Contacts of the helix formed by residues 114 - 125 (chain A) in PDB entry 1KB9
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 ASP 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLY 4.6 2.4 + - - +
112A SER* 3.0 1.2 - - - +
113A THR* 1.3 83.3 - - + +
115A LYS* 1.3 67.3 + - + +
116A SER 3.1 4.7 - - - -
117A LEU* 3.2 19.7 + - - +
118A ASP* 3.4 22.3 + - - +
222A SER* 3.6 26.0 + - - +
226A LYS* 4.9 9.8 + - - -
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Residues in contact with LYS 115 (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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89A GLU* 4.0 41.8 + - + +
91A LEU* 3.5 14.3 - - + +
112A SER* 3.1 21.5 + - - +
114A ASP* 1.3 83.8 - - + +
116A SER* 1.3 60.6 + - - +
118A ASP* 3.6 26.1 + - + +
119A PHE* 3.4 15.8 + - - +
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Residues in contact with SER 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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51A VAL* 4.2 26.9 - - - -
91A LEU* 3.7 13.3 - - - +
106A VAL* 4.0 17.2 + - - +
108A SER* 3.0 33.9 + - - -
112A SER 3.5 3.4 + - - -
113A THR 4.2 3.1 - - - -
114A ASP 3.1 0.4 - - - -
115A LYS* 1.3 77.1 - - - +
117A LEU* 1.3 59.4 + - - +
119A PHE* 3.4 3.6 + - - +
120A LEU* 3.0 30.9 + - - +
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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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51A VAL* 3.8 24.0 - - + -
113A THR 4.0 14.8 - - - +
114A ASP* 3.2 10.3 + - - +
116A SER* 1.3 76.6 - - - +
118A ASP* 1.3 58.5 + - - +
120A LEU* 3.6 10.2 - - + +
121A ASN* 3.1 30.3 + - - +
208A VAL* 5.1 4.9 - - + -
219A LEU* 3.8 21.8 - - + -
222A SER* 3.6 33.0 - - - +
223A ILE* 4.4 19.7 - - + -
226A LYS* 4.4 11.8 + - - +
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Residues in contact with ASP 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 ASP* 3.4 20.4 + - - +
115A LYS* 3.6 35.7 - - + +
116A SER 3.3 0.2 - - - -
117A LEU* 1.3 79.0 - - - +
119A PHE* 1.3 57.8 + - - +
121A ASN* 4.1 2.8 - - - +
122A GLN* 2.9 33.1 + - - +
226A LYS* 2.9 28.0 + - - +
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Residues in contact with PHE 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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77A PHE* 5.1 4.5 - + - -
82A ASN* 3.0 53.4 - - - -
85A VAL* 3.6 25.4 - - + -
86A ALA* 3.5 20.0 - - + -
89A GLU* 6.2 1.1 - - + -
91A LEU* 4.1 9.9 - - + -
93A LEU* 3.6 29.6 - - + -
106A VAL* 4.3 9.4 - - + -
115A LYS 3.4 10.4 + - - +
116A SER 3.4 8.0 + - - +
117A LEU 3.3 0.2 - - - -
118A ASP* 1.3 77.0 - - - +
120A LEU* 1.3 64.5 + - - +
122A GLN* 4.0 16.3 - - - +
123A SER* 3.0 36.4 + - - -
127A GLN* 5.3 0.7 - - - -
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Residues in contact with LEU 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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51A VAL* 4.6 4.3 - - + +
52A GLY* 4.5 11.4 - - - +
53A VAL* 3.7 29.8 - - + +
77A PHE* 4.9 9.2 - - + -
104A TYR 4.4 14.8 - - - +
106A VAL* 3.6 28.0 - - + -
116A SER 3.0 15.5 + - - +
117A LEU* 3.6 16.8 - - + +
119A PHE* 1.3 77.2 - - - +
121A ASN* 1.3 60.8 + - - +
123A SER* 3.4 1.8 + - - -
124A PHE* 3.2 42.5 + - + +
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Residues in contact with ASN 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 3.1 16.2 + - - +
118A ASP* 4.1 3.6 - - - +
120A LEU* 1.3 74.8 - - - +
122A GLN* 1.3 66.5 + - - +
123A SER 3.1 0.7 - - - -
124A PHE* 4.5 2.9 - - - +
125A ILE* 3.1 57.8 + - - +
126A GLN* 3.6 2.3 + - - +
226A LYS* 5.5 13.6 - - + +
228A LEU* 6.0 0.8 - - - +
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Residues in contact with GLN 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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85A VAL* 4.1 10.6 - - - +
118A ASP 2.9 20.7 + - - +
119A PHE* 4.0 21.3 - - - +
120A LEU 3.4 0.2 - - - -
121A ASN* 1.3 78.6 + - - +
123A SER* 1.3 53.4 + - - +
126A GLN* 3.3 32.5 - - + +
127A GLN* 2.7 49.4 + - - +
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Residues in contact with SER 123 (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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77A PHE* 4.7 6.5 - - - -
82A ASN* 3.1 28.6 + - - -
119A PHE* 3.0 27.8 + - - -
120A LEU* 4.0 2.9 - - - -
121A ASN 3.1 0.4 - - - -
122A GLN* 1.3 80.6 - - - +
124A PHE* 1.3 69.4 + - - +
125A ILE 3.6 0.9 - - - -
127A GLN* 4.1 9.8 + - - -
128A LYS* 3.4 24.9 + - - +
131A LEU* 3.9 15.9 - - - +
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Residues in contact with PHE 124 (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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53A VAL* 4.3 5.8 - - + -
55A PHE* 3.6 35.2 - + - -
77A PHE* 3.5 29.8 - + - -
104A TYR* 3.6 33.4 - + + -
120A LEU* 3.2 34.7 + - + +
121A ASN* 3.3 2.4 + - - +
123A SER* 1.3 86.1 - - - +
125A ILE* 1.3 66.4 + - + +
128A LYS* 3.6 43.3 - - - +
131A LEU* 6.5 0.2 - - + -
201A PHE* 4.3 5.8 - + + -
230A LEU* 5.4 4.0 - - - +
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Residues in contact with ILE 125 (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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121A ASN* 3.1 37.7 + - - +
123A SER 3.6 0.8 - - - -
124A PHE* 1.3 88.4 - - + +
126A GLN* 1.3 68.1 + - + +
127A GLN 3.7 0.2 - - - -
128A LYS* 4.1 11.0 + - - +
228A LEU* 4.6 22.2 - - + +
230A LEU* 4.2 37.7 - - + -
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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