Contacts of the strand formed by residues 190 - 195 (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 TRP 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 3.6 28.3 - - + -
189A LEU* 1.3 74.6 - - - +
191A GLY* 1.3 63.3 + - - +
192A THR* 3.5 21.4 + - - -
208A VAL* 3.5 30.1 - - + +
210A PRO* 3.9 35.7 - - + -
239A PHE* 3.8 22.9 - + + -
467A GLY 4.3 2.9 - - - -
468A LYS 4.6 0.4 - - - -
469A GLY* 3.5 39.3 - - - -
470A ILE* 3.3 19.0 - - + +
471A ASP* 2.7 32.9 + - - +
474A CYS* 3.3 8.3 - - - -
497A ILE* 4.6 2.2 - - + -
498A VAL 3.1 11.9 - - - +
499A ILE* 4.1 4.3 - - + -
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Residues in contact with GLY 191 (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* 1.3 76.5 - - - +
192A THR* 1.3 67.1 + - - -
470A ILE* 4.5 0.4 - - - -
474A CYS* 3.2 3.4 - - - +
475A GLN* 3.4 29.4 - - - -
478A ALA* 4.2 5.8 - - - -
497A ILE* 3.3 3.8 - - - +
498A VAL 2.8 32.9 + - - -
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Residues in contact with THR 192 (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* 3.5 19.4 + - - -
191A GLY* 1.3 78.0 + - - -
193A VAL* 1.3 64.9 + - - +
206A PHE* 3.5 48.4 - - + -
208A VAL* 4.0 10.0 - - - +
470A ILE* 4.9 2.7 - - - +
475A GLN* 2.7 34.2 + - - +
478A ALA* 4.3 2.9 - - - -
495A SER* 6.4 0.2 - - - -
496A ILE 3.3 12.1 - - - +
497A ILE* 4.0 7.5 - - + +
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Residues in contact with VAL 193 (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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192A THR* 1.3 76.9 - - - +
194A SER* 1.3 65.2 + - - +
195A ILE* 3.8 22.9 - - + -
478A ALA* 3.6 21.7 - - + +
479A ASP* 4.4 13.7 - - - +
482A SER* 3.6 23.8 - - - +
494A ILE 4.1 2.7 - - - +
495A SER* 3.2 2.1 - - - -
496A ILE* 2.8 62.2 + - + +
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Residues in contact with SER 194 (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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192A THR* 4.7 0.6 - - - +
193A VAL* 1.3 79.0 - - - +
195A ILE* 1.3 64.1 - - - +
202A MET* 3.3 18.8 - - - +
204A ASP* 4.1 5.7 + - - +
205A ALA* 4.7 0.3 + - - -
206A PHE* 3.6 34.6 - - - -
494A ILE 3.3 4.9 - - - -
495A SER* 2.6 21.5 + - - -
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Residues in contact with ILE 195 (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* 3.8 16.4 - - + -
194A SER* 1.3 80.1 - - - +
196A GLN* 1.3 59.0 + - - +
197A GLY* 4.0 10.1 - - - +
202A MET* 3.5 11.1 - - - +
482A SER* 4.1 26.2 - - - +
486A LEU* 4.1 23.3 - - + -
493A ASN* 3.6 1.0 - - - -
494A ILE* 3.0 45.8 + - + +
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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