Contacts of the strand formed by residues 208 - 214 (chain E) in PDB entry 1K9A
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 ASP 208 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200E THR* 5.9 2.9 - - - -
202E GLY 3.5 8.3 - - - +
203E LYS* 2.9 40.1 + - + +
207E GLY* 1.3 75.3 - - - -
209E VAL* 1.3 65.9 + - - +
210E MET* 5.2 9.3 - - + +
221E VAL 3.7 1.3 - - - +
222E LYS* 3.4 4.7 - - - +
223E CYS* 3.2 44.6 + - - +
225E LYS* 2.9 24.8 + - - +
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Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E THR* 3.3 3.5 - - - -
201E ILE* 2.9 35.3 + - + -
202E GLY* 2.8 28.6 + - - +
207E GLY 5.0 3.6 - - - +
208E ASP* 1.3 79.2 - - - +
210E MET* 1.3 73.5 + - - +
220E ALA* 4.3 17.5 - - + -
221E VAL 3.4 6.1 - - - +
222E LYS* 4.2 22.7 - - + -
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Residues in contact with MET 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E LEU* 3.7 38.1 - - + -
198E LEU 4.6 1.6 - - - +
199E GLN 3.6 11.2 - - - +
200E THR* 3.7 24.0 - - + +
201E ILE* 4.2 5.1 - - - +
208E ASP* 5.2 6.3 - - + +
209E VAL* 1.3 81.2 - - - +
211E LEU* 1.3 66.6 + - - +
220E ALA* 3.4 5.2 - - - -
221E VAL* 2.9 38.4 + - + +
223E CYS* 5.4 9.0 - - - -
263E TYR* 3.4 38.6 - - + +
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Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E LEU* 3.9 1.2 - - - +
198E LEU* 3.0 42.5 + - + +
199E GLN* 2.9 41.0 + - + +
201E ILE* 3.9 16.9 - - + +
210E MET* 1.3 77.7 - - - +
212E GLY* 1.3 71.1 + - - +
218E LYS* 4.2 12.6 - - + -
219E VAL 3.5 14.1 - - - +
221E VAL* 4.9 0.9 - - - -
268E TYR* 3.5 40.2 - - + +
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Residues in contact with GLY 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E LEU* 4.3 8.1 - - - -
196E LYS 3.5 10.1 - - - -
197E LEU* 4.5 1.3 - - - -
198E LEU* 4.1 6.4 - - - +
210E MET 3.9 0.4 + - - -
211E LEU* 1.3 81.0 - - - +
213E ASP* 1.3 60.9 + - - +
218E LYS* 3.4 8.1 - - - +
219E VAL* 2.9 41.2 + - - -
221E VAL* 4.6 2.2 - - - -
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Residues in contact with ASP 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E GLU 3.2 4.2 - - - +
195E LEU* 4.1 2.7 - - - +
196E LYS* 3.0 46.2 + - + +
198E LEU* 4.6 10.8 - - + -
212E GLY* 1.3 74.1 - - - +
214E TYR* 1.3 57.2 + - - +
215E ARG 4.1 0.5 + - - -
216E GLY* 3.1 41.1 + - - +
217E ASN 3.0 6.9 + - - +
218E LYS* 5.5 0.6 - - - +
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Residues in contact with TYR 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E GLY* 5.1 8.8 - - - -
190E LEU* 3.7 42.3 - - + +
191E ASN* 3.1 34.3 + - - -
194E GLU* 3.4 30.7 - - + -
195E LEU* 4.1 11.2 - - + +
212E GLY 4.1 0.8 - - - -
213E ASP* 1.3 70.7 - - - +
215E ARG* 1.3 94.8 + - + +
216E GLY 2.9 1.8 + - - -
217E ASN* 3.0 21.8 + - - +
219E VAL* 4.1 25.0 - - + +
252E LEU* 6.3 2.7 - - + -
255E ILE* 6.2 0.2 - - + -
265E VAL* 5.3 2.2 - - + -
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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