Contacts of the strand formed by residues 560 - 573 (chain G) in PDB entry 1P8J
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 TYR 560 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458E PRO* 3.9 27.4 - - + -
494E SER* 4.2 11.4 - - - -
562E THR* 3.1 35.9 - - + +
564E THR* 3.1 23.2 - - + +
460G ASP* 5.8 1.6 - - - +
462G GLY* 5.1 7.6 - - - -
495G TYR* 3.3 11.8 - - - -
496G ASN* 2.7 63.5 + - + +
558G ASN* 3.9 5.6 - - - +
559G ASN* 1.3 83.4 - - - +
561G GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 561 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460G ASP* 3.4 9.8 + - - +
461G ILE* 3.0 26.6 + - - -
462G GLY 4.6 2.4 - - - +
494G SER* 2.9 17.7 - - - -
495G TYR* 3.7 7.1 - - - -
560G TYR* 1.3 79.5 - - - +
562G THR* 1.3 67.6 + - - -
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Residues in contact with THR 562 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E TYR* 3.3 42.9 - - + +
458G PRO* 3.8 19.1 - - + -
459G LYS 3.2 21.8 - - - +
460G ASP* 4.4 5.4 + - - +
461G ILE* 4.1 5.2 - - - -
493G LEU* 3.1 3.8 - - - -
494G SER* 2.8 41.9 + - - -
561G GLY* 1.3 77.8 + - - -
563G LEU* 1.3 68.6 + - - +
564G THR* 3.6 4.0 + - + +
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Residues in contact with LEU 563 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455G LEU* 4.0 23.8 - - + +
458G PRO* 3.3 1.9 - - - +
459G LYS* 2.7 44.3 + - + +
461G ILE* 3.9 6.5 - - + +
465G LEU* 3.8 28.0 - - + -
467G VAL* 4.2 3.1 - - + -
491G LEU* 4.4 13.2 - - + -
492G THR 3.6 16.6 - - - +
493G LEU* 3.9 11.9 - - + -
549G LEU* 3.9 16.6 - - + -
551G ILE* 3.8 19.1 - - + -
562G THR* 1.3 69.3 - - - +
564G THR* 1.3 58.8 + - - +
565G LYS 3.6 17.5 - - - +
566G PHE* 4.6 3.1 - - + -
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Residues in contact with THR 564 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E TYR* 3.1 36.1 - - + +
455G LEU* 3.8 6.0 - - - +
456G VAL* 3.6 20.3 - - - +
458G PRO* 4.2 8.5 - - + +
492G THR* 2.9 33.0 + - - +
493G LEU* 5.1 2.0 - - - -
494G SER* 5.1 3.1 - - - +
562G THR* 3.9 14.8 - - + +
563G LEU* 1.3 76.4 - - - +
565G LYS* 1.3 62.8 + - - +
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Residues in contact with LYS 565 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F THR* 6.1 0.7 - - - -
233F ASP* 4.7 7.1 - - - +
234F ALA* 6.5 0.4 - - + -
4036F SO4 2.7 45.1 + - - +
455G LEU* 3.7 11.6 - - - +
490G ARG 4.0 2.7 - - - +
491G LEU* 3.4 4.5 - - - -
492G THR* 3.1 51.5 + - + +
530G ASP* 4.2 24.3 + - - +
563G LEU* 3.6 7.1 - - - +
564G THR* 1.3 81.7 - - - +
566G PHE* 1.3 66.2 + - - +
567G THR* 3.9 21.3 - - - +
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Residues in contact with PHE 566 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453G GLU* 3.9 0.7 - - - -
454G ILE* 2.9 69.0 + - + +
455G LEU* 3.6 20.6 + - + +
467G VAL* 4.2 9.2 - - + -
489G ALA* 4.0 22.2 - - + -
490G ARG 3.3 3.1 - - - -
491G LEU* 3.5 20.4 - - + -
505G LEU* 4.2 15.9 - - + -
547G TRP* 5.9 4.9 - - + -
549G LEU* 3.7 37.9 - - + -
563G LEU* 4.6 3.4 - - + -
565G LYS* 1.3 77.6 - - - +
567G THR* 1.3 73.4 + - - +
568G LEU* 4.3 10.3 - - + -
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Residues in contact with THR 567 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F ALA* 4.6 10.3 - - + +
269F LEU* 4.2 10.6 - - + +
451G ILE* 3.8 27.1 - - + -
452G VAL 3.6 12.3 - - - +
453G GLU* 4.6 5.4 - - - +
454G ILE 4.5 0.2 - - - +
488G GLN 3.7 1.2 - - - +
489G ALA 3.8 0.3 - - - -
490G ARG* 2.8 51.5 + - - +
565G LYS* 3.9 20.4 - - - +
566G PHE* 1.3 76.6 + - - +
568G LEU* 1.3 62.4 + - - +
569G VAL* 4.1 12.6 - - + -
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Residues in contact with LEU 568 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451G ILE* 3.8 0.3 - - - -
452G VAL* 2.8 49.0 + - + +
454G ILE* 4.0 13.9 - - + +
471G VAL* 4.2 13.7 - - + -
487G VAL* 4.0 18.8 - - + -
488G GLN 3.5 12.1 - - - +
505G LEU* 4.1 15.3 - - + -
547G TRP* 3.9 34.8 - - + +
566G PHE* 4.1 14.7 + - + -
567G THR* 1.3 70.9 - - - +
569G VAL* 1.3 61.2 + - - +
570G LEU* 3.7 23.6 - - + -
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Residues in contact with VAL 569 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F LEU* 4.4 9.2 - - + -
449G LYS* 4.0 26.9 - - + -
450G CYS 3.4 5.2 - - - +
451G ILE* 4.5 8.7 - - + -
486G HIS 4.2 0.5 - - - +
487G VAL* 3.6 3.6 - - - -
488G GLN* 2.9 53.4 + - + +
490G ARG* 4.1 23.8 - - + +
567G THR* 4.1 10.3 - - + -
568G LEU* 1.3 75.8 - - - +
570G LEU* 1.3 65.3 + - - +
571G TYR* 3.7 25.9 + - + -
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Residues in contact with LEU 570 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449G LYS* 3.4 3.6 - - - +
450G CYS* 2.7 48.1 + - + +
452G VAL* 4.7 3.4 - - + -
471G VAL* 4.3 16.2 - - + -
473G ALA* 4.1 19.1 - - + -
481G ILE* 3.2 10.9 - - + +
484G LEU* 3.9 20.2 - - + -
486G HIS 4.1 1.6 - - - -
487G VAL* 4.1 8.5 - - + -
543G PRO* 3.7 23.1 - - + -
547G TRP* 4.0 13.2 - - + +
568G LEU* 3.7 30.5 - - + -
569G VAL* 1.3 78.3 - - - +
571G TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 571 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F GLU* 3.9 10.4 + - - -
276F ARG* 4.4 3.1 - - - -
312G ILE* 3.8 22.4 - - + +
313G TYR* 5.0 3.5 + - - -
447G GLN* 3.4 38.8 - - + +
448G ARG 3.4 7.4 - - - -
449G LYS* 3.3 44.2 + - + -
481G ILE* 3.6 2.9 - - - -
484G LEU* 3.6 7.3 - - - +
485G GLU* 2.8 25.1 + - + -
486G HIS* 3.0 41.9 + - + +
488G GLN* 4.2 20.2 + - + -
569G VAL* 3.7 18.4 - - + +
570G LEU* 1.3 76.1 - - - +
572G GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 572 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447G GLN* 3.6 3.7 - - - +
448G ARG* 2.7 38.6 + - - +
481G ILE* 3.5 11.1 - - - +
483G ARG 3.2 11.9 - - - -
485G GLU* 3.8 15.8 - - - +
571G TYR* 1.3 76.7 - - - +
573G THR* 1.3 65.5 + - - +
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Residues in contact with THR 573 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391G ARG* 3.6 13.5 - - - +
395G HIS* 5.8 1.7 - - + +
444G VAL* 5.1 2.2 - - + -
445G ALA* 3.4 42.0 - - + +
446G PRO 3.5 7.0 - - - +
448G ARG* 4.2 5.8 - - - -
481G ILE* 3.7 3.8 - - - +
482G THR* 3.0 23.4 + - - -
483G ARG* 2.9 33.8 + - - +
485G GLU* 4.0 5.8 + - - +
572G GLY* 1.3 79.7 - - - +
574G ALA* 1.3 62.4 + - - +
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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