Contacts of the strand formed by residues 455 - 463 (chain M) in PDB entry 2JA7
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 MET 455 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443M LEU* 3.4 34.3 - - + +
444M PHE 3.2 5.6 - - - -
445M ASN* 3.1 33.4 - - + +
449M SER* 4.7 0.7 - - - -
452M LYS 3.1 7.2 + - - +
453M MET 2.7 0.8 + - - -
454M SER* 1.3 86.0 - - - +
456M MET* 1.3 63.2 + - - +
490M HIS* 4.3 6.3 - - + -
505M CYS* 4.9 0.2 - - - +
1130N PHE* 4.1 7.9 - - + -
1134N GLU* 3.5 46.7 - - + +
1137N CYS* 4.0 13.9 - - + -
1138N MET* 3.8 13.9 - - - +
1141N HIS* 3.1 25.0 + - - +
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Residues in contact with MET 456 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443M LEU* 3.6 4.9 - - - -
444M PHE 2.8 30.8 + - - +
453M MET* 3.4 22.0 - - - +
455M MET* 1.3 77.9 - - - +
457M ALA* 1.3 63.4 + - - +
458M HIS* 3.6 5.0 - - - -
474M VAL* 3.3 30.5 - - + -
477M PRO* 3.7 17.0 - - + -
478M TYR* 3.2 32.5 + - + +
505M CYS 3.5 5.4 - - - +
507M VAL* 3.4 17.0 - - + -
510M GLN* 3.6 38.6 - - + -
521M MET* 3.7 10.5 - - + -
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Residues in contact with ALA 457 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362M ASP* 4.5 1.0 - - - +
441M PRO* 5.4 2.0 - - + -
442M VAL 2.9 14.1 - - - +
443M LEU* 4.4 0.7 - - - +
456M MET* 1.3 72.7 - - - +
458M HIS* 1.3 61.3 + - - +
501M LEU* 3.8 26.2 - - + +
502M SER* 4.5 1.6 - - - +
505M CYS* 2.8 17.7 + - + +
506M ALA* 3.3 25.8 - - + +
507M VAL* 3.0 26.0 + - - +
508M PRO* 4.8 0.7 - - - +
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Residues in contact with HIS 458 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361M LEU 4.2 2.0 - - - -
362M ASP 3.0 13.1 + - - +
363M GLN 2.9 18.9 + - - -
364M VAL* 3.6 21.3 - - + -
441M PRO* 3.5 6.8 - - - +
442M VAL* 2.9 30.2 + - - +
444M PHE* 3.0 40.3 - + + -
456M MET 3.6 2.7 - - - -
457M ALA* 1.3 74.4 - - - +
459M ARG* 1.3 62.9 + - - +
470M LEU* 5.7 1.3 - - + -
474M VAL* 4.0 22.0 - - + -
478M TYR* 2.4 26.9 + - - -
507M VAL* 3.1 25.5 - - + +
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Residues in contact with ARG 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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360M GLU* 3.8 16.8 - - - +
362M ASP* 2.6 51.4 + - + +
363M GLN* 3.4 30.0 - - + +
364M VAL* 2.9 27.0 + - - +
439M ASN* 3.8 41.7 + - - +
440M ASP 4.8 0.9 - - - -
441M PRO* 5.0 2.0 - - - -
458M HIS* 1.3 75.0 - - - +
460M VAL* 1.3 63.8 + - - +
461M LYS 3.4 0.2 + - - -
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Residues in contact with VAL 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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363M GLN* 5.5 0.2 + - - -
364M VAL* 4.0 2.5 - - - -
366M VAL* 3.6 25.4 - - + -
371M ALA* 5.9 0.4 - - + -
436M ILE* 3.7 22.7 - - + -
437M MET* 3.3 23.6 - - - +
438M ASP* 3.2 3.9 - - - +
439M ASN* 2.6 30.0 + - - +
440M ASP 3.4 32.4 + - - +
442M VAL* 3.6 18.8 - - + -
458M HIS 4.0 0.2 + - - -
459M ARG* 1.3 72.0 - - - +
461M LYS* 1.3 64.6 + - - +
462M VAL* 4.2 8.7 - - + +
489M LEU* 5.1 1.1 - - + -
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Residues in contact with LYS 461 (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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359M LEU* 4.5 18.6 - - + +
363M GLN* 3.3 32.7 + - + +
364M VAL 3.3 15.6 + - - +
365M GLY* 3.4 5.4 - - - -
366M VAL 2.8 24.3 + - - -
438M ASP* 3.0 17.9 - - - +
439M ASN* 5.8 0.9 - - - +
459M ARG 4.5 1.8 - - - +
460M VAL* 1.3 75.1 - - - +
462M VAL* 1.3 74.2 + - - +
463M ILE* 3.3 12.8 + - + +
65W HIS* 6.0 1.4 + - - +
68W PHE* 5.8 10.2 - - - -
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Residues in contact with VAL 462 (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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366M VAL* 3.3 12.1 - - + +
368M LYS* 4.0 13.2 - - + -
371M ALA* 3.2 33.4 - - + -
399M HIS* 3.7 29.4 - - + +
436M ILE 4.7 0.2 - - - +
437M MET* 4.4 3.1 - - - -
438M ASP* 2.8 38.1 + - - +
460M VAL* 4.0 3.5 - - + +
461M LYS* 1.3 78.2 - - - +
463M ILE* 1.3 62.0 + - - +
68W PHE* 5.4 4.5 - - - -
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Residues in contact with ILE 463 (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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359M LEU* 5.6 6.7 - - + -
365M GLY* 3.4 22.0 - - - -
366M VAL 2.8 18.3 + - - +
367M PRO* 3.3 1.0 - - - +
368M LYS* 2.8 32.1 + - - -
461M LYS* 3.7 21.1 - - + +
462M VAL* 1.3 79.4 - - - +
464M PRO* 1.3 78.0 - - + +
467M THR 3.7 5.6 - - - +
469M ARG* 3.3 43.3 - - + -
65W HIS* 5.8 4.3 - - + -
67W PHE* 4.7 6.1 - - + -
68W PHE* 5.4 5.8 - - + -
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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