Contacts of the helix formed by residues 572 - 586 (chain E) in PDB entry 6BAA
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 SER 572 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570E ASP* 3.0 12.4 + - - -
571E LEU* 1.3 77.3 - - - +
573E PRO* 1.3 74.1 - - - +
574E SER* 3.2 19.5 + - - -
575E VAL* 3.5 9.1 + - - +
576E ALA* 3.2 20.1 + - - +
1038E THR* 4.0 2.2 - - - -
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Residues in contact with PRO 573 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324E VAL* 3.6 15.9 - - + +
572E SER* 1.3 88.7 - - - +
574E SER* 1.3 55.1 + - - +
576E ALA* 3.7 3.8 - - + +
577E PHE* 2.9 56.2 + - + +
1038E THR* 3.6 32.5 - - - +
1039E ASP* 4.6 1.6 - - - +
1278E ALA* 3.8 23.3 - - + -
1279E GLY* 3.9 11.2 - - - +
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Residues in contact with SER 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E ILE* 5.0 0.7 - - - -
321E PHE* 3.2 51.6 - - - +
324E VAL* 3.4 23.9 - - - +
325E ASP* 3.8 11.5 + - - +
572E SER* 3.7 12.7 - - - -
573E PRO* 1.3 76.8 - - - +
575E VAL* 1.3 67.3 + - - +
578E ALA* 3.3 16.7 - - - +
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Residues in contact with VAL 575 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E PHE* 4.7 10.8 - - + -
455E ILE* 3.9 22.5 - - + +
456E LEU* 3.7 28.0 - - + -
570E ASP 4.3 17.3 - - - +
571E LEU* 5.7 2.7 - - - -
572E SER* 3.5 12.0 + - - +
574E SER* 1.3 85.0 + - - +
576E ALA* 1.3 66.9 + - + +
579E SER* 3.1 23.0 + - - -
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Residues in contact with ALA 576 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456E LEU* 6.0 0.2 - - - -
571E LEU* 5.5 6.1 - - + -
572E SER 3.2 15.6 + - - +
573E PRO* 4.1 5.4 - - + +
575E VAL* 1.3 82.6 - - + +
577E PHE* 1.3 69.4 + - + +
579E SER* 2.4 23.2 + - - -
580E LEU* 2.9 14.0 + - - +
1034E LEU* 6.6 0.2 - - + -
1038E THR* 5.3 6.1 - - - -
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Residues in contact with PHE 577 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E ILE* 4.4 8.7 - - + +
324E VAL* 5.5 0.2 - - + -
573E PRO* 2.9 29.4 + - + +
576E ALA* 1.3 84.0 - - + +
578E ALA* 1.3 61.3 + - - +
580E LEU* 3.4 17.3 - - + +
581E SER* 2.9 33.1 + - - -
1034E LEU* 4.5 16.2 - - + -
1035E ALA* 4.2 16.8 - - - -
1038E THR* 5.5 1.1 - - - -
1279E GLY* 3.0 33.9 - - - -
1282E GLY* 3.4 26.0 - - - +
1283E LEU* 3.3 33.4 - - + -
1286E THR* 4.0 8.4 + - - +
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Residues in contact with ALA 578 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E PRO* 3.5 34.6 - - + +
320E ILE* 4.2 6.4 - - - +
321E PHE* 4.1 8.3 - - + +
455E ILE* 4.0 17.0 - - + -
574E SER 3.3 21.0 + - - +
575E VAL 3.6 2.4 + - - +
576E ALA 3.4 0.4 - - - -
577E PHE* 1.3 78.1 - - - +
579E SER* 1.3 56.4 + - - +
581E SER 3.3 0.5 + - - -
582E LEU* 3.0 33.5 + - - +
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Residues in contact with SER 579 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E LEU* 4.3 4.3 - - - -
455E ILE* 4.5 4.4 - - - +
456E LEU* 3.9 32.4 - - - +
575E VAL 3.1 12.4 + - - -
576E ALA* 2.4 32.6 + - - -
578E ALA* 1.3 78.7 - - - +
580E LEU* 1.3 53.5 + - - +
582E LEU* 3.4 12.9 + - - +
583E PHE* 3.0 41.5 + - - -
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Residues in contact with LEU 580 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551E PRO 5.9 1.3 - - - +
555E VAL* 4.8 17.0 - - + -
576E ALA 2.9 14.5 + - - +
577E PHE* 3.2 29.1 + - + +
579E SER* 1.3 76.7 + - - +
581E SER* 1.3 58.3 + - - +
583E PHE* 3.0 14.0 + - + +
584E HIS* 2.9 51.6 + - + +
1031E ASP* 5.6 5.6 - - + -
1283E LEU* 4.7 8.1 - - + -
1286E THR* 3.7 21.8 - - + +
1287E TYR* 5.8 3.1 - - + -
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Residues in contact with SER 581 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E PRO* 4.3 5.6 - - - -
320E ILE* 3.8 10.3 - - - +
577E PHE 2.9 11.0 + - - -
578E ALA 3.3 3.1 + - - -
580E LEU* 1.3 72.8 - - - +
582E LEU* 1.3 60.7 + - - +
584E HIS* 3.2 11.3 + - - +
585E ILE* 2.9 33.9 + - - +
1286E THR* 3.0 37.3 + - - +
1289E LEU* 3.8 20.6 - - - +
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Residues in contact with LEU 582 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E PHE* 4.6 19.3 - - + -
317E PRO* 3.7 22.8 - - + +
448E GLY* 4.4 13.5 - - - +
451E LEU* 4.4 11.7 - - + -
452E LEU* 3.8 41.3 - - + +
455E ILE* 4.1 20.2 - - + -
578E ALA 3.0 17.8 + - - +
579E SER* 3.4 8.7 - - - +
581E SER* 1.3 77.0 - - - +
583E PHE* 1.3 57.4 + - + +
585E ILE* 3.0 8.0 + - + +
586E LEU* 3.0 38.9 + - + +
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Residues in contact with PHE 583 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E LEU* 3.6 42.2 - - + -
456E LEU* 4.7 4.3 - - + -
459E SER 5.8 0.4 - - - -
463E GLY* 4.7 16.2 - - - -
551E PRO* 5.3 10.5 - - + +
554E ALA* 4.7 9.9 - - + -
555E VAL* 4.4 31.9 - - + -
558E THR* 4.5 17.5 - - - -
579E SER* 3.0 29.5 + - - -
580E LEU* 3.0 14.8 + - + +
582E LEU* 1.3 79.2 - - + +
584E HIS* 1.3 61.5 + - + +
586E LEU* 3.6 15.8 + - + +
587E VAL* 3.4 22.5 + - - +
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Residues in contact with HIS 584 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551E PRO* 5.8 9.2 - - + +
580E LEU* 2.9 53.1 + - + +
581E SER* 3.6 8.5 - - - +
582E LEU 3.2 0.4 - - - -
583E PHE* 1.3 76.5 - - - +
585E ILE* 1.3 66.0 + - + +
587E VAL* 4.2 10.2 + - - +
588E THR* 4.9 3.8 + - - -
1286E THR* 3.8 18.5 - - + +
1287E TYR* 5.0 9.8 - + - -
1290E MET* 3.4 50.7 - - + +
1294E TYR* 5.1 4.5 - - - -
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Residues in contact with ILE 585 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLY* 3.7 28.9 - - - +
314E PHE* 4.2 19.5 - - + -
317E PRO* 4.2 16.8 - - + -
444E GLN* 5.7 4.5 - - + +
581E SER 2.9 19.8 + - - +
582E LEU* 3.4 10.5 - - + +
584E HIS* 1.3 79.4 - - + +
586E LEU* 1.3 76.0 + - + +
587E VAL 3.0 7.2 + - - -
588E THR* 3.7 9.0 + - - -
589E PRO* 3.4 12.6 - - + +
1289E LEU* 6.0 3.8 - - + -
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Residues in contact with LEU 586 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E PHE* 4.5 4.7 - - + -
444E GLN* 3.9 24.9 - - + +
445E ILE* 4.6 8.3 - - + +
448E GLY* 4.1 26.2 - - - +
449E VAL* 5.9 2.0 - - + -
452E LEU* 6.0 3.6 - - + -
467E ILE* 5.4 1.2 - - + +
582E LEU* 3.0 24.8 + - + +
583E PHE* 3.6 14.0 + - + +
584E HIS 3.4 1.2 - - - -
585E ILE* 1.3 92.5 - - + +
587E VAL* 1.3 61.4 + - - +
589E PRO* 3.5 18.8 - - + -
590E LEU* 3.2 25.4 - - + +
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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