Contacts of the strand formed by residues 494 - 500 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A VAL* 3.7 1.7 - - - +
194A SER* 3.3 2.1 + - - -
195A ILE* 3.0 44.0 + - + +
197A GLY* 5.2 0.4 - - - -
431A SER* 4.0 1.6 - - - -
433A GLY* 3.8 22.0 - - - +
434A LEU 4.8 1.8 - - - +
482A SER* 4.0 16.8 - - - +
485A ALA* 4.2 13.9 - - + -
486A LEU* 3.7 36.3 - - + -
490A SER* 4.0 9.6 - - - +
492A ASP 3.5 10.5 + - - +
493A ASN* 1.3 77.9 - - - +
495A SER* 1.3 62.9 + - - +
496A ILE* 3.9 27.8 - - + -
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Residues in contact with SER 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A VAL 3.2 5.4 - - - -
194A SER* 2.6 27.8 + - - -
202A MET* 4.4 0.2 - - - +
204A ASP* 2.8 30.0 + - - +
205A ALA 4.7 3.8 + - - -
206A PHE* 5.2 4.0 - - - -
241A VAL* 4.2 19.7 - - - +
429A LEU 4.5 0.2 - - - -
430A ALA* 3.1 7.8 - - - +
431A SER* 3.1 33.9 + - - +
434A LEU* 5.2 0.3 - - - +
494A ILE* 1.3 74.2 - - - +
496A ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLY 3.9 0.2 - - - +
192A THR* 3.3 6.3 - - - +
193A VAL* 2.8 51.7 + - + +
428A ILE* 4.0 24.0 - - + -
429A LEU 3.3 4.9 - - - +
430A ALA* 4.3 2.0 - - + -
434A LEU* 3.7 27.4 - - + -
478A ALA* 4.0 4.0 - - + +
481A LEU* 3.7 26.5 - - + -
482A SER 3.8 12.8 - - - +
494A ILE* 3.9 14.4 - - + -
495A SER* 1.3 80.1 - - - +
497A ILE* 1.3 65.8 + - - +
498A VAL* 4.2 16.3 + - + -
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Residues in contact with ILE 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A TRP* 4.6 2.2 - - + -
191A GLY 3.3 9.6 - - - +
192A THR* 4.0 19.1 - - + +
206A PHE* 4.6 5.2 - - + -
207A ALA 4.4 0.2 - - - +
208A VAL* 3.9 19.1 - - + -
239A PHE* 4.0 18.6 - - + -
240A GLY 3.7 21.8 - - - +
241A VAL* 3.5 25.4 - - + -
427A LEU 3.7 1.2 - - - +
428A ILE* 3.4 6.2 - - - +
429A LEU* 2.8 37.2 + - + +
496A ILE* 1.3 78.6 - - - +
498A VAL* 1.3 64.0 + - - +
499A ILE* 3.9 23.7 - - + +
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Residues in contact with VAL 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A TRP* 3.1 5.5 - - - +
191A GLY 2.8 37.3 + - - +
426A CYS* 5.0 1.6 - - + -
427A LEU 3.8 2.7 - - - +
428A ILE* 4.1 11.9 - - + -
447A ALA* 4.6 6.3 - - + -
451A ILE* 3.9 28.9 - - + -
474A CYS* 3.6 17.4 - - + +
477A ALA* 4.1 9.9 - - + -
478A ALA* 3.9 25.1 - - + +
481A LEU* 4.0 19.7 - - + -
496A ILE* 4.1 4.2 - - + -
497A ILE* 1.3 74.4 - - - +
499A ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 6.4 0.4 - - + -
189A LEU 3.3 11.7 - - - +
190A TRP* 4.1 1.6 - - + -
239A PHE* 3.6 58.8 - - + -
334A VAL* 4.9 5.8 - - + -
426A CYS* 3.1 8.3 - - - +
427A LEU* 2.9 66.5 + - + +
429A LEU* 4.7 5.2 - - + -
474A CYS* 4.2 1.1 - - - -
497A ILE* 3.9 10.3 - - + -
498A VAL* 1.3 78.5 - - - +
500A ASP* 1.3 68.4 + - - +
501A LEU* 3.6 16.1 + - + -
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Residues in contact with ASP 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE 5.4 1.0 - - - +
189A LEU* 2.9 41.7 + - + +
425A GLU 4.0 2.0 - - - -
426A CYS* 4.5 2.2 - - - -
451A ILE* 3.8 13.6 - - + +
455A HIS* 4.4 6.2 + - - -
471A ASP* 4.8 2.1 - - - +
474A CYS* 3.5 21.5 - - - -
499A ILE* 1.3 76.0 - - - +
501A LEU* 1.3 63.7 + - - +
502A LYS 3.1 13.8 + - - +
505A ARG* 2.8 49.5 + - - +
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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