Contacts of the strand formed by residues 200 - 205 (chain D) in PDB entry 3L43
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 THR 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D ILE* 3.4 10.9 - - - +
173D ALA* 4.2 11.2 - - + -
187D LEU* 4.7 2.5 - - + -
190D ALA* 3.8 30.4 + - + +
194D ASP* 2.6 28.9 + - - +
197D GLY* 3.8 13.7 + - - +
198D LEU 3.7 2.2 - - - -
199D ARG* 1.4 76.2 + - - +
201D ILE* 1.3 63.0 + - - +
202D GLY 4.3 0.7 + - - -
227D LEU* 4.1 29.6 - - + +
229D ARG* 3.3 23.6 + - - +
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D LEU* 3.7 31.2 - - + -
171D ILE 3.0 8.1 + - - +
172D LEU* 3.6 18.9 - - + +
173D ALA 3.0 23.4 + - - -
200D THR* 1.3 78.1 - - - +
202D GLY* 1.3 73.7 + - - +
203D VAL 3.7 0.3 + - - -
229D ARG* 3.8 31.2 - - + +
230D GLY 4.1 6.7 - - - +
232D VAL* 4.2 20.0 - - + -
277D LEU* 4.5 6.1 - - + -
280D VAL* 3.8 27.1 - - + +
281D LEU* 4.1 9.4 - - + +
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Residues in contact with GLY 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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173D ALA* 3.6 8.1 - - - -
201D ILE* 1.3 75.0 - - - +
203D VAL* 1.3 58.9 + - - +
227D LEU* 3.7 12.9 - - - +
230D GLY 3.2 11.1 + - - -
231D TYR* 3.4 25.9 - - - -
232D VAL* 2.7 31.0 + - - -
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Residues in contact with VAL 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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47D VAL* 4.5 9.6 - - + -
172D LEU* 3.7 29.8 - - + -
173D ALA 2.7 15.3 + - - +
174D VAL* 3.3 17.5 - - + -
175D THR 2.9 26.7 + - - -
201D ILE* 4.3 1.1 - - + +
202D GLY* 1.3 77.5 - - - +
204D ILE* 1.3 66.4 + - - +
205D THR* 4.1 8.2 + - + -
231D TYR* 4.6 0.4 - - - -
232D VAL 3.3 7.6 - - - +
234D VAL* 4.3 24.5 - - + -
277D LEU* 3.8 25.4 - - + -
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Residues in contact with ILE 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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173D ALA 5.4 0.4 - - - +
175D THR* 3.3 17.0 - - + +
177D ALA* 3.7 29.4 - - + -
181D LEU* 3.7 25.4 - - + -
203D VAL* 1.3 79.7 - - - +
205D THR* 1.3 59.7 + - - +
207D LEU* 3.7 13.7 - - + +
216D ALA* 4.8 5.8 - - + -
219D VAL* 3.8 7.6 - - + -
220D LEU* 3.8 24.5 - - + -
231D TYR* 3.6 31.2 - - + -
232D VAL 2.9 10.4 + - - +
233D GLY* 3.5 1.7 - - - -
234D VAL* 2.8 33.8 + - - +
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Residues in contact with THR 205 (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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42D ALA 2.6 28.6 + - - +
43D GLY 4.1 4.9 - - - +
47D VAL* 5.1 0.7 - - + -
174D VAL* 3.8 17.9 - - + -
175D THR 3.2 4.1 + - - -
176D PRO* 3.3 14.4 - - - +
177D ALA* 2.6 35.5 + - - +
203D VAL* 4.3 4.0 - - + -
204D ILE* 1.3 73.4 - - - +
206D LYS* 1.3 61.2 + - - +
207D LEU 3.3 2.7 - - - -
234D VAL* 3.6 17.9 - - + -
236D ASN* 3.5 27.4 - - - +
901D GDP 4.2 3.4 - - - -
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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