Contacts of the strand formed by residues 496 - 503 (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 THR 496 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397M LEU* 3.4 29.2 - - + +
459M PHE* 4.1 12.3 - - + -
460M ILE 5.4 3.4 - - - +
470M PRO* 3.4 27.4 - - + +
474M TYR 6.0 0.2 - - - +
475M GLN* 3.6 8.4 + - - +
492M ILE* 3.4 3.0 - - - -
493M VAL* 2.6 34.4 + - - +
494M GLY 3.5 0.4 - - - -
495M ASN* 1.3 83.4 + - - +
497M LYS* 1.3 73.3 + - - +
498M VAL* 3.9 7.0 - - + -
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Residues in contact with LYS 497 (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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459M PHE* 4.0 4.9 - - - +
460M ILE 5.3 0.2 + - - -
475M GLN* 2.7 32.8 + - + +
476M VAL* 4.0 33.0 + - + +
477M HIS* 5.8 0.4 - - - -
490M GLU* 3.3 48.6 + - + +
491M LYS 3.4 7.4 - - - +
492M ILE* 4.3 21.1 - - + +
496M THR* 1.3 80.1 - - - +
498M VAL* 1.3 70.2 + - - +
519M LEU* 5.8 6.3 - - - +
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Residues in contact with VAL 498 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397M LEU* 4.5 9.9 - - + -
457M GLN* 4.2 22.9 - - + +
458M ILE 3.1 23.3 - - - +
459M PHE* 3.9 10.5 - - + -
476M VAL* 4.4 0.2 - - - -
489M TYR 3.8 1.6 - - - +
491M LYS* 2.6 47.6 + - + +
493M VAL* 4.2 15.3 - - + -
496M THR* 3.9 21.1 - - + +
497M LYS* 1.3 84.2 - - - +
499M LEU* 1.3 72.7 + - - +
500M GLU* 5.1 0.2 - - - +
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Residues in contact with LEU 499 (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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457M GLN* 3.5 0.5 - - - -
458M ILE* 2.8 45.5 + - + -
476M VAL* 3.4 26.8 - - + +
477M HIS 4.4 0.9 - - - +
478M ARG* 3.7 32.3 - - + +
488M SER* 4.4 8.7 - - - -
489M TYR 3.2 7.6 - - - +
490M GLU* 4.1 15.0 - - + +
498M VAL* 1.3 80.9 - - - +
500M GLU* 1.3 63.0 + - - +
501M ILE* 5.7 0.2 - - + -
515M CYS* 3.3 41.7 - - - +
516M ALA* 4.2 12.3 - - + -
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Residues in contact with GLU 500 (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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455M GLY* 4.0 19.3 - - - -
456M LEU 3.1 16.4 - - - +
457M GLN* 3.3 26.7 + - + +
488M SER* 3.9 0.5 - - - -
489M TYR* 2.9 45.4 + - + +
491M LYS* 3.6 15.3 + - + -
498M VAL 5.1 1.3 - - - +
499M LEU* 1.3 77.2 - - - +
501M ILE* 1.3 67.7 + - - +
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Residues in contact with ILE 501 (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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455M GLY* 3.7 2.3 - - - -
456M LEU* 2.8 52.2 + - + +
458M ILE* 4.3 10.3 - - + +
486M THR* 3.5 21.8 - - - +
487M THR 3.1 21.1 - - - +
488M SER* 3.7 7.2 - - - -
499M LEU* 4.3 0.4 - - + -
500M GLU* 1.3 75.8 - - - +
502M PRO* 1.3 79.2 - - + +
503M LEU 4.5 0.2 - - - +
511M ALA* 3.5 22.4 - - + -
513M ILE* 4.2 15.3 - - + -
515M CYS* 3.6 18.4 - - - -
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Residues in contact with PRO 502 (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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453M PRO* 5.3 3.1 - - + -
454M LEU 3.5 9.2 - - - +
455M GLY* 4.7 0.7 - - - -
486M THR* 5.4 2.4 - - - -
487M THR* 3.4 36.1 - - + +
489M TYR* 5.9 2.9 - - + -
500M GLU 4.6 0.9 - - - +
501M ILE* 1.3 99.6 - - + +
503M LEU* 1.3 60.7 + - - +
504M GLU* 3.6 25.6 + - + +
510M ARG 5.0 1.4 - - - +
511M ALA* 4.4 5.0 - - - +
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Residues in contact with LEU 503 (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* 5.2 3.6 - - + -
443M VAL 4.5 3.1 - - - +
444M GLN* 4.9 0.9 - - - -
445M LEU* 4.5 13.9 - - + +
453M PRO* 3.7 0.3 - - - +
454M LEU* 2.9 26.0 + - + +
455M GLY 4.8 0.2 - - - -
456M LEU* 3.7 42.0 - - + +
502M PRO* 1.3 72.2 - - - +
504M GLU* 1.3 61.4 + - - +
509M MET* 2.9 65.2 - - + +
510M ARG 3.8 1.6 - - - +
511M ALA* 3.8 22.9 - - + +
548M VAL* 4.4 19.1 - - + -
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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