Contacts of the helix formed by residues 97 - 115 (chain A) in PDB entry 6DMY
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 ASN 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A TYR* 2.9 54.8 + - - +
94A ILE* 3.2 8.2 + - - +
95A GLN 3.2 1.8 - - - -
96A LYS* 1.3 89.8 - - - +
98A CYS* 1.3 65.1 + - - +
99A GLY 3.6 1.3 - - - -
100A LYS* 3.9 25.8 - - + +
101A PHE* 3.3 41.0 + - + +
594A ALA* 5.2 1.0 - - - +
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Residues in contact with CYS 98 (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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94A ILE 4.3 3.8 - - - -
95A GLN 4.3 3.8 - - - +
96A LYS 3.6 2.8 - - - -
97A ASN* 1.3 78.0 - - - +
99A GLY* 1.3 72.6 + - - +
100A LYS* 4.6 4.2 - - - +
102A LEU* 3.8 5.9 + - - +
594A ALA* 3.7 23.1 - - - +
597A SER* 3.3 31.2 - - - +
598A MET* 3.7 31.9 - - + +
601A TYR* 3.9 18.6 - - + -
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Residues in contact with GLY 99 (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 CYS* 1.3 88.1 - - - +
100A LYS* 1.3 62.4 + - - +
101A PHE 3.4 0.2 - - - -
102A LEU* 3.3 8.7 + - - +
103A VAL* 3.0 34.6 + - - +
598A MET* 4.5 7.6 - - - +
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Residues in contact with LYS 100 (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 LYS 4.8 3.8 - - - +
97A ASN* 4.1 34.1 - - + +
98A CYS* 3.3 4.6 - - - +
99A GLY* 1.3 81.1 - - - +
101A PHE* 1.3 64.3 + - + +
103A VAL* 3.2 8.0 + - - +
104A VAL* 2.9 32.0 + - + +
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Residues in contact with PHE 101 (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 TYR* 4.0 28.0 - + - -
94A ILE* 3.6 32.5 - - + -
97A ASN* 3.3 42.2 + - + +
100A LYS* 1.3 81.1 - - + +
102A LEU* 1.3 61.2 + - - +
104A VAL* 4.2 21.5 - - + -
105A GLY 2.9 21.1 + - - -
590A LEU 5.3 2.0 - - - +
591A ILE* 3.5 20.3 - - + +
594A ALA* 4.8 9.6 - - + -
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Residues in contact with LEU 102 (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 CYS 3.8 12.6 + - - +
99A GLY* 3.3 13.5 + - - +
100A LYS 3.3 0.4 - - - -
101A PHE* 1.3 78.2 - - - +
103A VAL* 1.3 65.0 + - + +
106A LEU* 3.0 52.0 + - + +
591A ILE* 4.6 19.3 - - + +
594A ALA* 4.3 11.7 - - + +
595A ILE* 5.2 19.3 - - + +
598A MET* 6.2 2.9 - - + -
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Residues in contact with VAL 103 (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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99A GLY 3.0 19.6 + - - +
100A LYS* 3.2 10.1 + - - +
102A LEU* 1.3 84.3 - - + +
104A VAL* 1.3 62.3 + - + +
107A LEU* 2.9 53.5 + - + +
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Residues in contact with VAL 104 (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 LYS* 2.9 23.2 + - + +
101A PHE* 4.2 22.9 - - + -
103A VAL* 1.3 79.1 - - + +
105A GLY* 1.3 59.7 + - - +
107A LEU* 3.8 1.7 - - - +
108A ILE* 3.0 50.0 + - + +
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Residues in contact with GLY 105 (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 PHE 2.9 17.9 + - - -
104A VAL* 1.3 77.8 - - - +
106A LEU* 1.3 57.8 + - - +
108A ILE* 3.4 9.1 - - - +
109A PHE* 3.0 40.6 + - - +
591A ILE* 3.8 20.4 - - - -
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Residues in contact with LEU 106 (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 LEU* 3.0 36.8 + - + +
103A VAL 4.4 0.2 - - - +
105A GLY* 1.3 75.3 - - - +
107A LEU* 1.3 74.2 + - + +
109A PHE* 3.2 3.1 + - - -
110A GLY* 3.0 28.1 + - - -
476A LEU* 6.1 3.4 - - + -
479A LEU* 3.7 30.5 - - + -
587A MET* 5.6 7.6 - - + -
591A ILE* 5.1 3.9 - - + +
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Residues in contact with LEU 107 (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* 2.9 45.5 + - + +
104A VAL* 4.0 2.2 - - - +
106A LEU* 1.3 93.8 - - + +
108A ILE* 1.3 61.3 + - + +
110A GLY* 4.3 4.1 + - - +
111A ALA* 4.4 9.0 + - - +
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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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104A VAL* 3.0 35.7 + - + +
105A GLY* 3.4 12.3 - - - +
107A LEU* 1.3 78.9 - - + +
109A PHE* 1.3 85.3 + - + +
110A GLY 3.4 0.7 - - - -
111A ALA* 3.6 18.5 + - - +
112A PHE* 4.0 12.0 + - - -
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Residues in contact with PHE 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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105A GLY* 3.0 21.6 + - - +
106A LEU* 3.2 3.8 + - + +
108A ILE* 1.3 98.0 - - + +
110A GLY* 1.3 64.0 + - - +
111A ALA 3.2 1.1 + - - -
112A PHE* 3.8 8.3 + + - +
113A ALA 3.7 2.9 + - - -
479A LEU* 3.3 27.4 - - + +
480A SER* 6.0 0.2 - - - -
483A ALA* 3.5 15.7 - - - +
583A PHE* 3.5 40.4 - + + -
586A ALA* 5.5 4.7 - - + -
587A MET* 3.5 52.3 - - + -
591A ILE* 4.3 11.9 - - + -
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Residues in contact with GLY 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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106A LEU* 3.0 15.3 + - - -
107A LEU* 4.3 2.4 - - - -
108A ILE 3.4 0.4 - - - -
109A PHE* 1.3 77.5 - - - +
111A ALA* 1.3 55.6 + - - +
113A ALA* 3.0 9.6 + - - +
114A VAL* 3.0 32.9 + - - +
479A LEU* 4.2 8.6 - - - +
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Residues in contact with ALA 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 LEU 4.4 7.9 + - - +
108A ILE* 3.6 15.5 + - - +
109A PHE 3.2 0.8 - - - -
110A GLY* 1.3 77.4 - - - +
112A PHE* 1.3 64.4 + - + +
114A VAL* 3.6 3.7 + - - +
115A GLY* 2.9 26.0 + - - -
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Residues in contact with PHE 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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108A ILE 4.0 11.3 + - - -
109A PHE* 3.8 8.1 + + - +
111A ALA* 1.3 82.4 - - + +
113A ALA* 1.3 62.0 + - - +
115A GLY* 3.3 13.3 + - - +
483A ALA* 3.6 25.4 - - + +
486A GLY* 3.5 20.4 - - - -
487A LEU* 4.2 33.9 - - + +
490A LEU* 4.7 13.2 - - + -
583A PHE* 3.9 33.4 - + - -
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Residues in contact with ALA 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 PHE 3.7 10.0 + - - +
110A GLY* 3.0 13.2 + - - +
112A PHE* 1.3 80.2 - - - +
114A VAL* 1.3 61.8 + - + +
116A LEU* 3.3 22.0 - - - +
479A LEU* 4.7 8.1 - - + -
482A ALA* 4.5 14.0 - - + +
483A ALA* 4.1 18.6 - - + +
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Residues in contact with VAL 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 GLY 3.0 14.5 + - - +
111A ALA* 4.4 4.0 - - - +
113A ALA* 1.3 80.1 - - + +
115A GLY* 1.3 52.2 + - - +
116A LEU* 2.7 25.1 + - - +
117A LYS* 4.6 0.5 + - - +
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Residues in contact with GLY 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 ALA 2.9 19.7 + - - -
112A PHE* 3.3 6.5 + - - +
114A VAL* 1.3 73.6 - - - +
116A LEU* 1.3 56.6 + - - -
117A LYS* 3.6 10.5 - - - -
486A GLY 3.6 3.1 - - - +
489A SER* 3.5 3.1 + - - -
490A LEU* 3.4 36.2 - - - +
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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