Contacts of the strand formed by residues 120 - 129 (chain A) in PDB entry 1KN0
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 TYR 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ARG* 3.6 42.8 - - - +
113A VAL 3.1 13.9 - - - +
114A GLN* 4.2 1.6 - - + -
118A GLY 3.2 21.1 - - - +
119A SER* 1.3 77.7 + - - +
121A HIS* 1.3 66.3 + - - +
158A PHE* 4.7 2.5 - - - -
26K PHE* 4.1 3.8 - + - -
85K ALA* 2.8 50.5 + - + +
86K HIS 3.1 31.9 + - - -
87K SER* 3.7 16.2 + - - -
112K ARG* 4.9 9.0 + - - -
114K GLN* 3.5 34.9 + - - +
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Residues in contact with HIS 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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112A ARG* 3.6 1.7 - - - -
113A VAL* 2.8 33.6 + - - +
119A SER* 5.1 0.2 - - - -
120A TYR* 1.3 80.1 - - - +
122A GLU* 1.3 59.4 + - - +
154A ALA* 3.8 12.9 - - - +
157A SER* 3.4 31.1 - - - -
158A PHE* 3.3 47.3 - + + -
81K TYR 4.1 4.9 - - - -
84K TRP* 3.3 39.8 + + - -
86K HIS* 2.9 43.1 - + - +
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Residues in contact with GLU 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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89A THR* 2.9 36.9 + - - +
110A PHE* 4.1 5.6 - - + +
111A VAL 3.1 17.3 - - - +
112A ARG* 3.7 17.0 - - + -
121A HIS* 1.3 76.6 - - - +
123A ASP* 1.3 67.2 + - - +
154A ALA* 4.5 1.1 - - - -
86K HIS* 3.1 29.1 + - - -
87K SER* 3.4 17.9 - - - -
88K ILE* 2.6 57.4 + - + +
147K VAL* 4.7 0.3 - - - +
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Residues in contact with ASP 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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110A PHE* 3.3 5.0 - - - -
111A VAL* 2.9 32.3 + - - +
122A GLU* 1.3 75.9 - - - +
124A VAL* 1.3 77.4 + - - +
150A GLY 4.4 3.1 - - - +
153A ARG* 3.1 49.5 + - + +
154A ALA* 3.8 23.9 - - + +
157A SER* 4.7 3.5 + - - -
86K HIS* 4.5 7.3 - - + -
88K ILE* 3.7 12.7 - - - +
147K VAL* 3.8 11.5 - - - +
148K THR* 5.4 1.2 + - - -
151K LEU* 6.0 0.5 - - - +
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Residues in contact with VAL 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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108A CYS* 4.4 7.0 - - + -
109A ALA 3.2 7.4 - - - +
110A PHE* 3.4 30.7 - - + -
123A ASP* 1.3 85.5 + - - +
125A GLY* 1.3 68.0 + - - +
126A TYR* 5.9 0.2 - - + -
150A GLY* 4.0 2.5 - - - -
153A ARG* 2.9 29.3 + - - +
88K ILE* 4.2 2.2 - - + -
91K GLN* 3.9 9.2 - - - +
143K ARG* 3.9 17.5 - - + +
144K LYS* 4.4 8.1 - - + -
147K VAL* 3.0 36.8 - - + -
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Residues in contact with GLY 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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108A CYS* 3.3 7.3 - - - +
109A ALA 2.7 28.5 + - - -
124A VAL* 1.3 78.0 - - - +
126A TYR* 1.3 61.2 + - - +
146A ALA 3.3 9.6 - - - -
149A ASP* 3.4 6.3 - - - -
150A GLY* 3.3 26.8 - - - -
144K LYS* 4.6 1.1 - - - -
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Residues in contact with TYR 126 (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 ASP* 2.6 35.4 + - - +
95A PHE* 4.0 1.2 - - - -
106A GLY* 3.6 11.4 - - - -
107A VAL 3.3 16.2 - - - -
108A CYS* 3.6 17.0 - - + -
124A VAL* 5.9 0.2 - - + -
125A GLY* 1.3 72.8 - - - -
127A GLY* 1.3 80.0 + - - +
128A VAL* 3.7 14.0 + - + +
145A GLU* 4.1 3.1 - - - +
146A ALA* 3.5 7.9 + - - +
149A ASP* 2.9 21.4 + - - +
136K ALA 3.5 15.7 - - - -
139K LEU* 3.4 21.7 - - + +
140K GLU* 3.5 49.2 - - + +
143K ARG* 3.8 12.6 - - + -
144K LYS* 4.0 4.9 - - + -
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Residues in contact with GLY 127 (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 GLY* 3.7 0.5 - - - -
107A VAL 2.7 37.2 + - - +
126A TYR* 1.3 74.2 - - - +
128A VAL* 1.3 67.6 + - - +
142A ALA* 3.2 27.7 - - - +
145A GLU* 3.9 7.0 - - - -
146A ALA* 3.4 8.4 - - - +
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Residues in contact with VAL 128 (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 VAL 3.5 4.9 - - - +
126A TYR* 3.7 23.8 - - + +
127A GLY* 1.3 80.7 - - - +
129A SER* 1.3 63.9 + - - +
130A GLU* 3.5 28.5 - - + +
141A LYS* 2.9 32.4 + - - +
142A ALA* 3.8 4.5 - - - +
145A GLU* 3.7 7.1 + - - +
136K ALA* 3.6 21.1 - - + -
137K LEU* 4.7 8.5 - - + -
140K GLU* 4.8 11.0 - - - +
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Residues in contact with SER 129 (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 PHE 3.4 1.6 - - - +
104A TYR* 3.4 1.9 - - - -
105A VAL* 2.7 39.2 + - - +
128A VAL* 1.3 78.4 - - - +
130A GLU* 1.3 61.2 + - - +
131A GLY 4.6 0.2 + - - -
132A LEU* 3.7 14.7 - - - +
138A SER* 3.2 49.6 + - - -
141A LYS* 3.9 13.2 - - - +
142A ALA* 4.6 0.2 - - - -
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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