Contacts of the strand formed by residues 120 - 129 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E PHE* 4.2 11.7 - + - -
85E ALA* 2.8 48.6 - - + +
86E HIS 3.1 29.1 + - - -
87E SER* 3.8 15.5 + - - -
112E ARG* 4.9 7.8 + - - -
114E GLN* 3.8 28.8 + - - +
112F ARG* 3.8 41.7 - - + +
113F VAL 3.1 13.2 - - - +
114F GLN* 4.1 2.2 - - + -
118F GLY 3.2 20.0 - - - +
119F SER* 1.3 79.6 + - - +
121F HIS* 1.3 68.4 + - - +
158F PHE* 4.7 1.6 - - - -
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Residues in contact with HIS 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E TYR 4.0 5.8 - - - -
84E TRP* 3.2 46.3 + + - -
86E HIS* 3.0 39.0 - + - +
111F VAL 4.1 0.2 - - - +
112F ARG* 3.5 2.3 - - - -
113F VAL* 2.7 37.5 + - - +
119F SER* 4.8 0.2 - - - -
120F TYR* 1.3 76.6 - - - +
122F GLU* 1.3 58.8 + - - +
154F ALA* 3.7 20.3 - - - +
157F SER* 3.4 20.8 - - - -
158F PHE* 3.2 47.2 - + + -
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Residues in contact with GLU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E HIS* 3.2 28.3 + - - +
87E SER* 3.3 18.6 - - - -
88E ILE* 2.5 56.8 + - + +
147E VAL* 4.9 0.2 - - - +
89F THR* 2.7 37.3 + - - +
110F PHE* 4.2 5.5 - - + +
111F VAL 3.1 15.7 - - - +
112F ARG* 3.7 16.1 - - + -
121F HIS* 1.3 75.2 - - - +
123F ASP* 1.3 65.5 + - - +
154F ALA* 4.7 1.6 - - - -
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Residues in contact with ASP 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E HIS* 4.5 8.4 - - + -
88E ILE* 3.8 10.5 - - - -
147E VAL* 3.6 18.6 - - - +
148E THR* 5.1 2.3 + - - -
151E LEU* 5.9 0.5 - - - +
110F PHE* 3.5 2.8 - - - +
111F VAL* 2.9 33.6 + - - +
122F GLU* 1.3 76.1 - - - +
124F VAL* 1.3 75.1 + - - +
150F GLY 4.4 2.9 - - - +
153F ARG* 3.1 66.9 + - + +
154F ALA* 3.9 5.4 - - - +
157F SER* 4.7 2.3 + - - -
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Residues in contact with VAL 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ILE* 4.1 3.6 - - + -
91E GLN* 3.8 8.1 - - - +
143E ARG* 4.0 17.0 - - + +
144E LYS* 4.4 8.5 - - + -
147E VAL* 3.0 36.3 - - + -
108F CYS* 4.3 7.4 - - + -
109F ALA 3.2 9.0 - - - +
110F PHE* 3.6 29.2 - - + -
123F ASP* 1.3 82.3 + - - +
125F GLY* 1.3 69.5 + - - +
126F TYR* 5.8 0.2 - - + -
150F GLY* 4.0 3.6 - - - -
153F ARG* 2.8 29.6 + - - +
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Residues in contact with GLY 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E LYS* 4.5 1.1 - - - -
108F CYS* 3.3 7.6 - - - +
109F ALA 2.6 28.3 + - - -
124F VAL* 1.3 79.1 - - - +
126F TYR* 1.3 61.1 + - - +
146F ALA* 3.2 22.4 - - - -
149F ASP* 3.4 4.9 - - - -
150F GLY* 3.3 14.5 - - - -
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Residues in contact with TYR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ALA 3.5 15.6 + - - -
139E LEU* 3.2 22.7 - - + +
140E GLU* 3.3 50.7 - - + +
143E ARG* 3.8 13.7 - - + -
144E LYS* 3.9 4.5 - - + -
94F ASP* 2.6 34.1 + - - +
95F PHE* 4.1 0.9 - - - -
106F GLY* 3.7 9.5 - - - -
107F VAL 3.1 23.1 - - - -
108F CYS* 3.6 16.4 - - + -
124F VAL* 5.8 0.4 - - + -
125F GLY* 1.3 72.8 - - - -
127F GLY* 1.3 76.9 - - - +
128F VAL* 3.6 13.2 - - + +
145F GLU* 4.2 2.6 - - - +
146F ALA* 3.4 7.3 + - - +
149F ASP* 2.9 21.6 + - - +
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Residues in contact with GLY 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F VAL 3.9 0.2 - - - +
106F GLY* 3.8 0.5 - - - -
107F VAL 2.7 32.3 + - - +
126F TYR* 1.3 74.6 - - - +
128F VAL* 1.3 68.6 + - - +
142F ALA* 3.2 27.5 - - - +
145F GLU* 3.9 7.4 - - - -
146F ALA* 3.2 9.4 - - - +
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Residues in contact with VAL 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ALA* 3.4 27.4 - - + -
137E LEU* 4.6 11.4 - - + -
140E GLU* 4.8 7.6 - - - +
105F VAL 3.5 6.1 - - - +
126F TYR* 3.6 23.3 - - + +
127F GLY* 1.3 81.9 - - - +
129F SER* 1.3 60.6 + - - +
130F GLU* 3.5 23.3 - - + +
141F LYS* 2.8 38.0 + - - +
142F ALA* 3.9 4.1 - - - +
145F GLU* 3.9 7.0 + - - +
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Residues in contact with SER 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F PHE 3.2 3.9 - - - +
104F TYR* 3.4 0.2 - - - -
105F VAL* 2.8 35.8 + - - -
128F VAL* 1.3 78.6 - - - +
130F GLU* 1.3 62.4 + - - +
131F GLY 4.5 0.5 + - - -
132F LEU* 3.7 14.9 - - - +
138F SER* 3.3 49.6 + - - -
141F LYS* 4.0 14.4 - - - +
142F ALA* 4.7 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