Contacts of the strand formed by residues 205 - 210 (chain B) in PDB entry 4RUH
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 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B TYR 3.6 23.8 - - - -
198B TRP* 3.8 3.2 - - - -
199B LEU* 3.7 19.7 - - + +
203B LYS 5.0 0.4 - - - +
204B PRO* 1.3 75.1 - - - +
206B ILE* 1.3 68.8 + - - +
207B THR* 4.5 5.2 - - - -
401B MET* 3.7 4.9 - - - +
409B PRO* 3.9 2.0 - - - -
410B ASP* 3.1 18.6 - - + +
412B THR* 4.0 26.0 - - + +
436B PRO* 3.0 31.0 - - - +
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Residues in contact with ILE 206 (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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205B CYS* 1.3 81.4 - - - +
207B THR* 1.3 64.5 + - - +
208B TYR 4.1 0.2 + - - -
394B TYR* 3.8 14.8 - - + +
397B GLY* 3.4 39.5 - - - +
398B ARG* 3.5 11.7 - - + +
401B MET* 4.0 8.3 - - + -
409B PRO* 3.8 21.1 - - + -
410B ASP 2.8 5.5 + - - -
411B LEU* 3.2 16.8 - - + +
412B THR* 2.9 23.8 + - - -
433B MET* 3.7 24.0 - - + -
434B LEU 3.3 14.4 - - - +
435B LEU* 3.9 7.4 - - + -
436B PRO* 4.2 0.4 - - - -
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ASN* 3.1 26.5 + - + +
197B TYR 5.1 0.7 + - - -
205B CYS* 4.5 3.6 - - - -
206B ILE* 1.3 71.4 - - - +
208B TYR* 1.3 62.2 + - - +
209B GLY 3.3 24.0 - - - +
210B LEU* 4.3 0.7 - - + -
385B TRP* 3.8 2.6 - - + -
394B TYR* 3.5 7.7 + - - -
412B THR* 3.2 21.4 + - - +
414B GLU* 4.0 18.0 - - + +
434B LEU* 3.1 50.6 + - + +
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Residues in contact with TYR 208 (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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207B THR* 1.3 75.4 - - - +
209B GLY* 1.3 55.5 + - - +
309B TRP* 5.4 3.8 - - - -
385B TRP* 3.6 7.1 - - - -
386B VAL* 3.4 10.2 - - + -
387B SER* 2.6 50.0 + - - +
389B PHE* 3.9 30.2 - + + -
394B TYR* 3.5 28.0 - - + +
411B LEU* 3.7 28.3 + - + -
412B THR 3.1 31.0 + - - -
413B ARG* 3.4 32.4 + - + +
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 3.3 11.3 - - - +
208B TYR* 1.3 81.9 - - - +
210B LEU* 1.3 65.0 + - - +
385B TRP* 3.0 15.3 - - - -
386B VAL* 4.0 3.1 - - - -
412B THR 4.1 2.2 + - - -
413B ARG* 4.0 18.6 - - - +
414B GLU 3.1 22.7 + - - -
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Residues in contact with LEU 210 (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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207B THR* 4.3 0.7 - - + -
209B GLY* 1.3 81.5 - - - +
211B ARG* 1.3 66.6 + - - +
309B TRP 5.8 1.3 - - - -
346B PRO* 5.3 0.3 - - - +
384B PRO* 3.5 4.7 - - - +
385B TRP* 2.6 48.0 + - + +
386B VAL* 5.2 1.6 - - - +
413B ARG* 5.3 4.4 + - - +
414B GLU* 3.7 14.6 - - + +
416B GLY 3.8 14.6 - - - +
417B SER* 4.8 0.4 - - - -
418B ILE* 3.7 40.6 - - + +
421B THR* 3.9 14.1 - - + +
434B LEU* 3.7 20.4 - - + -
501B BES 4.0 25.1 - - + -
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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