Contacts of the strand formed by residues 533 - 539 (chain A) in PDB entry 6C90
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A THR* 3.8 0.8 - - - +
315A PRO 2.8 12.9 + - - -
316A LEU* 3.2 22.6 - - - +
317A GLN* 2.7 34.3 + - - +
494A ARG 3.7 7.4 - - - -
525A GLY* 3.9 11.0 - - - -
532A ARG* 1.3 75.7 - - - +
534A ILE* 1.3 59.6 + - - -
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Residues in contact with ILE 534 (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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317A GLN* 3.6 6.5 - - + +
319A TYR* 4.1 19.5 - - + -
386A PHE* 3.2 52.7 - - + -
494A ARG* 3.1 15.4 + - + +
495A THR* 3.2 19.8 - - + +
496A VAL 2.9 24.6 + - - -
524A ALA* 3.5 4.5 - - - +
532A ARG* 5.1 7.6 - - + +
533A GLY* 1.3 76.9 - - - +
535A VAL* 1.3 62.7 + - - +
536A ILE* 3.9 25.1 - - + -
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Residues in contact with VAL 535 (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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316A LEU* 4.2 13.9 - - + -
317A GLN 2.8 15.3 + - - +
318A HIS* 3.4 14.4 - - + +
319A TYR* 2.6 34.5 + - - -
496A VAL* 3.5 6.3 - - + +
498A PHE* 3.9 14.4 - - + -
517A TYR* 3.2 24.9 - - + +
521A SER* 3.8 39.0 - - - +
524A ALA* 4.1 6.3 - - + -
534A ILE* 1.3 78.4 - - - +
536A ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 536 (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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319A TYR* 3.3 14.4 - - + +
321A PHE* 4.0 14.8 - - + +
328A LEU* 3.8 39.7 - - + -
377A ILE* 4.2 4.9 - - + -
381A ILE* 4.0 30.5 - - + -
386A PHE* 5.0 2.0 - - + -
495A THR* 4.2 4.7 - - + -
496A VAL 3.0 7.6 + - - +
497A LEU* 3.5 22.3 - - + +
498A PHE* 2.9 30.6 + - - -
534A ILE* 3.9 20.2 - - + -
535A VAL* 1.3 80.7 - - - +
537A LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 537 (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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319A TYR 2.7 15.0 + - - +
320A ILE* 3.3 12.6 - - + -
321A PHE 3.1 19.3 + - - -
498A PHE* 3.6 27.4 - - + -
501A ALA* 3.9 25.6 - - + -
512A ILE* 5.1 2.9 - - + -
517A TYR* 4.5 20.2 - - + +
536A ILE* 1.3 71.2 - - - +
538A MET* 1.3 68.7 + - - +
539A VAL* 3.5 16.3 + - + +
543A MET* 5.1 3.1 - - + -
551A LEU* 4.1 15.5 - - + -
552A LEU* 3.8 29.6 - - + -
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Residues in contact with MET 538 (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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321A PHE* 3.7 26.2 - - + +
370A GLY* 4.8 2.2 - - - +
373A ASN* 3.8 41.7 - - + +
374A VAL* 4.0 14.1 - - + -
377A ILE* 4.0 15.3 - - + -
497A LEU* 3.8 16.2 - - + -
498A PHE 3.0 18.7 + - - +
499A THR* 3.7 31.9 - - - +
500A ASN* 4.3 2.4 - - - -
501A ALA* 3.8 20.4 + - - +
536A ILE 3.9 0.2 + - - -
537A LEU* 1.3 74.2 - - - +
539A VAL* 1.3 62.8 + - - +
540A ASP* 4.3 0.8 + - - -
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Residues in contact with VAL 539 (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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320A ILE* 3.6 30.3 - - + -
321A PHE 3.5 5.3 + - - -
322A PRO* 3.5 3.5 - - + +
323A ALA* 2.9 25.6 + - - +
347A MET* 4.6 4.9 - - + -
350A LEU* 4.1 8.9 - - + +
501A ALA* 4.9 5.6 - - + -
511A TRP* 5.0 7.2 - - + -
537A LEU* 3.5 16.5 + - + +
538A MET* 1.3 79.6 - - - +
540A ASP* 1.3 60.5 + - - +
541A GLU* 3.1 26.0 - - + +
543A MET* 4.1 31.0 - - + -
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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