Contacts of the strand formed by residues 533 - 539 (chain M) in PDB entry 6D6Q
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314M THR* 3.9 2.2 - - - +
315M PRO 3.1 8.1 + - - -
316M LEU* 3.4 18.6 - - - -
317M GLN* 2.9 26.7 + - - +
494M ARG 3.3 10.5 - - - -
524M ALA* 4.4 0.4 - - - -
525M GLY 4.4 8.7 - - - -
532M ARG* 1.3 76.6 - - - +
534M ILE* 1.3 68.0 + - - +
535M VAL 4.0 0.2 - - - -
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Residues in contact with ILE 534 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317M GLN* 3.4 31.0 - - + +
319M TYR* 4.0 19.1 - - + -
328M LEU* 5.9 0.9 - - + -
386M PHE* 4.5 37.5 - - + -
494M ARG* 3.1 11.9 + - + +
495M THR* 2.2 41.9 + - - +
496M VAL* 2.9 11.8 + - - +
524M ALA* 4.6 0.4 - - - +
532M ARG* 4.1 17.7 - - + +
533M GLY* 1.3 80.3 - - - +
535M VAL* 1.3 61.4 + - - +
536M ILE* 4.0 18.2 - - + -
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Residues in contact with VAL 535 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316M LEU* 3.9 28.9 - - + -
317M GLN 2.9 11.1 + - - +
318M HIS* 3.2 38.6 - - + +
319M TYR* 2.9 23.7 + - - +
496M VAL* 3.4 19.5 - - + -
498M PHE* 3.7 25.1 - - + -
517M TYR* 3.6 12.6 - - - +
521M SER* 4.2 4.5 - - - +
524M ALA* 4.5 0.2 - - + -
533M GLY 4.0 0.2 - - - -
534M ILE* 1.3 71.4 - - - +
536M ILE* 1.3 72.9 + - - +
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Residues in contact with ILE 536 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319M TYR* 3.2 22.2 - - + +
320M ILE* 5.7 0.2 - - - -
321M PHE* 5.8 2.7 - - + +
328M LEU* 4.6 20.4 - - + -
377M ILE* 3.7 27.8 - - + -
381M ILE* 4.2 11.9 - - + -
495M THR* 4.8 2.7 - - - +
496M VAL 2.9 8.5 + - - +
497M LEU* 3.2 30.0 - - + -
498M PHE* 2.9 30.1 + - - -
534M ILE* 4.0 18.6 - - + +
535M VAL* 1.3 84.5 - - - +
537M LEU* 1.3 61.3 + - - +
538M MET* 5.7 5.6 - - + +
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Residues in contact with LEU 537 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319M TYR 2.9 11.3 + - - +
320M ILE* 3.4 14.6 - - + +
321M PHE* 2.9 24.0 + - - +
498M PHE* 3.3 33.4 - - + +
500M ASN 4.7 0.2 - - - -
501M ALA* 4.6 20.6 - - + +
512M ILE* 6.0 1.1 - - + -
517M TYR* 4.7 13.0 - - + +
536M ILE* 1.3 77.0 - - - +
538M MET* 1.3 74.6 + - - +
539M VAL* 4.2 12.3 - - + -
543M MET* 5.8 3.4 - - + -
551M LEU* 4.5 25.4 - - + -
552M LEU* 4.5 13.0 - - + -
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Residues in contact with MET 538 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321M PHE* 3.4 22.4 - - + +
373M ASN* 4.2 28.3 - - + +
374M VAL* 4.5 27.4 - - + +
377M ILE* 4.9 7.6 - - + -
497M LEU* 5.0 6.1 - - + -
498M PHE 3.0 13.9 + - - +
499M THR* 3.3 41.5 - - + +
500M ASN* 4.1 12.6 - - - +
501M ALA* 4.6 2.4 + - - +
502M ARG* 5.5 1.4 + - - -
536M ILE* 5.7 7.4 - - + -
537M LEU* 1.3 82.1 - - - +
539M VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 539 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320M ILE* 3.5 28.0 - - + -
321M PHE 2.9 13.9 + - - +
322M PRO* 3.5 8.5 - - + +
323M ALA* 3.3 22.0 + - - +
347M MET* 4.9 4.5 - - + -
350M LEU* 4.1 19.4 - - + +
501M ALA* 6.3 1.6 - - + -
502M ARG* 5.4 3.8 - - - +
537M LEU* 4.2 17.9 - - + -
538M MET* 1.3 81.4 - - - +
540M ASP* 1.3 60.4 + - - +
541M GLU 3.8 2.2 - - - +
543M MET* 4.2 24.9 - - - -
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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