Contacts of the strand formed by residues 211 - 217 (chain D) in PDB entry 2WLM
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 SER 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195C PHE* 6.1 0.5 - - - -
162D ARG* 4.5 9.5 + - - -
163D LEU 3.2 11.6 + - - -
164D ALA* 4.6 5.4 - - - -
208D PHE* 3.8 5.0 - - - -
210D LEU* 1.3 81.9 + - - +
212D TRP* 1.3 67.4 + - - +
213D THR* 4.3 2.1 + - - -
274D VAL* 5.0 6.1 - - - +
275D PHE* 3.6 31.2 - - - -
285D LEU* 5.2 3.6 - - - -
290D PHE* 3.9 14.2 - - - -
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Residues in contact with TRP 212 (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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162D ARG* 3.1 2.3 - - - -
163D LEU* 2.7 57.5 + - + +
174D ALA* 4.0 14.6 - - + -
175D ASP* 4.1 8.1 - - - -
176D VAL* 4.0 17.3 - - + -
202D ARG* 3.4 40.9 + - + +
203D SER* 3.3 27.8 - - - -
204D ARG 4.2 6.7 - - - -
205D SER* 3.8 29.4 - - - -
208D PHE* 3.6 24.2 - + + -
211D SER* 1.3 77.5 + - - +
213D THR* 1.3 81.2 + - - +
214D VAL* 3.7 9.7 + - + +
243D PHE* 4.7 2.2 - + - -
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Residues in contact with THR 213 (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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160D MET* 4.2 15.5 - - + -
161D MET 3.5 12.3 - - - +
162D ARG* 3.6 24.1 + - + +
211D SER* 4.3 2.6 + - - -
212D TRP* 1.3 81.2 + - - +
214D VAL* 1.3 67.4 + - - +
215D MET* 3.7 30.4 + - + +
271D PHE* 4.8 10.0 - - + +
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Residues in contact with VAL 214 (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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160D MET* 2.9 28.2 - - - +
161D MET* 2.8 32.5 + - - +
163D LEU* 4.2 13.7 - - + -
176D VAL* 3.5 22.2 - - + -
178D LEU* 5.4 5.5 - - + +
200D LEU* 3.2 38.1 - - + -
202D ARG 4.0 8.7 - - - +
212D TRP* 4.1 18.4 - - - +
213D THR* 1.3 74.9 - - - +
215D MET* 1.3 61.6 + - - +
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Residues in contact with MET 215 (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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194C ARG* 5.9 0.4 - - - -
153D PHE* 4.1 40.6 - - + -
158D THR* 3.4 12.3 - - + -
159D LEU 3.4 3.6 - - - -
160D MET* 3.7 24.5 - - + +
200D LEU* 3.1 11.5 - - - +
201D THR* 2.9 47.8 + - + +
202D ARG 5.2 1.6 + - - +
213D THR* 3.7 28.7 + - + +
214D VAL* 1.3 83.2 - - - +
216D HIS* 1.3 60.4 + - - +
217D PRO* 3.7 0.7 - - - -
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Residues in contact with HIS 216 (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 THR* 3.3 2.9 - - - -
159D LEU* 2.7 36.2 + - + +
178D LEU* 4.6 6.7 - - + +
198D LEU* 3.3 33.2 - - + +
199D THR* 2.8 32.6 + - - +
200D LEU* 3.9 11.2 - - + +
215D MET* 1.3 73.6 - - - +
217D PRO* 1.3 75.4 + - - +
218D ILE* 3.4 3.2 + - + +
222D SER* 2.4 41.8 + - - -
223D PRO* 4.5 1.1 - - + -
224D ILE* 3.7 21.6 - - + +
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Residues in contact with PRO 217 (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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156D LYS* 5.1 8.7 - - + -
157D PRO 3.8 0.2 - - - +
158D THR* 3.4 17.4 - - + +
199D THR* 3.9 12.8 - - + +
200D LEU 5.2 0.4 - - - -
201D THR* 3.0 37.5 - - + +
215D MET 3.5 1.3 - - - +
216D HIS* 1.3 102.3 + - - +
218D ILE* 1.3 61.4 + - - +
219D ASP* 3.9 10.3 + - + +
222D SER* 4.0 1.0 - - - -
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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