Contacts of the strand formed by residues 140 - 149 (chain D) in PDB entry 1KLG
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 ARG 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D TYR* 3.9 3.6 - - - -
137D GLU 2.9 33.6 + - - +
138D ASN 3.9 9.0 - - - +
139D LYS* 1.3 83.6 - - + +
141D ASN* 1.3 67.7 + - - +
142D THR* 3.0 7.1 + - + +
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Residues in contact with ASN 141 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D ARG* 4.1 13.9 - - - +
135D VAL 3.2 19.7 + - - +
136D TYR* 3.5 27.8 + - + -
140D ARG* 1.3 71.1 - - - +
142D THR* 1.3 59.8 + - - +
143D ILE 3.3 15.3 - - - +
144D SER* 3.3 17.7 + - - -
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Residues in contact with THR 142 (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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135D VAL* 2.8 22.1 + - - +
137D GLU* 2.8 54.7 + - + +
140D ARG* 3.0 11.2 + - + +
141D ASN* 1.3 75.1 - - - +
143D ILE* 1.3 75.8 + - - +
171D LYS* 5.0 2.5 - - - +
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Residues in contact with ILE 143 (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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135D VAL* 2.8 50.0 + - + -
141D ASN* 3.3 3.4 - - - +
142D THR* 1.3 95.2 + - - +
144D SER* 1.3 66.8 + - - +
145D PHE* 4.3 3.6 - - + -
166D PHE* 4.0 28.0 - - + -
167D LEU* 4.3 7.9 - - + -
170D LYS* 5.4 3.6 - - + -
171D LYS* 4.0 28.5 - - + +
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Residues in contact with SER 144 (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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132D LEU* 4.7 6.5 - - - -
133D VAL 3.3 10.1 - - - -
134D ARG* 3.4 17.8 - - - +
141D ASN* 3.3 21.3 + - - -
143D ILE* 1.3 80.0 + - - +
145D PHE* 1.3 66.8 + - - +
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Residues in contact with PHE 145 (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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132D LEU* 3.7 3.7 - - - +
133D VAL* 2.7 69.1 + - + -
135D VAL* 3.7 15.9 - - + -
143D ILE* 4.3 6.7 - - + -
144D SER* 1.3 80.6 - - - +
146D GLU* 1.3 82.5 + - - +
147D VAL* 3.8 19.3 - - + -
163D ALA* 4.2 11.0 - - - -
166D PHE* 3.3 65.5 - + + -
167D LEU* 4.1 4.9 - - + -
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Residues in contact with GLU 146 (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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130D ASN* 3.8 38.7 + - + +
131D VAL 3.1 15.9 - - - +
132D LEU* 4.2 12.8 + - + +
145D PHE* 1.3 94.4 - - - +
147D VAL* 1.3 65.6 + - - +
148D GLN* 5.2 2.8 - - - +
166D PHE* 5.8 0.5 - - - -
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D GLN 3.7 0.3 - - - +
130D ASN* 3.4 4.0 - - - -
131D VAL* 2.9 40.7 + - + +
133D VAL* 3.9 13.2 - - + -
145D PHE* 3.8 21.5 - - + -
146D GLU* 1.3 78.5 - - - +
148D GLN* 1.3 63.2 + - - +
159D LEU* 3.8 33.9 - - + +
162D LYS* 4.1 15.9 - - + +
163D ALA* 4.0 22.4 - - + +
166D PHE* 5.7 0.2 - - + -
230D ILE* 5.8 0.4 - - + -
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Residues in contact with GLN 148 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D LEU* 3.6 38.1 - - + +
129D GLN 3.3 7.6 - - - +
130D ASN* 3.4 24.1 - - - +
146D GLU 5.2 2.7 - - - +
147D VAL* 1.3 80.4 - - - +
149D THR* 1.3 55.5 + - - +
159D LEU* 5.1 0.4 - - - +
162D LYS* 2.8 37.4 + - - +
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Residues in contact with THR 149 (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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123D PHE* 4.1 0.2 - - - -
128D LEU* 3.4 7.8 - - - -
129D GLN* 2.9 37.3 + - + +
131D VAL* 4.6 1.6 - - + -
148D GLN* 1.3 78.8 - - - +
150D ASP* 1.3 61.6 + - - +
151D LYS* 3.1 25.4 + - - +
154D VAL* 3.6 17.5 - - + +
158D GLU* 3.1 17.8 + - - -
159D LEU* 4.4 14.8 - - + -
162D LYS* 3.8 6.3 - - - +
225D SER* 3.8 17.5 - - - -
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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