Contacts of the helix formed by residues 559 - 571 (chain f) in PDB entry 5T0J
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 ASP 559 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557f ASP* 3.3 9.0 + - - +
558f ALA* 1.3 76.4 - - - +
560f PRO* 1.3 70.2 - - - +
561f GLU* 2.9 26.4 + - - +
562f VAL* 2.9 45.6 + - + +
563f SER* 3.2 24.3 + - - -
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Residues in contact with PRO 560 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558f ALA 3.4 6.0 - - - +
559f ASP* 1.3 88.6 - - - +
561f GLU* 1.3 82.1 + - - +
563f SER* 3.8 1.8 - - - -
564f TYR* 2.9 29.8 + - - +
596f ASP* 5.4 7.2 - - + +
598f ASN* 3.2 36.1 + - + +
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Residues in contact with GLU 561 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529f ARG* 3.6 36.3 - - + +
559f ASP* 2.9 23.7 - - - +
560f PRO* 1.3 91.1 - - - +
562f VAL* 1.3 59.4 + - + +
564f TYR* 3.0 7.2 + - - +
565f ASN* 2.9 35.2 + - - +
681f LEU 5.1 10.8 - - - +
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Residues in contact with VAL 562 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528f ARG* 5.0 5.2 - - + +
529f ARG* 4.1 28.5 - - + +
532f PRO* 5.8 1.6 - - - +
554f PHE* 3.7 14.1 - - + +
557f ASP* 3.3 34.5 - - + +
559f ASP* 2.9 29.4 + - + +
561f GLU* 1.3 75.6 - - - +
563f SER* 1.3 63.0 + - - +
565f ASN* 4.0 7.1 - - - +
566f SER* 3.2 22.5 + - - -
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Residues in contact with SER 563 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554f PHE 4.0 4.7 - - - -
555f SER 3.8 15.0 + - - -
557f ASP 3.8 14.6 + - - -
559f ASP 3.2 20.1 + - - -
560f PRO* 3.9 5.8 - - - -
561f GLU 3.2 0.8 - - - -
562f VAL* 1.3 77.3 - - - +
564f TYR* 1.3 61.2 + - - +
566f SER* 2.7 21.7 + - - -
567f ILE* 3.8 10.4 - - - +
598f ASN* 5.0 14.8 + - - +
602f MET* 4.8 9.2 - - - +
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Residues in contact with TYR 564 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560f PRO 2.9 17.7 + - - +
561f GLU* 3.0 8.0 + - - +
563f SER* 1.3 78.7 - - - +
565f ASN* 1.3 69.8 + - - +
566f SER 3.5 0.7 + - - -
567f ILE* 3.8 2.8 - - - +
568f PHE* 3.3 20.2 + + + +
597f PRO* 5.2 3.8 - - + -
598f ASN* 4.0 24.2 - - + -
601f PHE* 3.2 60.7 - + + -
677f GLU* 6.0 0.2 - - - -
680f PRO* 3.2 47.4 + - + +
681f LEU* 4.6 7.9 - - + +
683f VAL* 5.2 13.2 - - + +
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Residues in contact with ASN 565 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529f ARG* 2.8 44.2 - - - +
532f PRO* 3.7 13.7 - - + +
533f LEU* 4.2 10.8 - - + +
561f GLU* 2.9 18.2 + - - +
562f VAL* 4.0 4.9 - - - +
564f TYR* 1.3 79.7 - - - +
566f SER* 1.3 59.0 + - - +
568f PHE* 4.0 9.3 - - - +
569f ALA* 3.1 26.7 + - - +
681f LEU* 3.2 39.3 - - - +
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Residues in contact with SER 566 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532f PRO* 5.2 1.1 - - - -
551f LEU* 3.3 35.3 - - - +
554f PHE* 3.8 25.6 - - - -
555f SER* 3.7 16.9 - - - -
562f VAL 3.2 14.8 + - - -
563f SER* 2.7 26.3 + - - -
565f ASN* 1.3 74.8 - - - +
567f ILE* 1.3 70.0 + - - +
568f PHE 3.1 0.7 - - - -
569f ALA 3.1 10.4 + - - -
570f MET 3.4 0.2 + - - -
602f MET* 4.5 1.2 - - - -
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Residues in contact with ILE 567 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555f SER* 5.7 0.2 - - - -
563f SER 3.8 14.6 - - - +
564f TYR 3.8 1.3 - - - +
566f SER* 1.3 80.7 + - - +
568f PHE* 1.3 61.0 + - - +
570f MET* 3.4 12.4 + - + -
571f GLY* 2.8 24.8 + - - -
585f MET* 5.2 3.1 - - + -
601f PHE* 3.6 29.6 - - + +
602f MET* 3.5 46.2 - - + +
605f LEU* 3.6 18.2 - - + +
606f ALA* 3.8 26.7 - - + -
609f LEU* 4.5 9.9 - - + -
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Residues in contact with PHE 568 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533f LEU* 3.5 43.3 - - + -
536f ALA* 5.2 15.3 - - + +
564f TYR* 3.3 20.8 + + + +
565f ASN* 4.1 7.4 - - - +
566f SER 3.1 0.4 - - - -
567f ILE* 1.3 80.6 - - - +
569f ALA* 1.3 68.9 + - - +
571f GLY* 3.3 16.7 + - - +
572f MET 4.8 0.2 + - - -
601f PHE* 4.3 15.3 - + + -
605f LEU* 5.0 4.3 - - + -
677f GLU* 3.1 59.5 - - + -
678f LEU* 5.1 6.7 - - + -
681f LEU* 4.6 7.9 - - + -
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Residues in contact with ALA 569 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532f PRO* 3.5 28.9 - - + +
533f LEU 6.1 0.2 - - - -
535f LEU* 3.6 32.0 - - + +
536f ALA* 4.5 3.8 + - - +
547f ILE* 4.5 0.7 - - - +
551f LEU* 3.7 4.5 - - + -
565f ASN 3.1 20.2 + - - +
566f SER 3.1 7.7 + - - +
568f PHE* 1.3 82.2 - - - +
570f MET* 1.3 64.0 + - - +
573f VAL* 3.6 14.0 - - - +
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Residues in contact with MET 570 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547f ILE* 3.6 33.2 - - + -
548f LEU* 4.0 22.9 - - + -
551f LEU* 3.6 14.8 - - + +
566f SER 3.4 4.5 + - - +
567f ILE* 3.5 17.3 - - + +
569f ALA* 1.3 82.6 - - - +
571f GLY* 1.3 60.6 + - - +
573f VAL* 3.2 6.0 - - - +
574f GLY* 2.7 36.3 + - - +
582f LEU* 4.1 18.6 - - + -
585f MET* 4.7 17.3 - - + -
609f LEU* 3.5 29.2 - - + -
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Residues in contact with GLY 571 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567f ILE 2.8 17.6 + - - -
568f PHE* 3.3 17.0 - - - -
570f MET* 1.3 74.8 - - - +
572f MET* 1.3 60.6 + - - -
575f SER* 3.3 21.2 + - - -
605f LEU* 4.0 17.3 - - - +
609f LEU* 3.5 10.0 - - - +
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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