Contacts of the strand formed by residues 120 - 129 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26J PHE* 4.1 12.1 - + - -
85J ALA* 2.8 51.0 - - + +
86J HIS* 3.2 29.4 + - - -
87J SER* 3.9 14.7 + - - -
112J ARG* 5.0 7.4 + - - -
114J GLN* 3.8 26.1 + - - +
112K ARG* 3.7 41.3 - - + +
113K VAL 3.2 13.9 - - - +
114K GLN* 4.2 2.2 - - + +
118K GLY 3.1 20.6 - - - +
119K SER* 1.3 78.1 + - - +
121K HIS* 1.3 66.4 + - - +
158K PHE* 4.7 2.9 - - - -
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Residues in contact with HIS 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J TYR 4.1 7.6 - - - -
84J TRP* 3.3 37.0 + + - -
86J HIS* 2.9 41.1 - + - +
112K ARG* 4.5 1.6 - - - -
113K VAL* 2.8 32.6 + - - +
120K TYR* 1.3 78.5 - - - +
122K GLU* 1.3 60.0 + - - +
154K ALA* 3.8 13.9 - - - +
157K SER* 3.3 37.2 - - - -
158K PHE* 3.3 41.4 - + + -
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Residues in contact with GLU 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J HIS* 3.1 31.2 + - - -
87J SER* 3.3 19.6 - - - -
88J ILE* 2.6 54.1 + - + +
147J VAL* 4.9 0.3 - - - +
89K THR* 2.9 37.2 + - - +
110K PHE* 4.1 5.7 - - - +
111K VAL 3.1 16.4 - - - +
112K ARG* 3.7 17.1 - - + -
121K HIS* 1.3 74.7 - - - +
123K ASP* 1.3 65.2 + - - +
154K ALA* 4.6 0.7 - - - -
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Residues in contact with ASP 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J HIS* 4.5 7.8 - - + -
88J ILE* 3.6 14.3 - - - +
147J VAL* 4.0 10.4 - - - +
148J THR* 5.4 0.9 + - - -
151J LEU* 6.0 0.5 - - - +
110K PHE* 3.3 4.7 - - - -
111K VAL 3.0 30.4 + - - -
122K GLU* 1.3 75.5 - - - +
124K VAL* 1.3 76.6 + - - +
150K GLY 4.4 2.5 - - - +
153K ARG* 2.9 53.4 + - + +
154K ALA* 3.8 23.7 - - + +
157K SER* 4.7 2.9 + - - -
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Residues in contact with VAL 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J ILE* 4.1 2.7 - - + -
91J GLN* 3.9 9.2 - - - +
143J ARG* 3.9 18.2 - - + +
144J LYS* 4.5 7.3 - - + -
147J VAL* 2.9 38.6 - - + -
108K CYS* 4.4 7.2 - - + -
109K ALA 3.4 7.0 - - - +
110K PHE* 3.5 30.3 - - + +
123K ASP* 1.3 78.4 + - - +
125K GLY* 1.3 68.1 + - - +
126K TYR* 5.8 0.2 - - + -
150K GLY* 4.0 2.7 - - - -
153K ARG* 2.9 30.8 + - - +
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Residues in contact with GLY 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J LYS* 4.6 2.0 - - - -
108K CYS* 3.3 7.3 - - - +
109K ALA 2.7 27.5 + - - -
124K VAL* 1.3 78.0 - - - +
126K TYR* 1.3 61.0 + - - +
146K ALA 3.3 9.6 - - - -
149K ASP* 3.3 11.7 - - - -
150K GLY* 3.3 21.5 - - - -
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Residues in contact with TYR 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ALA 3.7 14.8 - - - -
139J LEU* 3.3 24.4 - - + +
140J GLU* 3.6 45.7 - - + +
143J ARG* 3.7 18.8 - - + -
144J LYS* 4.0 4.5 - - + -
94K ASP* 2.5 35.0 + - - +
95K PHE* 4.1 1.2 - - - -
106K GLY* 3.6 11.1 - - - -
107K VAL 3.3 28.3 - - - -
108K CYS* 3.6 12.1 - - + -
124K VAL* 5.8 0.2 - - + -
125K GLY* 1.3 72.2 - - - -
127K GLY* 1.3 71.2 + - - +
128K VAL* 3.7 13.8 - - + +
145K GLU* 4.1 2.8 - - - +
146K ALA* 3.4 8.8 + - - +
149K ASP* 2.9 20.9 + - - +
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Residues in contact with GLY 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106K GLY* 3.6 2.4 - - - -
107K VAL 2.8 35.0 + - - +
126K TYR* 1.3 75.4 - - - +
128K VAL* 1.3 66.1 + - - +
142K ALA* 3.2 27.9 - - - +
145K GLU* 3.9 7.4 - - - -
146K ALA* 3.4 8.2 - - - +
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Residues in contact with VAL 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ALA* 3.3 29.2 - - + -
137J LEU* 4.7 8.3 - - + -
140J GLU* 4.9 11.9 - - - +
105K VAL 3.4 6.1 - - - +
126K TYR* 3.7 22.4 - - + +
127K GLY* 1.3 80.0 - - - +
129K SER* 1.3 64.3 + - - +
130K GLU* 3.6 23.1 - - + +
141K LYS* 2.9 32.0 + - - +
142K ALA* 4.1 4.1 - - - +
145K GLU* 3.6 7.4 + - - +
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Residues in contact with SER 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K PHE 3.4 3.2 - - - +
104K TYR* 3.4 0.2 - - - -
105K VAL* 2.8 37.3 + - - +
128K VAL* 1.3 77.7 - - - +
130K GLU* 1.3 61.8 + - - +
131K GLY 4.6 0.5 + - - -
132K LEU* 3.7 14.2 - - - +
138K SER* 3.1 49.7 + - - -
141K LYS* 3.9 13.9 - - - +
142K 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