Contacts of the strand formed by residues 229 - 235 (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 LYS 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D LEU* 4.1 32.9 - - + +
134D ARG* 5.4 10.9 - - - +
188D PHE* 3.6 1.9 - - - -
189D ILE* 2.7 63.8 + - + +
227D SER 4.4 7.4 - - - +
228D VAL* 1.3 78.3 - - - +
230D ILE* 1.3 65.2 + - - +
231D GLU* 5.8 1.1 - - + +
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Residues in contact with ILE 230 (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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131D VAL* 3.2 30.3 - - + -
132D LEU* 3.0 14.7 + - - +
133D VAL* 3.2 27.3 - - + -
134D ARG* 3.0 23.2 + - - +
147D VAL* 5.8 0.2 - - + -
159D LEU* 4.0 13.0 - - + -
163D ALA* 5.1 1.6 - - + -
186D ILE* 3.7 30.3 - - + -
187D LYS 3.4 3.4 - - - +
188D PHE* 3.6 38.4 - - + -
228D VAL* 4.1 4.3 - - + -
229D LYS* 1.3 77.3 - - - +
231D GLU* 1.3 71.4 + - - +
232D VAL* 4.3 0.9 - - + -
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Residues in contact with GLU 231 (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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134D ARG* 3.3 23.3 + - + +
136D TYR* 3.8 23.3 - - + +
186D ILE* 3.6 0.5 - - - -
187D LYS* 2.8 53.5 + - + +
189D ILE* 2.7 33.4 - - + +
229D LYS* 5.8 0.8 - - + +
230D ILE* 1.3 79.1 - - - +
232D VAL* 1.3 62.7 + - - +
233D HIS* 2.9 32.9 + - + -
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Residues in contact with VAL 232 (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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133D VAL* 4.1 19.5 - - + -
134D ARG 2.8 11.7 + - - +
135D VAL* 3.4 6.8 - - + +
136D TYR 2.6 34.3 + - - +
163D ALA* 4.9 3.6 - - + -
167D LEU* 3.8 23.8 - - + -
185D TYR 3.6 3.1 - - - -
186D ILE* 4.2 21.8 - - + -
200D MET* 3.8 19.3 - - + -
230D ILE* 4.3 1.5 - - + -
231D GLU* 1.3 73.3 - - - +
233D HIS* 1.3 57.6 + - - +
234D LEU* 3.6 30.1 - - + -
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Residues in contact with HIS 233 (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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136D TYR* 3.5 33.4 - + + -
139D LYS* 5.7 6.3 - - + -
183D THR* 4.5 0.5 + - - -
184D GLY* 3.2 3.5 - - - -
185D TYR* 3.0 76.2 + + + -
187D LYS* 5.1 3.6 - - + -
231D GLU* 2.9 46.7 + - + -
232D VAL* 1.3 73.7 - - - +
234D LEU* 1.3 62.9 + - - +
235D THR* 5.4 1.5 - - + +
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Residues in contact with LEU 234 (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* 4.5 13.9 - - + -
136D TYR 2.6 16.6 + - - +
137D GLU* 4.3 3.1 - - + -
138D ASN* 2.9 23.9 + - - -
139D LYS 4.5 0.9 + - - -
167D LEU* 5.1 5.6 - - + -
171D LYS* 5.8 2.5 - - + -
173D LEU* 4.3 13.7 - - + -
181D TYR* 3.6 50.3 - - + +
183D THR 3.4 4.9 - - - +
184D GLY* 3.7 20.4 - - - -
200D MET* 4.1 11.2 - - + -
201D MET* 5.5 0.7 - - + -
232D VAL* 3.6 28.5 - - + +
233D HIS* 1.3 73.1 - - - +
235D THR* 1.3 70.7 + - - +
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Residues in contact with THR 235 (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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11D LEU* 6.3 0.4 - - + -
137D GLU* 5.3 0.2 - - - +
138D ASN* 3.6 19.5 - - - +
139D LYS* 5.5 2.7 - - + +
181D TYR* 3.3 7.8 - - - +
182D GLU* 2.6 35.3 + - - +
183D THR* 2.5 39.6 + - - +
233D HIS* 5.4 1.6 - - + +
234D LEU* 1.3 81.7 - - - +
236D THR* 1.3 59.8 + - - +
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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