Contacts of the strand formed by residues 120 - 129 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C PHE* 4.0 12.6 - + - -
85C ALA* 2.8 50.4 - - + +
86C HIS* 3.1 29.9 + - - -
87C SER* 3.9 13.9 + - - -
112C ARG* 5.1 7.6 + - - -
114C GLN* 3.6 28.6 + - - +
112D ARG* 3.7 39.0 - - + +
113D VAL 3.1 13.2 - - - +
114D GLN* 4.2 1.3 - - - -
118D GLY 3.2 19.7 - - - +
119D SER* 1.3 79.4 + - - +
121D HIS* 1.3 68.7 - - - +
158D PHE* 4.8 1.8 - - - -
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Residues in contact with HIS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C TYR 4.1 4.9 - - - -
84C TRP* 3.3 47.8 + + - -
86C HIS* 2.9 36.8 - + + +
112D ARG* 4.5 0.9 - - - -
113D VAL* 2.7 34.7 + - - +
119D SER* 4.9 0.2 - - - -
120D TYR* 1.3 78.6 + - - +
122D GLU* 1.3 57.6 + - - +
154D ALA* 3.7 16.6 - - - +
157D SER* 3.4 30.8 - - - -
158D PHE* 3.3 45.9 - + + -
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 3.1 37.4 + - - +
87C SER* 3.4 11.0 - - - -
88C ILE* 2.6 55.9 + - + +
147C VAL* 4.8 0.2 - - - +
89D THR* 2.7 37.7 + - - +
110D PHE* 4.3 5.1 - - + +
111D VAL 3.2 14.6 - - - +
112D ARG* 3.7 17.7 - - + -
121D HIS* 1.3 76.3 - - - +
123D ASP* 1.3 65.0 + - - +
154D ALA* 4.4 1.1 - - - -
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Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 4.6 6.9 - - - -
88C ILE* 3.7 10.9 - - - +
147C VAL* 3.7 12.5 - - - +
148C THR* 5.4 0.9 + - - -
151C LEU* 6.0 0.2 - - - +
110D PHE* 3.3 6.4 - - - +
111D VAL 2.9 31.0 + - - -
122D GLU* 1.3 76.7 - - - +
124D VAL* 1.3 79.4 + - - +
150D GLY 4.4 2.7 - - - +
153D ARG* 3.2 50.7 + - + +
154D ALA* 3.9 23.0 - - + +
157D SER* 4.7 3.1 + - - -
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 4.1 2.7 - - + -
91C GLN* 3.8 8.5 - - - +
143C ARG* 3.8 20.4 - - + +
144C LYS* 4.3 7.6 - - + -
147C VAL* 3.1 36.1 - - + -
108D CYS* 4.5 6.7 - - + -
109D ALA 3.3 6.3 - - - +
110D PHE* 3.4 31.6 - - + -
123D ASP* 1.3 84.6 + - - +
125D GLY* 1.3 69.4 + - - +
126D TYR* 5.8 0.4 - - + -
150D GLY* 4.0 2.7 - - - -
153D ARG* 2.8 30.2 + - - +
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Residues in contact with GLY 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LYS* 4.7 1.1 - - - -
108D CYS* 3.3 7.3 - - - +
109D ALA 2.7 29.7 + - - -
124D VAL* 1.3 76.9 - - - +
126D TYR* 1.3 61.1 + - - +
146D ALA 3.2 22.0 - - - -
149D ASP* 3.3 5.6 - - - -
150D GLY* 3.3 15.5 - - - -
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Residues in contact with TYR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ALA 3.6 17.3 - - - -
139C LEU* 3.2 22.2 - - + +
140C GLU* 3.4 49.1 - - + +
143C ARG* 3.8 14.4 - - + -
144C LYS* 4.2 3.8 - - + -
94D ASP* 2.5 35.6 + - - +
95D PHE* 4.1 1.0 - - - -
106D GLY* 3.7 10.6 - - - -
107D VAL 3.1 22.0 - - - -
108D CYS* 3.5 17.7 - - + -
124D VAL* 5.8 0.2 - - + -
125D GLY* 1.3 72.9 - - - -
127D GLY* 1.3 79.1 + - - +
128D VAL* 3.7 11.8 + - + +
145D GLU* 4.2 3.5 - - - +
146D ALA* 3.5 4.7 + - - -
149D ASP* 2.8 26.2 + - - +
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Residues in contact with GLY 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLY* 3.6 1.2 - - - -
107D VAL 2.7 35.5 + - - +
126D TYR* 1.3 74.5 - - - +
128D VAL* 1.3 66.8 + - - +
142D ALA* 3.2 28.2 - - - +
145D GLU* 3.9 6.7 - - - -
146D ALA* 3.3 9.2 - - - +
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Residues in contact with VAL 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ALA* 3.4 28.5 - - + -
137C LEU* 4.7 10.8 - - + -
140C GLU* 5.0 8.5 - - - +
105D VAL 3.5 5.2 - - - +
126D TYR* 3.7 24.4 + - + +
127D GLY* 1.3 79.9 - - - +
129D SER* 1.3 65.8 + - - +
130D GLU* 3.5 23.6 - - + +
141D LYS* 2.9 33.2 + - - +
142D ALA* 3.9 4.7 - - - +
145D GLU* 3.7 6.9 + - - +
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Residues in contact with SER 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D PHE 3.3 3.6 + - - +
104D TYR* 3.4 0.2 - - - -
105D VAL* 2.8 36.4 + - - +
128D VAL* 1.3 78.8 - - - +
130D GLU* 1.3 61.5 + - - +
131D GLY 4.6 0.2 + - - -
132D LEU* 3.8 13.2 - - - +
138D SER* 3.1 51.0 + - - -
141D LYS* 4.0 13.8 - - - +
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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