Contacts of the helix formed by residues 500 - 515 (chain T) in PDB entry 2P8Z
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 500 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495T VAL* 3.8 10.3 - - + +
497T ASN* 2.6 44.9 + - - +
499T ASN* 1.3 70.1 - - - +
501T LEU* 1.3 64.4 + - - +
502T PRO* 3.1 5.2 - - - -
503T LYS* 2.8 43.6 + - - +
504T LEU 3.3 6.6 + - - -
552T VAL* 3.0 38.9 - - + +
553T PRO* 4.8 1.7 - - - +
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Residues in contact with LEU 501 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494T GLU* 5.3 6.1 - - + -
495T VAL* 3.6 31.9 - - + +
498T ALA* 3.1 25.3 + - + +
500T ASP* 1.3 75.9 - - - +
502T PRO* 1.3 68.4 - - + +
504T LEU* 3.2 9.6 + - + +
505T VAL* 3.0 31.9 + - + +
528T HIS* 5.0 12.6 - - + +
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Residues in contact with PRO 502 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498T ALA 4.7 0.2 - - - +
499T ASN 3.2 15.3 - - - +
500T ASP* 2.8 6.0 - - - -
501T LEU* 1.3 95.9 - - + +
503T LYS* 1.3 64.2 + - + +
505T VAL* 3.5 7.0 + - + +
506T GLU* 3.1 23.6 + - - +
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Residues in contact with LYS 503 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499T ASN 5.7 0.9 - - - -
500T ASP* 2.8 31.3 + - - +
502T PRO* 1.3 73.7 - - + +
504T LEU* 1.3 55.6 + - - +
506T GLU* 3.3 6.7 + - - +
507T GLY* 2.7 32.9 + - - -
549T HIS 4.5 0.3 - - - +
550T ALA* 3.6 21.5 - - - +
552T VAL* 3.4 25.8 - - + +
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Residues in contact with LEU 504 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493T VAL* 4.0 16.6 - - + +
494T GLU* 3.9 14.1 - - - +
495T VAL* 3.6 42.8 - - + +
500T ASP 3.3 2.0 + - - -
501T LEU* 3.2 12.9 + - + +
503T LYS* 1.3 76.4 - - - +
505T VAL* 1.3 66.7 + - - +
507T GLY* 3.0 1.4 + - - -
508T LEU* 2.9 49.5 + - + +
528T HIS* 4.3 14.8 - - + +
545T LEU* 4.2 8.3 - - + -
550T ALA* 4.0 7.4 - - + +
552T VAL* 5.7 1.0 - - + +
554T LEU* 4.1 16.8 - - + -
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Residues in contact with VAL 505 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501T LEU* 3.0 22.0 + - + +
502T PRO* 3.8 6.3 - - + +
504T LEU* 1.3 74.8 - - + +
506T GLU* 1.3 61.2 + - - +
508T LEU* 3.9 12.3 + - + +
509T LYS* 3.4 37.9 + - - +
528T HIS* 4.0 27.1 - - + +
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Residues in contact with GLU 506 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502T PRO 3.1 18.1 + - - +
503T LYS* 3.6 6.7 - - - +
504T LEU 3.0 0.4 - - - -
505T VAL* 1.3 77.5 - - - +
507T GLY* 1.3 66.3 + - - +
509T LYS* 3.2 22.2 + - - +
510T ARG* 3.1 52.1 + - - +
513T LYS* 5.2 5.2 + - - -
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Residues in contact with GLY 507 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503T LYS 2.7 18.6 + - - -
504T LEU 3.0 2.2 + - - -
506T GLU* 1.3 75.7 - - - +
508T LEU* 1.3 56.1 + - - +
510T ARG* 3.2 4.5 + - - +
511T LEU* 2.8 30.5 + - - +
545T LEU* 3.5 9.2 - - - -
549T HIS* 3.3 32.7 - - - +
550T ALA* 3.9 1.8 - - - -
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Residues in contact with LEU 508 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493T VAL* 5.5 0.7 - - + -
504T LEU* 2.9 33.6 + - + +
505T VAL* 4.0 10.5 - - + +
507T GLY* 1.3 75.2 - - - +
509T LYS* 1.3 58.2 + - + +
511T LEU* 3.5 4.5 - - + +
512T SER* 2.8 35.6 + - - -
520T THR* 3.8 23.6 + - + +
528T HIS* 3.8 33.4 - - + +
529T ILE 5.7 0.2 - - - +
530T VAL* 3.6 30.3 - - + -
545T LEU* 3.6 21.7 - - + +
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Residues in contact with LYS 509 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505T VAL* 3.4 32.3 - - - +
506T GLU* 3.2 25.7 + - - +
508T LEU* 1.3 78.2 - - + +
510T ARG* 1.3 62.1 - - - +
512T SER* 3.3 6.8 + - - -
513T LYS* 3.1 43.5 + - - +
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Residues in contact with ARG 510 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392T GLY* 5.9 7.3 - - - -
394T PHE* 4.2 9.9 - - + -
506T GLU* 3.1 37.8 + - - +
507T GLY* 3.5 7.0 - - - +
509T LYS* 1.3 80.5 - - - +
511T LEU* 1.3 61.7 + - - +
513T LYS* 3.5 12.4 + - + +
514T SER* 3.2 24.1 + - - -
548T ASP 4.6 3.6 + - - -
549T HIS* 3.2 43.9 + - - +
550T ALA 5.8 0.4 - - - -
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Residues in contact with LEU 511 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507T GLY 2.8 20.0 + - - +
508T LEU* 3.5 4.9 - - + +
510T ARG* 1.3 71.3 - - - +
512T SER* 1.3 65.6 + - - +
514T SER* 3.0 18.1 + - - +
515T ASP* 3.1 11.9 + - + -
518T VAL* 3.5 23.2 - - + +
520T THR* 4.6 9.2 - - + -
530T VAL* 4.4 15.5 - - + -
541T CYS* 4.1 31.6 - - + +
544T ASP* 5.3 1.1 - - + +
545T LEU* 4.0 26.7 - - + -
549T HIS* 3.8 27.1 + - + +
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Residues in contact with SER 512 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464T LEU* 5.8 1.3 - - - -
465T LYS* 6.1 0.2 - - - +
508T LEU 2.8 26.6 + - - -
509T LYS* 3.3 6.4 + - - -
511T LEU* 1.3 73.4 - - - +
513T LYS* 1.3 61.8 + - - +
515T ASP 2.7 23.6 - - - +
516T PRO* 4.9 0.3 - - - +
518T VAL* 3.6 16.0 - - - +
519T LEU* 5.5 0.2 - - - -
520T THR* 3.1 27.0 + - - +
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Residues in contact with LYS 513 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385T MET* 4.5 11.6 - - - +
394T PHE* 4.0 23.3 - - + -
464T LEU* 3.4 52.9 - - + +
465T LYS* 5.2 5.2 + - - +
506T GLU* 5.2 5.5 + - - -
509T LYS* 3.1 34.0 + - - +
510T ARG* 3.8 10.7 - - - +
511T LEU 3.3 0.2 - - - -
512T SER* 1.3 77.2 - - - +
514T SER* 1.3 58.9 + - - +
515T ASP 3.6 1.4 + - - -
516T PRO* 5.6 1.0 - - - +
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Residues in contact with SER 514 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385T MET 4.9 7.1 - - - +
387T PRO* 4.7 12.3 - - - +
394T PHE* 3.1 33.6 - - - -
510T ARG 3.2 8.3 + - - -
511T LEU* 3.0 13.5 + - - +
513T LYS* 1.3 79.8 - - - +
515T ASP* 1.3 59.6 + - - +
516T PRO* 3.9 6.7 - - - +
549T HIS* 3.5 19.5 + - - -
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Residues in contact with ASP 515 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114T GLU* 5.6 0.3 - - - +
465T LYS* 5.2 0.2 - - - -
511T LEU* 3.1 13.1 + - + +
512T SER 2.7 19.8 + - - +
513T LYS 4.9 0.9 - - - -
514T SER* 1.3 81.2 - - - +
516T PRO* 1.3 67.3 - - - +
517T CYS* 3.0 24.3 + - - +
518T VAL* 3.1 32.2 + - + +
537T HIS* 3.0 29.4 + - - -
541T CYS* 3.8 8.1 - - - -
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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