Contacts of the helix formed by residues 534 - 546 (chain G) in PDB entry 4P0S
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 PRO 534 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517G GLU 4.1 2.4 - - - +
518G THR* 4.6 15.3 - - + -
521G SER* 3.3 25.1 - - - +
531G ASN* 6.1 0.2 - - + -
533G GLY* 1.3 76.6 - - - -
535G ALA* 1.3 59.2 + - + +
537G SER* 3.6 9.4 - - - -
538G ARG* 3.1 26.9 + - - +
9M G 2.7 32.8 - - - +
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Residues in contact with ALA 535 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533G GLY* 3.0 1.8 - - - -
534G PRO* 1.3 82.7 - - + +
536G LEU* 1.3 63.8 + - + +
538G ARG* 3.2 13.2 + - - +
539G THR* 3.1 29.4 + - - -
8M T 3.9 46.7 - - - +
9M G 5.1 0.2 - - - +
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Residues in contact with LEU 536 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482G VAL* 5.4 2.0 - - + -
483G ARG 3.7 9.4 - - - +
484G GLY* 3.1 46.4 - - - +
485G VAL* 4.4 11.7 - - + +
489G LYS* 4.2 5.6 - - + -
532G LEU* 3.5 48.0 - - + +
533G GLY* 4.0 1.6 - - - -
535G ALA* 1.3 81.2 - - + +
537G SER* 1.3 60.8 + - - +
538G ARG 3.1 0.4 - - - -
539G THR* 3.3 9.1 + - - +
540G LEU* 2.9 37.1 + - + +
30N C 5.9 0.7 - - - -
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Residues in contact with SER 537 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507G TYR* 3.8 4.7 + - - -
516G GLN 4.3 1.0 + - - -
517G GLU 2.5 27.9 + - - +
519G LEU 3.8 0.2 + - - -
520G LEU* 3.3 34.4 + - - +
521G SER* 3.5 17.7 + - - -
532G LEU* 4.7 1.9 - - - +
533G GLY 3.9 2.2 - - - -
534G PRO* 3.6 17.6 - - - -
535G ALA 3.2 0.4 - - - -
536G LEU* 1.3 78.6 - - - +
538G ARG* 1.3 56.0 + - - +
540G LEU* 3.9 4.0 - - - +
541G SER* 3.2 25.3 + - - -
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Residues in contact with ARG 538 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517G GLU* 3.6 35.4 + - + +
534G PRO 3.1 21.0 + - - +
535G ALA* 3.3 12.2 + - - +
537G SER* 1.3 75.3 - - - +
539G THR* 1.3 82.2 + - - +
540G LEU 3.2 1.1 - - - -
541G SER* 2.9 19.9 + - - -
542G GLN* 3.3 31.0 + - + +
473H LEU* 1.9 58.0 + - - +
8M T 5.8 1.2 + - - -
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Residues in contact with THR 539 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482G VAL* 4.3 10.3 - - + -
535G ALA 3.1 15.2 + - - -
536G LEU* 3.3 10.4 + - - +
538G ARG* 1.3 87.3 + - - +
540G LEU* 1.3 61.3 + - + +
542G GLN* 3.2 23.4 + - - +
543G LEU* 3.3 11.3 + - - +
471H VAL* 3.6 44.5 + - + +
472H ASP 4.6 3.5 + - - -
478H LEU* 3.7 16.1 - - + +
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Residues in contact with LEU 540 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479G LEU* 4.6 13.2 - - + -
482G VAL* 4.6 12.3 - - + -
485G VAL* 4.5 19.3 - - + -
493G LEU* 3.9 24.9 - - + -
503G LEU* 5.6 2.7 - - + -
507G TYR* 3.7 10.0 + - - +
520G LEU* 3.6 24.9 - - + -
532G LEU* 4.5 7.6 - - + -
536G LEU 2.9 24.4 + - - +
537G SER* 3.9 2.2 - - - +
539G THR* 1.3 75.7 - - + +
541G SER* 1.3 65.0 + - - +
543G LEU* 3.3 7.5 + - + +
544G TYR* 3.2 47.0 + - + +
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Residues in contact with SER 541 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507G TYR* 3.5 13.2 + - - -
516G GLN* 3.6 31.9 - - - -
517G GLU* 3.8 16.4 - - - +
537G SER 3.2 9.8 + - - -
538G ARG 2.9 18.9 + - - -
540G LEU* 1.3 76.5 - - - +
542G GLN* 1.3 54.5 + - - +
545G CYS* 2.7 48.7 + - - +
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Residues in contact with GLN 542 (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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517G GLU* 6.5 0.2 - - + -
538G ARG* 3.4 45.0 - - + +
539G THR* 3.2 14.1 + - - +
540G LEU 3.1 0.8 - - - -
541G SER* 1.3 82.0 + - - +
543G LEU* 1.3 63.1 + - - +
546G SER* 3.2 30.4 + - - +
550G LEU* 4.2 4.5 - - - +
473H LEU 3.9 2.8 + - - +
474H ALA* 3.3 26.8 - - - +
475H GLY* 4.8 2.2 - - - +
478H LEU* 3.9 16.1 - - + +
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Residues in contact with LEU 543 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539G THR 3.3 9.1 + - - +
540G LEU* 3.3 12.5 + - + +
541G SER 3.3 0.4 - - - -
542G GLN* 1.3 81.1 - - - +
544G TYR* 1.3 76.4 + - + +
545G CYS 3.9 0.2 + - - -
546G SER* 5.0 0.9 + - - +
550G LEU* 3.5 28.1 - - + +
478H LEU* 3.5 39.5 - - + +
481H VAL* 4.9 5.6 - - + -
482H TRP* 4.5 4.0 - - + -
485H GLN* 3.8 29.4 - - - +
506H SER* 5.2 0.2 - - - -
507H PRO* 3.2 46.4 - - + +
508H GLN* 5.0 1.2 + - - +
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Residues in contact with TYR 544 (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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475G PHE* 3.7 13.9 - + - -
478G GLN* 4.6 5.8 + - - +
479G LEU* 3.3 29.1 - - + +
500G PRO* 5.8 5.2 - - + -
503G LEU* 3.6 29.8 - - + -
504G LEU* 3.9 19.3 - - + +
507G TYR* 4.2 15.6 - - + +
540G LEU* 3.2 35.0 + - + +
543G LEU* 1.3 100.8 - - + +
545G CYS* 1.3 52.0 + - - +
482H TRP* 5.9 0.4 - + - -
485H GLN* 3.9 15.6 + - - -
507H PRO* 4.4 19.0 - - + +
508H GLN* 2.3 37.3 + - - -
557H MET* 5.5 10.8 - - + -
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Residues in contact with CYS 545 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507G TYR* 3.8 29.4 - - - -
516G GLN* 3.4 36.8 - - - +
541G SER* 2.7 32.8 + - - +
542G GLN* 5.2 0.2 - - - -
543G LEU 3.6 0.6 - - - -
544G TYR* 1.3 80.3 - - - +
546G SER* 1.3 66.0 + - - +
547G TYR* 3.0 24.4 - - - -
508H GLN* 3.7 6.1 - - - +
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Residues in contact with SER 546 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G SER 4.3 0.2 + - - -
542G GLN* 3.2 23.9 + - - +
543G LEU 5.4 0.5 - - - +
545G CYS* 1.3 75.6 - - - +
547G TYR* 1.3 62.8 + - - +
548G GLY 3.5 9.6 + - - +
549G PRO 4.6 1.9 + - - -
550G LEU* 3.3 17.2 - - - +
506H SER* 4.0 6.2 + - - -
508H GLN* 3.7 12.0 - - - +
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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