Contacts of the helix formed by residues 100 - 115 (chain A) in PDB entry 1AKZ
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLY 3.7 4.2 - - - +
99A LYS* 1.3 85.8 - - + +
101A TYR* 1.3 63.9 + - - +
102A PHE 3.2 0.2 + - - -
103A ILE* 3.3 6.8 + - + +
104A LYS* 2.9 50.3 + - + +
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLU* 2.6 32.0 + - - +
99A LYS* 3.2 25.5 + - + -
100A PRO* 1.3 78.1 - - - +
102A PHE* 1.3 74.6 + + + +
104A LYS* 3.6 6.9 - - - +
105A LEU* 2.9 28.3 + - + +
220A ARG 4.5 3.3 - - - +
221A GLY* 3.4 32.3 - - - -
224A GLN* 3.7 20.4 - - + -
225A PHE* 3.3 38.7 - - + -
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Residues in contact with PHE 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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82A MET* 3.2 33.2 - - + -
96A GLU 3.2 23.6 - - - +
97A PHE* 3.7 31.0 - + - +
99A LYS 3.0 3.9 + - - +
101A TYR* 1.3 93.5 - + + +
103A ILE* 1.3 62.1 + - - +
105A LEU* 3.2 11.8 + - + +
106A MET* 2.9 57.7 + - + +
126A PHE* 4.7 7.4 - + - -
222A TRP* 4.4 0.9 - + - -
225A PHE* 3.6 44.4 - + - -
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Residues in contact with ILE 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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97A PHE 3.4 15.7 - - - +
98A GLY* 3.2 33.0 - - - +
99A LYS 3.1 8.2 + - - +
100A PRO* 3.8 6.1 - - + +
102A PHE* 1.3 76.2 - - - +
104A LYS* 1.3 70.4 + - + +
106A MET* 3.5 6.2 + - - +
107A GLY* 3.1 18.7 + - - -
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Residues in contact with LYS 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 PRO* 2.9 48.8 + - - +
101A TYR* 3.6 7.0 - - - +
103A ILE* 1.3 84.4 - - + +
105A LEU* 1.3 57.3 + - - +
107A GLY* 3.1 3.3 + - - -
108A PHE* 2.8 29.3 + - - +
220A ARG 5.2 1.3 - - - +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A TYR 2.9 19.4 + - - +
102A PHE* 3.2 16.8 + - + +
104A LYS* 1.3 75.9 - - - +
106A MET* 1.3 70.8 + - + +
108A PHE* 3.1 7.3 + - + +
109A VAL* 2.9 37.9 + - + +
220A ARG* 3.4 35.4 + - + +
221A GLY* 3.8 15.9 - - - +
222A TRP* 3.6 57.7 - - + +
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Residues in contact with MET 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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82A MET* 4.4 16.6 - - + +
102A PHE* 2.9 55.3 + - + +
103A ILE* 3.9 6.3 - - - +
104A LYS 3.4 0.2 - - - -
105A LEU* 1.3 83.1 - - + +
107A GLY* 1.3 57.2 + - - +
109A VAL* 3.5 7.9 + - + +
110A ALA* 2.9 30.5 + - - +
126A PHE* 4.7 5.4 - - + -
222A TRP* 3.4 36.8 - - + -
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Residues in contact with GLY 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 ILE 3.1 14.7 + - - -
104A LYS* 3.1 4.0 + - - -
106A MET* 1.3 77.4 - - - +
108A PHE* 1.3 56.7 + - - +
110A ALA* 3.2 6.6 + - - +
111A GLU* 2.9 30.0 + - - +
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Residues in contact with PHE 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 LYS 2.8 12.7 + - - +
105A LEU* 3.4 11.4 - - + +
107A GLY* 1.3 75.8 - - - +
109A VAL* 1.3 67.4 + - + +
111A GLU* 3.3 8.6 + - + +
112A GLU* 2.9 65.4 + - + +
210A ARG* 6.0 0.2 - - - -
216A SER 4.7 2.2 - - - -
217A HIS* 3.8 28.5 - + - -
220A ARG* 3.4 71.3 - - + +
222A TRP* 6.3 0.4 - + - -
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Residues in contact with VAL 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 LEU* 2.9 35.6 + - + +
106A MET* 3.9 11.0 - - + +
108A PHE* 1.3 82.8 - - + +
110A ALA* 1.3 64.5 + - - +
112A GLU* 3.2 7.1 + - - +
113A ARG* 3.0 45.4 + - + +
118A VAL* 4.7 4.7 - - + -
208A THR* 3.9 32.3 - - + +
217A HIS* 4.7 2.0 - - + +
222A TRP* 4.2 10.3 - - + +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A MET 2.9 18.7 + - - +
107A GLY* 3.5 7.6 - - - +
109A VAL* 1.3 77.1 - - - +
111A GLU* 1.3 63.7 + - - +
113A ARG* 3.2 17.9 + - - +
114A LYS* 3.3 24.9 + - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLY 2.9 13.8 + - - +
108A PHE* 3.5 12.6 - - + +
110A ALA* 1.3 76.6 - - - +
112A GLU* 1.3 64.7 + - + +
114A LYS* 3.1 37.1 + - - +
115A HIS* 2.7 56.3 + - + -
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Residues in contact with GLU 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 PHE* 2.9 49.9 + - + +
109A VAL 3.4 8.5 - - - +
111A GLU* 1.3 78.3 - - + +
113A ARG* 1.3 52.9 + - - +
115A HIS* 3.1 2.6 + - - -
116A TYR* 2.7 47.7 + - - +
118A VAL* 4.0 13.5 - - + -
210A ARG* 2.7 43.4 + - - +
217A HIS* 2.8 23.9 + - + +
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Residues in contact with ARG 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 VAL* 3.0 30.7 + - + +
110A ALA* 3.2 9.8 + - - +
112A GLU* 1.3 75.2 - - - +
114A LYS* 1.3 60.2 + - - +
116A TYR 3.5 16.5 - - - +
118A VAL* 3.0 50.6 + - + +
120A PRO 2.9 21.0 + - - -
121A PRO* 4.1 0.6 - - - +
122A PRO* 3.7 34.3 - - - +
125A VAL* 3.6 20.4 - - - +
208A THR* 4.1 5.1 - - - +
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ALA* 3.3 22.1 + - - +
111A GLU* 3.1 41.0 + - - +
113A ARG* 1.3 79.6 - - - +
115A HIS* 1.3 74.2 + - + +
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Residues in contact with HIS 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 GLU* 2.7 49.3 + - + -
112A GLU* 3.1 2.2 + - - +
114A LYS* 1.3 91.4 + - + +
116A TYR* 1.3 86.9 + + + +
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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