Contacts of the strand formed by residues 545 - 554 (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 GLY 545 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470G ALA* 4.3 3.4 - - - -
471G VAL* 2.6 45.7 + - - +
508G PRO* 3.6 9.6 - - - -
543G PRO 3.3 0.4 + - - -
544G ALA* 1.3 75.8 - - - +
546G GLU* 1.3 57.8 + - - -
547G TRP* 3.7 1.0 + - - -
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Residues in contact with GLU 546 (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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468G ARG* 2.9 53.0 + - - +
469G LYS 3.4 11.7 + - - +
470G ALA* 4.1 8.1 + - + +
506G ILE 4.2 0.3 - - - +
507G SER 4.1 1.9 - - - +
508G PRO* 3.4 24.5 - - - +
545G GLY* 1.3 71.8 - - - -
547G TRP* 1.3 69.9 + - - +
548G VAL* 4.0 7.2 + - + +
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Residues in contact with TRP 547 (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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454G ILE* 5.9 1.3 - - + -
467G VAL 3.7 0.9 - - - +
468G ARG* 3.4 0.9 - - - -
469G LYS* 2.9 36.7 + - + +
471G VAL* 3.6 28.0 - - + +
484G LEU* 3.9 27.6 - - + -
487G VAL* 4.1 18.2 - - + -
505G LEU* 3.7 39.5 - - + -
506G ILE 3.5 16.8 - - - -
507G SER* 3.7 20.6 - - - -
508G PRO* 3.3 23.6 - - + +
535G THR* 5.7 1.8 - - + -
538G SER* 4.6 3.6 - - - -
543G PRO* 3.0 23.6 + - + +
545G GLY 3.9 0.2 - - - -
546G GLU* 1.3 73.3 - - - +
548G VAL* 1.3 65.1 + - - +
566G PHE* 5.9 4.9 - - + -
568G LEU* 3.9 22.3 - - + +
570G LEU* 4.0 10.5 - - + +
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Residues in contact with VAL 548 (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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466G GLU* 3.7 32.3 - - + +
467G VAL 3.3 4.3 - - - +
468G ARG* 3.7 35.7 - - + +
504G HIS 3.7 0.5 - - - +
505G LEU* 3.4 7.8 - - - +
506G ILE* 2.8 56.8 + - + +
546G GLU* 4.0 10.1 - - + +
547G TRP* 1.3 82.1 - - - +
549G LEU* 1.3 63.9 + - - +
550G GLU* 4.1 11.8 + - + +
566G PHE* 5.6 0.2 - - - -
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Residues in contact with LEU 549 (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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465G LEU* 3.8 0.9 - - - +
466G GLU* 3.3 6.2 - - - +
467G VAL* 2.8 42.3 + - + +
491G LEU* 3.8 21.3 - - + -
503G ILE* 3.9 17.9 - - + -
504G HIS 3.5 12.8 - - - +
505G LEU* 4.4 4.7 - - + -
515G LEU* 4.2 14.4 - - + -
548G VAL* 1.3 73.5 - - - +
550G GLU* 1.3 61.5 + - - +
551G ILE* 4.2 13.2 - - + +
563G LEU* 3.9 21.3 - - + -
566G PHE* 3.7 45.3 - - + -
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Residues in contact with GLU 550 (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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464G ARG* 4.5 21.0 + - + +
465G LEU 3.6 4.5 - - - +
466G GLU* 4.3 14.7 - - + +
502G ALA 3.6 0.7 - - - +
503G ILE* 3.1 8.3 - - - +
504G HIS* 2.7 47.1 + - + +
506G ILE* 3.5 25.4 - - + +
512G ARG* 2.9 34.1 + - - -
548G VAL* 4.1 12.5 - - + +
549G LEU* 1.3 78.3 - - - +
551G ILE* 1.3 63.1 + - - +
552G GLU* 4.5 11.1 - - - +
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Residues in contact with ILE 551 (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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461G ILE* 3.9 24.6 - - + +
464G ARG* 3.4 2.5 - - - +
465G LEU* 2.8 53.3 + - + +
491G LEU* 4.8 3.8 - - + -
493G LEU* 4.3 11.9 - - + -
501G LEU* 3.9 18.6 - - + -
502G ALA 3.5 2.9 - - - +
503G ILE* 4.2 20.2 - - + -
549G LEU* 4.2 12.6 - - + -
550G GLU* 1.3 79.0 - - - +
552G GLU* 1.3 64.1 + - - +
563G LEU* 3.8 39.9 - - + -
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Residues in contact with GLU 552 (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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461G ILE* 5.5 1.1 - - - -
463G LYS* 3.6 9.9 - - - +
464G ARG* 4.3 24.8 + - + -
501G LEU* 3.5 9.1 - - - -
502G ALA* 3.0 50.2 + - + +
504G HIS* 4.7 11.2 + - - -
512G ARG* 4.7 5.3 + - - -
550G GLU* 4.5 17.0 - - - +
551G ILE* 1.3 77.1 - - - +
553G ASN* 1.3 64.0 + - - +
554G THR* 3.4 10.2 + - + +
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Residues in contact with ASN 553 (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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461G ILE* 5.5 0.2 - - - +
462G GLY 4.0 6.7 + - - +
463G LYS* 2.6 58.8 + - + +
495G TYR* 3.2 25.5 + - - +
500G ASP* 3.6 8.3 - - - +
501G LEU* 4.9 1.1 - - - -
552G GLU* 1.3 72.4 - - - +
554G THR* 1.3 55.3 + - - +
555G SER* 3.0 27.3 + - - -
557G ALA 3.0 26.9 + - - -
559G ASN* 3.0 23.5 + - - +
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Residues in contact with THR 554 (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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463G LYS* 4.4 1.6 - - - +
500G ASP* 2.7 29.9 + - - +
502G ALA* 3.4 32.8 - - + +
518G ALA* 3.6 20.1 - - + +
552G GLU* 4.1 11.4 - - + +
553G ASN* 1.3 72.9 - - - +
555G SER* 1.3 58.7 + - - +
556G GLU* 5.6 0.7 - - - +
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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