Contacts of the strand formed by residues 533 - 539 (chain B) in PDB entry 6IEH
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 GLY 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314B THR* 4.4 0.6 - - - +
315B PRO 2.8 12.8 + - - -
316B LEU* 3.3 11.1 - - - +
317B GLN* 2.9 29.6 + - - +
494B ARG 3.6 8.7 - - - -
524B ALA 4.4 0.4 - - - -
525B GLY* 4.0 18.8 - - - -
532B ARG* 1.3 75.1 - - - +
534B ILE* 1.3 62.2 + - - -
535B VAL 4.2 0.2 - - - -
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Residues in contact with ILE 534 (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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244A GLU* 3.7 14.6 - - - +
317B GLN* 3.6 20.9 - - + +
319B TYR* 3.9 23.6 - - + -
328B LEU* 5.5 1.1 - - + -
386B PHE* 3.5 50.7 - - + -
494B ARG* 3.1 10.3 + - + +
495B THR* 3.1 25.1 - - + +
496B VAL 2.9 22.9 + - - -
524B ALA* 3.7 3.0 - - - +
533B GLY* 1.3 79.4 - - - +
535B VAL* 1.3 66.5 + - - +
536B ILE* 4.0 12.3 - - + -
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Residues in contact with VAL 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 4.0 14.1 - - + -
317B GLN 3.4 4.2 + - - +
318B HIS* 3.6 26.5 - - + -
319B TYR* 2.8 27.3 + - - +
496B VAL* 3.5 8.7 - - + +
498B PHE* 3.8 17.3 - - + -
517B TYR* 3.8 11.2 - - - +
521B SER* 3.7 41.1 - - - +
524B ALA* 4.1 4.3 - - + -
534B ILE* 1.3 79.2 - - - +
536B ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 536 (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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319B TYR* 3.5 6.1 - - + +
321B PHE* 4.6 7.0 - - + -
328B LEU* 3.7 40.4 - - + -
377B ILE* 4.0 22.4 - - + -
380B MET* 5.4 2.0 - - - -
381B ILE* 4.5 6.5 - - + -
386B PHE* 6.0 1.3 - - + -
495B THR* 4.3 15.9 - - + -
496B VAL 2.7 13.0 + - - +
497B LEU* 3.4 21.8 - - + -
498B PHE* 2.9 33.4 + - - +
517B TYR* 5.9 0.2 - - - -
534B ILE* 4.0 14.1 - - + -
535B VAL* 1.3 80.2 - - - +
537B LEU* 1.3 69.5 + - - +
538B MET* 5.0 0.9 - - + -
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Residues in contact with LEU 537 (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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319B TYR 2.8 15.3 + - - +
320B ILE* 3.3 21.6 - - + +
321B PHE 2.8 23.8 + - - +
498B PHE* 3.5 28.9 - - + -
501B ALA* 4.1 24.5 - - + -
512B ILE* 4.6 4.0 - - + -
517B TYR* 4.3 18.8 - - + +
536B ILE* 1.3 74.1 - - - +
538B MET* 1.3 63.0 + - - +
539B VAL* 3.7 20.2 + - + -
543B MET* 4.7 3.8 - - + -
551B LEU* 4.1 21.5 - - + -
552B LEU* 4.5 3.6 - - + -
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Residues in contact with MET 538 (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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321B PHE* 3.6 33.4 - - + -
372B SER* 3.9 22.0 - - - +
373B ASN 4.0 3.6 - - - +
374B VAL* 4.0 28.5 - - + -
377B ILE* 4.0 14.8 - - + -
497B LEU* 3.9 20.0 - - + -
498B PHE 2.6 28.0 + - - +
499B THR* 3.4 18.2 - - - +
500B ASN* 3.8 3.6 - - - -
501B ALA* 3.4 20.1 + - - +
536B ILE* 5.0 1.3 - - + -
537B LEU* 1.3 73.9 - - - +
539B VAL* 1.3 62.4 + - - +
540B ASP* 4.2 4.6 + - - +
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Residues in contact with VAL 539 (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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320B ILE* 4.0 17.5 - - + -
321B PHE 3.1 12.8 + - - +
322B PRO* 4.1 0.8 - - + +
323B ALA* 3.5 19.6 + - - +
347B MET* 3.9 12.1 - - + -
350B LEU* 3.6 14.6 - - + +
501B ALA* 3.6 20.0 - - + -
511B TRP* 4.9 2.2 - - + -
537B LEU* 3.7 19.7 - - + -
538B MET* 1.3 79.0 - - - +
540B ASP* 1.3 62.6 + - - +
541B GLU 3.2 25.1 - - - +
543B MET* 4.3 10.5 - - + -
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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