - - - +
121A SER* 2.7 30.5 + - - +
345A ILE* 5.6 1.6 - - + -
360A LYS 5.5 2.9 - - - +
362A ASP 5.4 2.5 - - - +
365A LEU* 4.4 24.0 - - + -
366A LEU* 3.8 33.9 - - + -
531A LEU* 4.0 20.6 - - + -
535A LEU* 3.7 29.8 - - + -
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Residues in contact with THR 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 ARG* 2.7 21.8 + - + +
115A LEU* 2.6 26.5 + - - +
117A LEU* 1.3 76.7 - - - +
119A VAL* 1.3 57.5 + - - +
121A SER* 3.1 4.1 + - - -
122A ASN* 2.7 39.0 + - - +
366A LEU* 3.8 20.4 - - + +
369A ALA* 4.2 17.9 - - + -
371A PHE* 6.2 2.0 - - - -
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Residues in contact with VAL 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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115A LEU* 3.2 39.6 + - + +
116A VAL* 4.3 1.8 - - - +
117A LEU 3.2 0.2 + - - -
118A THR* 1.3 78.4 + - - +
120A ARG* 1.3 65.8 + - - +
122A ASN* 3.5 14.3 + - - +
123A LEU* 4.2 4.0 - - - +
751A BOG 3.1 47.7 + - + +
752A BOG 3.9 21.3 - - - +
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Residues in contact with ARG 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 VAL* 3.2 16.3 + - - +
117A LEU 3.0 2.7 + - - +
119A VAL* 1.3 78.7 - - - +
121A SER* 1.3 65.1 + - - +
122A ASN 3.0 1.6 + - - -
123A LEU* 3.1 21.8 + - - +
355A TYR* 4.5 3.8 + - - -
523A ILE* 4.1 14.3 + - - +
524A GLU* 3.0 39.2 + - - +
527A ALA* 3.8 21.6 - - + +
528A PRO* 3.7 23.8 - - + +
531A LEU* 4.6 11.4 - - + -
700A ACD 2.4 33.9 + - - -
751A BOG 3.2 57.8 + - - +
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Residues in contact with SER 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 LEU* 2.7 26.7 + - - +
118A THR* 3.7 3.4 - - - -
120A ARG* 1.3 67.6 - - - +
122A ASN* 1.3 55.4 + - - +
123A LEU 3.0 11.1 + - - -
124A ILE* 3.5 17.4 + - - +
366A LEU* 6.0 0.6 - - - +
371A PHE* 3.7 30.1 - - - -
528A PRO 4.5 10.1 - - - -
531A LEU* 3.8 12.3 + - - +
532A LYS* 3.6 28.2 + - - +
535A LEU* 5.7 0.7 - - - +
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Residues in contact with ASN 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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44A GLN* 5.9 0.2 + - - -
118A THR 2.7 22.5 + - - +
119A VAL* 3.7 10.3 - - - +
120A ARG 3.0 1.2 + - - -
121A SER* 1.3 71.7 - - - +
123A LEU* 1.3 66.1 + - - +
124A ILE 3.6 1.5 - - - -
370A GLN 5.7 1.4 - - - +
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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