Contacts of the strand formed by residues 541 - 551 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463M ALA* 3.7 29.9 + - + +
464M ASP* 5.5 2.0 - - - +
471M HIS* 3.2 15.8 + - - -
538M LYS 6.1 0.7 - - - -
539M ASN* 3.7 5.3 + - - +
540M THR* 1.3 78.7 - - - +
542M VAL* 1.3 72.0 + - - +
566M PRO* 3.5 36.8 - - - +
567M ILE 3.4 6.1 - - - +
568M GLU* 3.5 30.4 - - - +
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Residues in contact with VAL 542 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460M ILE* 3.4 21.8 - - + -
461M GLY 3.4 8.1 - - - +
463M ALA* 4.0 6.0 - - - +
471M HIS* 3.4 10.1 - - + -
474M TYR* 3.4 33.0 - - + -
518M ILE* 4.6 8.3 - - + -
541M ARG* 1.3 84.3 - - - +
543M ARG* 1.3 72.4 + - - +
566M PRO* 3.3 1.9 - - - +
567M ILE* 2.8 49.8 + - + +
569M CYS* 3.5 16.6 - - - -
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Residues in contact with ARG 543 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460M ILE* 3.8 1.8 - - - -
461M GLY 2.9 29.6 + - - -
462M THR 2.8 32.2 + - - +
463M ALA* 3.6 18.5 + - + +
464M ASP 4.0 7.1 + - - -
465M GLU 5.4 0.6 + - - -
466M ARG 4.6 1.4 + - - -
468M LEU* 3.0 31.8 - - + +
542M VAL* 1.3 88.2 - - - +
544M LEU* 1.3 64.0 + - - +
545M VAL* 3.3 1.6 + - + +
563M ALA* 3.8 18.7 - - + +
564M SER* 3.0 29.8 - - - +
565M ASN 3.6 8.3 - - - +
566M PRO* 3.9 13.5 - - + -
567M ILE* 4.9 0.9 - - - -
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Residues in contact with LEU 544 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416M PRO* 4.3 20.0 - - + -
433M VAL* 4.3 23.3 - - + -
441M PRO* 4.4 15.9 - - + -
458M ILE* 4.9 11.0 - - + -
459M PHE 4.0 1.8 - - - -
460M ILE* 3.6 25.8 - - + -
513M ILE* 5.1 4.9 - - + -
516M ALA* 5.1 5.4 - - + -
518M ILE* 4.9 0.9 - - + -
542M VAL* 6.3 0.2 - - + -
543M ARG* 1.3 69.1 - - - +
545M VAL* 1.3 59.3 + - - +
546M PHE* 3.6 32.1 - - + -
562M THR 3.6 1.7 - - - +
563M ALA* 3.4 3.5 - - - -
564M SER* 2.5 37.0 + - - +
567M ILE* 4.0 13.8 - - + +
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Residues in contact with VAL 545 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457M GLN 3.4 0.5 - - - +
458M ILE* 3.3 7.3 - - - +
459M PHE* 2.8 74.9 + - + +
461M GLY* 3.5 4.0 - - - +
468M LEU* 3.5 31.4 - - + -
543M ARG* 3.4 14.6 - - + +
544M LEU* 1.3 73.7 - - - +
546M PHE* 1.3 63.8 + - - +
561M GLN* 3.6 28.0 - - + +
562M THR 3.5 7.4 - - - +
563M ALA* 4.9 1.3 - - + +
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Residues in contact with PHE 546 (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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410M LEU* 3.4 6.0 - - + +
412M ILE* 3.1 35.4 - - + -
416M PRO* 6.1 0.4 - - + -
441M PRO* 5.2 4.0 - - + -
443M VAL* 3.5 21.8 - - + -
456M LEU* 4.0 16.6 - - + -
457M GLN 3.2 4.5 - - - +
458M ILE* 3.7 31.9 - - + -
513M ILE* 3.5 28.7 - - + -
544M LEU* 3.6 43.1 - - + -
545M VAL* 1.3 74.5 - - - +
547M ARG* 1.3 61.9 + - - +
561M GLN* 3.4 1.4 - - - +
562M THR* 2.7 45.7 + - - +
564M SER* 4.8 2.2 - - - -
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Residues in contact with ARG 547 (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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395M VAL* 3.5 25.7 + - - +
396M PRO 3.5 10.1 + - - -
397M LEU* 2.7 32.9 + - - +
399M TRP 4.1 3.4 + - - -
401M LEU* 3.5 24.8 - - - +
410M LEU* 4.0 2.7 - - - -
456M LEU* 3.6 3.9 - - - +
457M GLN* 2.7 72.4 + - + +
459M PHE* 4.4 13.2 - - + -
546M PHE* 1.3 76.5 - - - +
548M VAL* 1.3 58.2 + - - +
549M HIS* 4.0 20.0 + - - +
560M LEU 3.0 18.4 - - - +
561M GLN* 2.5 35.8 + - + +
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Residues in contact with VAL 548 (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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410M LEU* 4.2 20.4 - - + -
445M LEU* 4.3 15.0 - - + -
454M LEU* 3.4 35.2 - - + -
455M GLY 3.9 16.6 - - - +
456M LEU* 4.5 8.7 - - + -
503M LEU* 4.4 6.5 - - + -
547M ARG* 1.3 74.5 - - - +
549M HIS* 1.3 70.6 + - - +
550M ILE* 4.4 5.4 - - + -
558M VAL 4.0 0.7 - - - +
559M SER* 3.7 1.4 - - - -
560M LEU* 3.1 40.3 + - + +
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Residues in contact with HIS 549 (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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395M VAL* 4.7 20.7 + - + +
401M LEU* 5.6 0.4 - - + -
454M LEU* 3.8 12.6 - - - +
455M GLY 4.5 3.1 + - - -
457M GLN* 3.4 32.2 + - + -
547M ARG* 4.0 26.0 + - - -
548M VAL* 1.3 76.4 + - - +
550M ILE* 1.3 60.9 + - - +
551M PRO* 3.2 12.2 - - - +
557M ILE* 4.2 12.7 - - + +
558M VAL 3.8 3.4 - - - -
559M SER* 3.0 30.5 + - - -
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Residues in contact with ILE 550 (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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408M TYR* 3.3 66.6 - - + +
445M LEU* 3.8 25.4 - - + -
448M TYR* 4.3 15.9 - - + -
450M GLU* 6.3 0.2 - - + -
454M LEU* 4.3 4.0 - - + -
548M VAL* 4.4 7.2 - - + -
549M HIS* 1.3 71.9 - - - +
551M PRO* 1.3 74.2 - - + +
552M GLU* 3.6 1.8 + - + -
557M ILE* 3.4 4.6 - - - +
558M VAL* 2.8 51.4 + - + +
560M LEU* 4.0 11.9 - - + -
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Residues in contact with PRO 551 (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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408M TYR* 5.2 0.5 + - - -
448M TYR* 5.4 4.7 - - + +
450M GLU* 5.2 11.3 - - + +
454M LEU* 3.7 19.7 - - + -
549M HIS 3.2 11.4 - - - +
550M ILE* 1.3 92.4 - - + +
552M GLU* 1.3 63.5 + - - +
553M SER 4.1 0.5 + - - -
556M ARG 3.9 4.9 - - - +
557M ILE* 4.3 12.1 - - + -
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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