Contacts of the strand formed by residues 201 - 204 (chain D) in PDB entry 1L9W
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 ILE 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ILE* 6.0 1.1 - - + -
19D ILE* 4.3 12.3 - - + -
139D VAL* 5.0 9.0 - - + -
168D ILE* 3.7 24.2 - - + -
169D PRO 2.9 4.4 + - - -
170D LYS* 2.9 39.4 - - + +
171D ILE 2.9 24.6 + - - -
200D VAL* 1.3 82.0 - - - +
202D THR* 1.3 65.9 + - - +
203D MET* 4.2 13.7 - - + -
221D SER* 3.6 3.6 - - - -
222D ALA* 4.7 2.7 - - + -
223D ALA* 3.7 44.6 - - + +
225D PHE* 4.7 1.6 - - + -
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Residues in contact with THR 202 (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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158D LEU* 4.3 8.7 - - + -
171D ILE* 3.3 26.5 - - + -
184D LEU* 3.7 11.0 - - + +
185D LEU* 6.0 0.2 - - - +
188D THR* 2.5 43.7 + - + +
200D VAL* 3.8 18.6 - - + -
201D ILE* 1.3 80.0 - - - +
203D MET* 1.3 70.9 + - - +
212D SER 4.4 6.9 - - - +
213D ARG* 5.9 0.2 - - - -
221D SER* 3.2 20.2 + - - -
223D ALA 5.2 0.3 - - - +
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Residues in contact with MET 203 (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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170D LYS* 4.1 14.8 - - - -
171D ILE 3.0 11.3 + - - +
172D ALA* 3.3 26.4 - - + -
173D VAL* 3.0 26.9 + - - +
184D LEU* 4.0 9.0 - - - +
201D ILE* 4.2 10.5 - - + -
202D THR* 1.3 82.5 - - - +
204D SER* 1.3 63.1 + - - +
205D MET* 4.9 0.7 - - + -
212D SER* 3.7 9.6 - - - +
213D ARG* 3.8 29.6 - - + +
224D THR* 5.2 3.6 - - - +
225D PHE* 3.3 41.1 - - + +
304D DHS 3.8 16.2 - - - +
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Residues in contact with SER 204 (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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148D THR* 5.3 0.3 + - - -
173D VAL* 3.2 7.7 + - - +
175D PRO* 3.6 22.5 - - - +
180D ASP 4.9 0.5 + - - -
181D VAL* 3.8 12.0 - - - +
184D LEU* 4.1 16.8 - - - +
203D MET* 1.3 77.1 - - - +
205D MET* 1.3 60.1 + - - +
209D GLY* 3.4 28.6 - - - +
212D SER* 2.7 27.2 + - - -
213D ARG* 4.5 6.6 + - - -
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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