Contacts of the strand formed by residues 210 - 214 (chain B) in PDB entry 3OOT
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 CYS 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLN* 3.1 11.7 + - - +
194B MET* 2.9 36.0 + - - +
206B CYS* 2.0 47.1 - - + -
209B GLY* 1.3 71.0 - - - +
211B LEU* 1.3 64.1 + - - +
299B TRP* 3.7 26.9 - - + +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ILE* 4.0 33.4 - - + -
191B GLN* 3.9 24.9 - - + +
192B ILE 3.8 3.1 - - - +
193B GLN* 4.6 5.8 - - - +
194B MET* 4.4 2.0 - - - +
210B CYS* 1.3 82.9 - - - +
212B ALA* 1.3 61.0 + - - +
294B PRO 5.7 1.6 - - - +
295B THR 4.2 6.3 - - - +
296B GLY 5.6 1.3 - - - -
297B PRO 4.0 19.0 + - - +
298B THR* 3.3 14.7 - - + +
299B TRP* 3.0 33.1 + - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B GLN* 3.4 3.8 - - - -
192B ILE* 3.0 50.5 + - + +
194B MET* 4.2 24.7 - - + -
211B LEU* 1.3 75.1 - - - +
213B LEU* 1.3 62.4 + - - +
214B VAL 3.8 0.7 + - - -
262B LEU* 4.5 1.1 - - + -
299B TRP* 3.5 6.1 - - + -
301B LEU* 4.2 25.8 - - + -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR 5.1 0.4 - - - +
34B GLY* 4.9 15.7 - - - +
189B VAL* 3.8 26.2 - - + -
190B TRP* 3.4 22.2 - - + +
191B GLN* 4.2 5.6 - - + +
212B ALA* 1.3 71.6 - - - +
214B VAL* 1.3 62.5 + - - +
215B ASP* 3.4 27.0 + - + +
291B ILE* 5.0 9.2 - - + -
295B THR* 4.3 17.3 - - + -
298B THR* 3.7 14.8 - - + +
299B TRP 2.8 14.8 + - - +
300B ALA* 3.2 9.9 - - + -
301B LEU* 2.8 26.2 + - - +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR* 2.8 26.9 + - - -
190B TRP* 2.9 18.8 + - - +
192B ILE* 4.5 7.0 - - + -
212B ALA 4.5 5.8 - - - +
213B LEU* 1.3 72.4 - - - +
215B ASP* 1.3 54.5 + - - +
301B LEU* 3.8 25.1 - - + +
306B ILE* 4.5 9.9 - - + -
311B THR* 4.1 13.9 - - + -
313B PHE* 3.7 22.8 - - + -
320B ILE* 3.8 27.8 - - + -
322B PHE* 4.0 22.7 - - + -
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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