Contacts of the strand formed by residues 120 - 129 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G PHE* 4.0 12.8 - + - -
85G ALA* 2.7 50.3 - - + +
86G HIS* 3.1 29.2 + - - -
87G SER* 3.8 16.0 + - - -
112G ARG* 5.0 6.8 + - - -
114G GLN* 3.7 29.9 + - - +
112H ARG* 3.7 41.3 - - + +
113H VAL 3.1 12.6 - - - +
114H GLN* 4.1 4.7 - - + -
118H GLY 3.3 20.0 - - - +
119H SER* 1.3 80.2 + - - +
121H HIS* 1.3 67.2 + - - +
158H PHE* 4.8 1.8 - - - -
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Residues in contact with HIS 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G TYR 4.1 3.6 - - - -
84G TRP* 3.2 46.8 + + - -
86G HIS* 2.8 42.4 - + - +
112H ARG* 3.5 2.0 - - - -
113H VAL* 2.7 40.7 + - - +
119H SER* 4.9 0.2 - - - -
120H TYR* 1.3 77.1 - - - +
122H GLU* 1.3 57.4 + - - +
154H ALA* 3.8 13.1 - - - +
157H SER* 3.4 29.7 - - - -
158H PHE* 3.3 45.5 - + + -
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Residues in contact with GLU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G HIS* 3.2 27.2 + - - -
87G SER* 3.3 18.9 - - - -
88G ILE* 2.6 57.3 + - + +
147G VAL* 4.9 0.2 - - - +
89H THR* 2.6 39.5 + - - +
110H PHE* 4.2 4.8 - - + +
111H VAL 3.1 16.8 - - - +
112H ARG* 3.6 17.5 - - + -
121H HIS* 1.3 74.9 - - - +
123H ASP* 1.3 64.6 + - - +
154H ALA* 4.6 1.1 - - - -
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Residues in contact with ASP 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G HIS* 4.6 7.8 - - + -
88G ILE* 3.8 9.9 - - - -
147G VAL* 3.5 16.4 - - - +
148G THR* 5.2 1.7 + - - -
110H PHE* 3.5 2.6 - - - -
111H VAL* 2.9 33.8 + - - +
122H GLU* 1.3 76.4 - - - +
124H VAL* 1.3 75.9 + - - +
125H GLY 4.0 0.2 + - - -
150H GLY* 4.4 2.7 - - - +
153H ARG* 3.2 67.4 + - + +
154H ALA* 3.9 5.3 - - + +
157H SER* 4.7 2.8 + - - -
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Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ILE* 4.0 4.3 - - + -
91G GLN* 3.8 7.9 - - - +
143G ARG* 4.1 17.9 - - + +
144G LYS* 4.4 8.8 - - + -
147G VAL* 3.0 36.6 - - + -
108H CYS* 4.4 7.0 - - + -
109H ALA 3.2 8.5 - - - +
110H PHE* 3.6 30.3 - - + -
123H ASP* 1.3 81.7 + - - +
125H GLY* 1.3 70.3 - - - +
126H TYR* 5.8 0.4 - - + -
150H GLY* 4.0 2.5 - - - -
153H ARG* 2.9 29.3 + - - +
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Residues in contact with GLY 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LYS* 4.7 1.3 - - - -
108H CYS* 3.3 7.3 - - - +
109H ALA 2.6 29.1 + - - -
124H VAL* 1.3 78.8 - - - +
126H TYR* 1.3 61.6 + - - +
146H ALA 3.2 22.4 - - - -
149H ASP* 3.4 4.9 - - - -
150H GLY* 3.2 15.1 - - - -
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Residues in contact with TYR 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G ALA 3.7 13.7 - - - -
139G LEU* 3.2 26.1 - - + +
140G GLU* 3.7 41.4 - - + +
143G ARG* 3.7 15.0 - - + -
144G LYS* 4.2 5.6 - - + -
94H ASP* 2.6 35.3 + - - +
95H PHE* 4.0 1.4 - - - -
106H GLY* 3.6 11.0 - - - -
107H VAL 3.3 13.9 - - - -
108H CYS* 3.6 19.1 - - + -
124H VAL* 5.8 0.2 - - + -
125H GLY* 1.3 72.7 - - - -
127H GLY* 1.3 81.5 + - - +
128H VAL* 3.6 16.0 + - + +
145H GLU* 4.3 2.6 - - - +
146H ALA* 3.5 7.0 + - - -
149H ASP* 2.9 21.0 + - - +
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Residues in contact with GLY 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H GLY* 3.6 1.2 - - - -
107H VAL 2.6 35.9 + - - +
126H TYR* 1.3 74.0 - - - +
128H VAL* 1.3 67.9 + - - +
142H ALA* 3.1 30.0 - - - +
145H GLU* 3.9 5.6 - - - -
146H ALA* 3.2 8.6 - - - +
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Residues in contact with VAL 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ALA* 3.4 28.7 - - + -
137G LEU* 4.9 8.3 - - + -
140G GLU* 5.1 7.6 - - - +
105H VAL 3.4 7.4 - - - +
126H TYR* 3.6 24.2 - - + +
127H GLY* 1.3 81.5 - - - +
129H SER* 1.3 63.7 + - - +
130H GLU* 3.5 23.3 - - + +
141H LYS* 2.9 33.0 + - - +
142H ALA* 3.8 4.2 - - - +
145H GLU* 3.6 5.6 + - - +
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Residues in contact with SER 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H PHE 3.2 3.6 + - - +
104H TYR* 3.3 0.2 - - - -
105H VAL* 2.8 38.4 + - - +
128H VAL* 1.3 76.0 - - - +
130H GLU* 1.3 62.0 + - - +
131H GLY 4.4 0.9 + - - -
132H LEU* 3.8 13.9 - - - +
138H SER* 3.1 50.0 + - - -
141H LYS* 4.1 14.5 - - - +
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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