Contacts of the strand formed by residues 454 - 461 (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 LEU 454 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445M LEU* 3.8 11.4 - - + -
448M TYR* 4.0 24.0 - - + +
452M LYS* 6.2 0.4 - - + -
453M PRO* 1.3 79.0 - - - +
455M GLY* 1.3 61.4 + - - +
502M PRO* 3.5 7.6 - - - +
503M LEU* 2.9 31.0 + - + -
509M MET* 3.5 27.8 - - + -
548M VAL* 3.4 28.7 - - + -
549M HIS 3.8 9.2 - - - +
550M ILE* 4.3 4.9 - - + -
551M PRO* 3.7 28.3 - - + -
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Residues in contact with GLY 455 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454M LEU* 1.3 79.4 - - - +
456M LEU* 1.3 62.4 + - - -
457M GLN* 3.8 5.7 + - - +
500M GLU* 4.0 23.3 - - - -
501M ILE 3.7 5.4 - - - -
502M PRO* 4.7 0.2 - - - -
503M LEU* 4.8 0.4 - - - -
547M ARG 3.9 0.7 - - - +
548M VAL* 3.9 19.6 - - - +
549M HIS* 4.5 3.5 + - - -
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Residues in contact with LEU 456 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410M LEU* 4.5 3.1 - - + -
443M VAL* 3.9 26.5 - - + -
454M LEU 4.1 1.2 + - - -
455M GLY* 1.3 73.0 - - - -
457M GLN* 1.3 70.0 + - - +
458M ILE* 4.6 1.0 - - + +
500M GLU* 3.1 6.9 - - - +
501M ILE* 2.8 51.0 + - + +
503M LEU* 3.7 23.4 - - + +
511M ALA* 4.3 5.2 - - + -
513M ILE* 3.7 30.3 - - + -
546M PHE* 4.0 12.8 - - + -
547M ARG* 3.6 25.8 - - - +
548M VAL* 4.4 3.4 - - + +
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Residues in contact with GLN 457 (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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397M LEU* 5.8 3.8 - - - +
455M GLY 4.4 4.3 - - - +
456M LEU* 1.3 76.9 - - - +
458M ILE* 1.3 63.6 + - - +
459M PHE* 5.2 2.9 - - + -
491M LYS* 3.2 37.6 - - - +
498M VAL* 4.2 12.0 - - + +
499M LEU 3.5 3.6 - - - -
500M GLU* 3.3 15.5 + - + +
545M VAL 3.4 0.4 - - - +
546M PHE* 3.2 8.8 - - - +
547M ARG* 2.7 59.0 + - + +
549M HIS* 3.4 30.5 + - + -
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Residues in contact with ILE 458 (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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456M LEU* 4.6 5.4 - - + +
457M GLN* 1.3 82.0 - - - +
459M PHE* 1.3 67.8 + - - +
476M VAL* 4.0 14.2 - - + +
498M VAL* 3.1 8.1 - - - +
499M LEU* 2.8 53.8 + - + +
501M ILE* 4.3 17.7 - - + -
513M ILE* 3.7 36.3 - - + -
515M CYS* 5.2 0.9 - - - -
516M ALA* 4.7 12.1 - - + -
544M LEU* 4.9 7.2 - - + -
545M VAL 3.3 4.7 - - - +
546M PHE* 3.7 24.7 - - + -
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Residues in contact with PHE 459 (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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397M LEU* 4.5 22.2 - - + -
457M GLN* 5.2 1.8 - - + -
458M ILE* 1.3 82.6 - - - +
460M ILE* 1.3 67.3 + - - +
468M LEU* 4.2 10.1 - - + -
470M PRO* 3.9 30.7 - - + -
476M VAL* 3.3 12.1 - - - -
496M THR* 4.1 5.2 - - + -
497M LYS 4.0 4.7 - - - +
498M VAL* 3.9 21.8 - - + -
544M LEU* 3.8 0.9 - - - -
545M VAL* 2.8 80.5 + - + +
547M ARG* 4.4 17.9 - - + -
561M GLN* 3.8 13.9 - - - -
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Residues in contact with ILE 460 (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* 1.3 74.4 - - - +
461M GLY* 1.3 59.4 + - - +
470M PRO* 3.8 5.0 - - - +
471M HIS* 3.0 20.5 + - + +
474M TYR* 3.4 25.8 - - + +
475M GLN* 3.8 7.1 - - - +
476M VAL* 3.4 34.5 - - + +
496M THR* 5.4 3.2 - - - +
497M LYS 5.3 0.2 + - - -
517M GLY 4.6 0.7 - - - +
518M ILE* 3.9 22.7 - - + -
542M VAL* 3.4 38.8 - - + -
543M ARG 3.8 2.5 - - - +
544M LEU* 3.6 30.7 - - + -
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Residues in contact with GLY 461 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459M PHE* 4.4 0.2 - - - -
460M ILE* 1.3 74.7 - - - +
462M THR* 1.3 61.6 + - - -
468M LEU* 4.1 1.6 - - - -
469M LYS 3.3 12.3 - - - -
470M PRO* 4.1 2.9 - - - -
471M HIS* 3.6 9.5 - - - +
542M VAL* 3.4 11.1 - - - +
543M ARG* 2.9 30.5 + - - -
545M VAL* 3.5 18.7 - - - +
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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