Contacts of the strand formed by residues 494 - 500 (chain B) in PDB entry 3RT0
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 494 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B VAL* 3.8 1.8 - - + +
194B SER* 3.3 2.3 + - - -
195B ILE* 2.9 49.7 + - + +
197B GLY* 5.1 0.4 - - - -
431B SER* 4.0 1.3 - - - -
433B GLY* 3.8 15.9 - - - +
434B LEU* 4.7 9.4 - - + +
482B SER* 4.0 22.9 - - - +
485B ALA* 4.2 8.3 - - + -
486B LEU* 3.8 34.5 - - + -
490B SER* 4.1 9.4 - - - +
492B ASP 3.6 10.7 + - - +
493B ASN* 1.3 78.1 - - - +
495B SER* 1.3 64.2 + - - +
496B ILE* 3.9 27.8 - - + -
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Residues in contact with SER 495 (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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193B VAL 3.2 5.2 - - - -
194B SER* 2.8 26.5 + - - -
204B ASP* 2.8 29.8 + - - +
205B ALA 4.6 3.1 + - - -
206B PHE* 5.2 3.8 - - - -
241B VAL* 4.0 22.9 - - - -
430B ALA* 3.0 8.3 - - - +
431B SER* 3.0 32.2 + - - +
494B ILE* 1.3 73.0 - - - +
496B ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 496 (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 GLY 4.0 0.2 - - - +
192B THR* 3.3 5.9 - - - +
193B VAL* 2.8 47.9 + - + +
428B ILE* 4.0 13.5 - - + -
429B LEU 3.4 7.6 - - - +
430B ALA* 4.2 7.2 - - + -
434B LEU* 3.8 17.0 - - + -
478B ALA* 4.2 2.9 - - + +
481B LEU* 3.6 32.1 - - + -
482B SER 3.9 12.6 - - - +
494B ILE* 3.9 16.4 - - + -
495B SER* 1.3 80.8 - - - +
497B ILE* 1.3 66.8 + - - +
498B VAL* 4.0 24.0 - - + -
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Residues in contact with ILE 497 (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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190B TRP* 4.5 4.3 - - + -
191B GLY 3.4 9.6 - - - +
192B THR* 4.0 16.4 - - + +
206B PHE* 4.6 4.5 - - + -
207B ALA 4.4 0.2 - - - +
208B VAL* 3.9 18.4 - - + -
239B PHE* 4.0 25.8 - - + -
240B GLY 3.7 22.7 - - - +
241B VAL* 3.7 26.7 - - + -
427B LEU 3.6 1.6 - - - +
428B ILE* 3.3 6.8 - - - +
429B LEU* 2.8 39.6 + - + +
496B ILE* 1.3 76.8 - - - +
498B VAL* 1.3 64.6 + - - +
499B ILE* 4.0 13.6 - - + +
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Residues in contact with VAL 498 (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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190B TRP* 3.1 5.5 - - - +
191B GLY 2.9 32.5 + - - +
426B CYS* 4.9 1.8 - - + -
427B LEU 3.8 1.8 - - - -
428B ILE* 4.2 14.4 - - + -
447B ALA* 4.5 7.9 - - + -
451B ILE* 4.1 25.8 - - + -
474B CYS* 3.6 16.8 - - + +
477B ALA* 4.1 10.8 - - + -
478B ALA* 3.9 28.9 - - + +
481B LEU* 4.2 8.5 - - + -
496B ILE* 4.0 11.4 - - + -
497B ILE* 1.3 76.5 - - - +
499B ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 499 (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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188B PRO* 6.3 0.2 - - + -
189B LEU 3.3 13.2 - - - +
190B TRP* 4.1 8.3 - - + -
239B PHE* 3.6 45.1 - - + -
334B VAL* 4.6 6.1 - - + -
426B CYS* 3.0 9.3 - - - +
427B LEU* 2.8 67.9 + - + +
429B LEU* 4.8 5.2 - - + -
474B CYS* 4.3 0.7 - - - -
497B ILE* 4.0 14.8 - - + +
498B VAL* 1.3 79.5 - - - +
500B ASP* 1.3 67.7 + - - +
501B LEU* 3.6 17.3 + - + +
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Residues in contact with ASP 500 (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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187B ILE 5.5 0.5 - - - +
189B LEU* 2.9 41.3 + - + +
425B GLU 4.0 2.5 - - - -
426B CYS* 4.5 2.7 - - - -
451B ILE* 3.8 12.2 - - + +
455B HIS* 4.4 6.8 + - - -
466B ARG* 5.3 0.2 + - - -
471B ASP* 5.0 1.4 - - - +
474B CYS* 3.4 23.2 - - - -
499B ILE* 1.3 74.7 - - - +
501B LEU* 1.3 65.1 + - - +
502B LYS* 3.0 20.6 + - - +
505B ARG* 3.0 41.0 + - - +
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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