Contacts of the helix formed by residues 104 - 118 (chain A) in PDB entry 1KPI
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 SER 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.9 1.1 - - - +
21A ARG* 4.5 2.5 - - - -
24A TYR* 3.5 17.1 + - - -
25A ASP* 2.8 27.8 + - - -
102A THR* 3.1 5.9 + - - +
103A LEU* 1.3 78.8 - - - +
105A GLU* 1.3 58.0 + - - +
107A GLN* 3.0 46.1 + - - +
108A TYR* 3.2 25.3 + - - +
128A ILE* 4.1 2.6 - - - +
900A SAH 3.7 2.8 + - - -
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Residues in contact with GLU 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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21A ARG* 3.8 39.8 + - - +
25A ASP* 3.1 12.9 + - - +
104A SER* 1.3 71.4 - - - +
106A ASN* 1.3 66.1 + - - +
108A TYR* 3.4 3.8 + - - +
109A ALA* 2.9 29.2 + - - +
128A ILE* 4.1 14.5 - - + +
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Residues in contact with ASN 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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24A TYR 4.3 2.0 + - - +
25A ASP* 2.6 59.5 + - - +
27A SER* 4.0 14.1 - - - +
28A ASN* 3.0 36.4 + - - +
104A SER* 4.2 1.3 - - - +
105A GLU* 1.3 74.1 - - - +
107A GLN* 1.3 60.1 + - - +
109A ALA* 3.7 5.9 - - - +
110A HIS* 2.8 23.7 + - - +
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Residues in contact with GLN 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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24A TYR* 3.8 14.9 - - - +
82A GLY* 3.2 34.2 - - - +
83A TRP* 3.5 53.5 - - + +
102A THR* 2.9 14.7 + - + +
104A SER* 3.0 24.6 + - - +
106A ASN* 1.3 73.2 - - - +
108A TYR* 1.3 60.7 + - - +
110A HIS* 3.6 0.2 - - - +
111A ASP* 2.8 39.6 + - - +
900A SAH 2.5 27.0 + - - -
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Residues in contact with TYR 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 THR* 4.5 2.6 - - + +
104A SER 3.2 17.6 + - - +
105A GLU 3.5 5.6 - - - +
106A ASN 3.2 0.2 - - - -
107A GLN* 1.3 80.0 - - - +
109A ALA* 1.3 61.8 + - - +
111A ASP* 3.8 0.9 - - - +
112A LYS* 2.8 69.0 + - + +
126A VAL* 3.0 51.7 + - + -
127A ARG* 4.1 4.9 - - - -
128A ILE* 3.5 34.3 - - + -
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Residues in contact with ALA 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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28A ASN* 5.4 0.7 - - - +
105A GLU 2.9 17.7 + - - +
106A ASN* 3.7 7.6 - - - +
108A TYR* 1.3 83.5 - - + +
110A HIS* 1.3 61.3 + - - +
112A LYS* 3.5 7.1 + - - +
113A ALA* 3.3 23.0 + - - +
903A SO4 4.4 4.4 + - - +
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Residues in contact with HIS 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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28A ASN* 3.7 5.4 - - - +
32A LYS* 4.2 7.4 - - - -
39A MET* 3.8 22.9 - - - -
83A TRP* 3.6 29.8 + + + -
106A ASN 2.8 21.4 + - - +
107A GLN 3.6 2.9 - - - +
109A ALA* 1.3 74.6 - - - +
111A ASP* 1.3 79.4 + - - +
113A ALA* 3.5 3.8 + - - +
114A MET* 2.9 56.0 + - + +
903A SO4 3.0 41.0 + - - +
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Residues in contact with ASP 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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81A CYS* 4.1 4.3 - - - -
82A GLY 2.8 20.9 - - - +
83A TRP* 2.9 26.0 - - - +
84A GLY* 3.6 13.7 + - - -
102A THR* 5.1 0.2 - - - +
107A GLN 2.8 27.2 + - - +
108A TYR 4.0 1.8 - - - +
110A HIS* 1.3 76.1 - - - +
112A LYS* 1.3 66.5 + - - +
113A ALA 3.1 1.8 - - - -
114A MET* 4.1 5.5 - - - +
115A PHE* 2.9 40.7 + - + -
126A VAL* 3.9 27.2 - - + +
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Residues in contact with LYS 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 TYR* 2.8 50.4 + - + +
109A ALA* 3.7 7.2 - - - +
111A ASP* 1.3 77.3 - - - +
113A ALA* 1.3 60.5 + - - +
115A PHE* 3.9 4.6 + - - +
116A ASP* 3.5 25.1 + - - +
126A VAL* 4.0 14.3 - - + +
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Residues in contact with ALA 113 (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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109A ALA 3.3 14.4 + - - +
110A HIS* 3.8 4.3 - - - +
112A LYS* 1.3 76.9 - - - +
114A MET* 1.3 65.2 + - - +
115A PHE 3.2 1.6 - - - -
116A ASP* 3.1 22.3 + - - +
117A GLU* 3.3 14.3 + - - +
903A SO4 5.4 4.9 - - - +
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Residues in contact with MET 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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83A TRP 5.5 2.5 - - - +
88A ARG* 3.7 39.0 + - - +
110A HIS* 2.9 47.9 + - + +
111A ASP* 3.2 8.7 + - - +
113A ALA* 1.3 76.4 - - - +
115A PHE* 1.3 69.6 + - + +
117A GLU* 3.3 51.5 + - - +
118A VAL* 4.2 2.4 + - - +
903A SO4 6.0 0.2 - - - -
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Residues in contact with PHE 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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84A GLY* 4.4 11.2 - - - -
87A MET* 3.3 57.4 - - + -
88A ARG* 4.5 15.5 - - + -
111A ASP* 2.9 30.9 + - + +
112A LYS* 4.2 4.3 - - - +
114A MET* 1.3 83.4 - - + +
116A ASP* 1.3 61.8 + - - +
117A GLU 3.3 0.3 + - - -
118A VAL 2.9 27.0 + - - +
124A LYS* 3.2 55.5 + - + +
126A VAL* 4.3 13.5 - - + -
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Residues in contact with ASP 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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112A LYS* 3.5 17.5 + - - +
113A ALA* 3.1 14.1 + - - +
115A PHE* 1.3 78.0 - - - +
117A GLU* 1.3 66.0 + - + +
118A VAL 3.6 0.7 + - - -
119A ASP* 4.0 9.0 - - - +
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Residues in contact with GLU 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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88A ARG* 5.0 5.5 + - - +
113A ALA* 3.3 9.0 + - - +
114A MET* 3.3 52.7 + - - +
116A ASP* 1.3 80.7 - - - +
118A VAL* 1.3 66.1 + - + +
119A ASP* 3.5 8.8 - - - +
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Residues in contact with VAL 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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88A ARG* 5.0 14.8 - - - +
114A MET 4.2 2.2 + - - +
115A PHE 2.9 13.3 + - - +
116A ASP 4.4 0.4 - - - -
117A GLU* 1.3 84.7 - - + +
119A ASP* 1.3 70.5 + - - +
120A SER* 5.4 1.6 - - - -
124A LYS* 2.7 33.8 + - - +
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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