Contacts of the strand formed by residues 463 - 468 (chain B) in PDB entry 2I91
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 463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B LYS* 4.8 0.9 - - + -
370B ARG 3.2 3.8 + - - +
371B PHE* 3.5 32.8 - - + -
372B LEU 3.0 24.4 + - - -
461B ALA* 3.8 0.5 - - - +
462B ASP* 1.3 97.0 - - + +
464B PHE* 1.3 80.3 + - - +
465B ILE* 3.9 12.8 - - + -
495B LYS* 3.6 34.5 - - + +
497B ILE* 4.1 14.8 - - + -
533B PHE* 5.2 2.5 - - + -
534B THR* 3.6 35.0 - - + +
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 3.4 21.3 - - + +
450B PRO* 4.7 2.0 - - + -
451B MET* 3.2 54.1 - - + -
454B ALA* 3.7 22.2 - - + -
461B ALA* 3.3 26.5 - - + -
463B ILE* 1.3 87.0 - - - +
465B ILE* 1.3 64.0 + - - +
466B VAL* 4.1 3.4 - - + -
483B LEU* 4.1 12.6 - - + -
486B TYR* 3.8 22.4 - + - -
494B ALA* 4.9 2.5 - - + -
495B LYS 3.2 14.4 + - - +
496B LEU* 3.6 13.4 - - + +
497B ILE* 2.8 28.6 + - - +
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Residues in contact with ILE 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PHE* 4.5 4.7 - - + -
372B LEU* 2.9 8.3 + - - +
373B LEU* 3.5 24.4 - - + -
374B ALA* 2.8 28.6 + - - +
403B VAL* 4.1 11.9 - - + -
463B ILE* 3.9 11.4 - - + -
464B PHE* 1.3 79.6 - - - +
466B VAL* 1.3 62.1 + - - +
467B PHE* 3.2 33.1 + - + -
497B ILE* 3.3 16.2 - - + +
499B CYS* 4.4 9.0 - - + -
530B ILE* 3.8 40.6 - - + -
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 6.3 0.2 - - + -
374B ALA* 3.4 11.7 - - + -
415B PHE* 3.8 30.5 - - + -
447B CYS* 5.1 1.8 - - - +
450B PRO* 4.6 10.5 - - + -
451B MET* 4.6 11.4 - - + -
464B PHE* 4.9 1.8 - - + -
465B ILE* 1.3 77.7 - - - +
467B PHE* 1.3 60.2 + - - +
468B THR* 3.4 25.2 + - + +
496B LEU* 3.8 23.1 - - + -
497B ILE 3.0 8.8 + - - +
498B VAL* 3.7 7.9 - - + -
499B CYS* 2.9 26.5 + - - -
508B ILE* 4.6 9.0 - - + -
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Residues in contact with PHE 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 4.6 5.6 - - + -
374B ALA 2.8 22.3 + - - +
375B ILE* 4.6 3.1 - - + -
376B ASP* 3.1 25.4 + - - +
381B MET* 4.0 5.5 - - - +
396B ALA* 3.5 30.0 - - + +
399B MET* 3.3 34.3 - - + -
400B CYS* 3.9 32.3 - - + -
403B VAL* 4.9 9.0 - - + -
465B ILE* 3.2 32.3 - - + -
466B VAL* 1.3 69.8 - - - +
468B THR* 1.3 59.7 + - - +
499B CYS* 3.4 35.7 - - + +
501B MET* 4.2 7.0 - - - -
530B ILE* 5.8 2.2 - - + -
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Residues in contact with THR 468 (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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376B ASP* 2.7 28.5 + - - -
381B MET* 4.4 1.1 - - - -
447B CYS* 3.4 9.9 - - - -
466B VAL* 3.8 23.1 - - + +
467B PHE* 1.3 74.9 - - - +
469B ASP* 1.3 67.8 + - - +
470B CYS* 3.0 20.4 + - - +
498B VAL* 3.9 23.3 - - + -
499B CYS 3.2 8.1 + - - +
500B ALA* 3.5 4.3 - - - -
501B MET* 3.1 27.3 + - - +
508B ILE* 4.3 6.3 - - + -
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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
------------------------------------------------------------
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