Contacts of the strand formed by residues 541 - 551 (chain L) in PDB entry 2O93
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 ARG 541 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463L ALA* 3.0 36.9 + - + +
471L HIS* 3.2 21.8 + - - -
538L LYS 5.9 0.7 - - - +
539L ASN* 3.7 5.9 + - - +
540L THR* 1.3 79.8 - - - +
542L VAL* 1.3 64.0 + - - +
566L PRO* 2.9 42.9 - - - +
567L ILE 3.5 9.2 - - - +
568L GLU* 3.9 20.4 + - - +
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Residues in contact with VAL 542 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460L ILE* 3.3 23.1 - - + -
461L GLY 3.3 7.2 - - - +
463L ALA* 3.6 4.4 - - - +
471L HIS* 3.8 2.9 - - + -
474L TYR* 3.3 42.0 - - + -
518L ILE* 4.3 9.4 - - + -
541L ARG* 1.3 80.3 - - - +
543L ARG* 1.3 72.7 + - - +
544L LEU* 6.2 0.2 - - + -
566L PRO* 3.6 1.9 - - - +
567L ILE* 3.0 42.5 + - + +
569L CYS* 3.5 25.1 - - - -
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Residues in contact with ARG 543 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460L ILE* 3.3 7.2 - - - +
461L GLY* 2.6 40.2 + - - +
462L THR 3.2 23.4 + - - -
463L ALA* 3.5 18.6 - - + +
464L ASP 4.8 7.3 + - - -
466L ARG 5.0 1.6 + - - -
467L ILE 5.0 0.6 - - - -
468L LEU* 3.4 31.8 - - + +
542L VAL* 1.3 85.8 - - - +
544L LEU* 1.3 61.9 + - - +
545L VAL 3.6 0.2 - - - -
563L ALA* 4.2 19.0 + - + +
564L SER* 3.4 21.5 + - - +
565L ASN 3.7 17.5 - - - +
566L PRO* 4.6 4.4 - - - +
567L ILE* 5.3 0.9 - - - -
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Residues in contact with LEU 544 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416L PRO* 4.1 25.1 - - + -
433L VAL* 4.3 23.1 - - + -
441L PRO* 4.8 7.6 - - + -
458L ILE* 4.2 20.9 - - + -
459L PHE 3.8 0.7 - - - +
460L ILE* 3.5 26.0 - - + -
476L VAL* 5.2 1.1 - - + -
513L ILE* 5.2 3.1 - - + -
516L ALA* 5.5 5.6 - - + -
518L ILE* 5.5 1.3 - - + -
543L ARG* 1.3 70.1 - - - +
545L VAL* 1.3 63.2 + - - +
546L PHE* 3.7 23.3 - - + -
562L THR 3.7 1.4 - - - +
563L ALA* 3.3 1.2 - - - -
564L SER* 2.9 41.6 + - - +
567L ILE* 4.2 12.5 - - + +
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Residues in contact with VAL 545 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458L ILE* 3.4 6.1 - - - +
459L PHE* 2.7 72.3 + - + +
461L GLY* 3.7 22.7 - - - +
468L LEU* 3.7 21.1 - - + -
543L ARG 4.1 0.9 - - - +
544L LEU* 1.3 75.6 - - - +
546L PHE* 1.3 65.3 - - - +
561L GLN* 3.6 29.8 - - + +
562L THR 3.5 6.3 - - - +
563L ALA* 4.0 9.9 - - + +
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Residues in contact with PHE 546 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410L LEU* 4.0 3.0 - - + +
412L ILE* 3.2 29.4 - - + -
416L PRO* 6.2 0.9 - - + -
441L PRO* 5.4 3.1 - - + -
443L VAL* 3.5 26.0 - - + -
456L LEU* 4.4 13.9 - - + -
457L GLN 3.2 4.9 - - - +
458L ILE* 3.4 37.0 - - + -
513L ILE* 3.5 30.5 - - + -
544L LEU* 3.7 40.2 - - + -
545L VAL* 1.3 73.3 - - - +
547L ARG* 1.3 60.0 + - - +
561L GLN* 3.4 1.0 - - - +
562L THR* 2.5 51.6 + - + +
564L SER* 5.0 3.1 - - - -
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Residues in contact with ARG 547 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395L VAL* 2.8 39.8 + - - +
396L PRO 3.0 17.6 + - - -
397L LEU* 3.6 25.2 + - + +
399L TRP* 3.5 15.6 + - - +
401L LEU* 3.6 16.4 - - + +
410L LEU* 4.2 1.6 - - - -
456L LEU* 3.5 4.4 - - - +
457L GLN* 2.8 62.5 + - + +
459L PHE* 4.5 8.7 - - + -
546L PHE* 1.3 76.9 - - - +
548L VAL* 1.3 61.3 + - - +
549L HIS* 4.1 12.4 + - - -
560L LEU 3.2 13.9 - - - +
561L GLN* 2.7 37.0 + - + +
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Residues in contact with VAL 548 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401L LEU* 6.1 0.2 - - - +
410L LEU* 3.9 21.5 - - + -
445L LEU* 4.4 19.5 - - + -
454L LEU* 4.4 20.9 - - + -
455L GLY 3.4 25.6 - - - +
456L LEU* 4.0 9.2 - - + -
457L GLN* 5.5 0.9 - - - -
503L LEU* 4.5 7.6 - - + -
547L ARG* 1.3 76.9 - - - +
549L HIS* 1.3 74.9 + - - +
550L ILE* 3.8 6.6 + - + +
559L SER* 3.9 1.6 - - - -
560L LEU* 2.9 36.3 + - + +
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Residues in contact with HIS 549 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393L SER* 3.4 44.3 + - - -
395L VAL* 3.4 36.1 + - + +
401L LEU* 5.1 0.2 - - + -
454L LEU* 4.7 4.3 - - - +
455L GLY 4.7 2.5 + - - -
457L GLN* 3.7 25.9 + - + -
547L ARG* 4.1 17.8 + - - -
548L VAL* 1.3 81.2 - - - +
550L ILE* 1.3 60.0 + - - +
551L PRO* 3.4 10.9 - - - +
557L ILE* 4.3 13.2 - - + +
558L VAL 3.8 3.4 - - - -
559L SER* 3.2 22.3 + - - -
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Residues in contact with ILE 550 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408L TYR* 3.9 47.8 - - + +
445L LEU* 3.6 36.3 - - + -
448L TYR* 4.0 20.4 - - + -
450L GLU* 5.7 0.7 - - - +
454L LEU* 4.2 7.2 - - + -
548L VAL* 3.8 9.4 + - + +
549L HIS* 1.3 71.1 - - - +
551L PRO* 1.3 74.7 - - + +
552L GLU* 3.7 4.5 + - + +
557L ILE* 3.2 5.5 - - - +
558L VAL* 2.9 44.9 + - + +
560L LEU* 4.8 7.9 - - + +
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Residues in contact with PRO 551 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448L TYR* 5.5 1.3 - - - +
450L GLU* 4.2 18.2 - - - +
454L LEU* 4.1 17.0 - - + -
549L HIS 3.4 9.4 - - - +
550L ILE* 1.3 89.4 - - + +
552L GLU* 1.3 65.2 + - - +
556L ARG 4.1 3.6 - - - +
557L ILE* 4.4 16.4 - - + -
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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