Contacts of the helix formed by residues 572 - 586 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570H ASP* 3.0 12.6 + - - -
571H LEU* 1.3 77.1 - - - +
573H PRO* 1.3 72.8 - - - +
574H SER* 3.2 19.2 + - - -
575H VAL* 3.5 9.3 + - - +
576H ALA* 3.2 20.1 + - - +
1038H THR* 4.0 2.5 - - - -
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Residues in contact with PRO 573 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H VAL* 3.6 15.1 - - + +
572H SER* 1.3 87.6 - - - +
574H SER* 1.3 56.1 + - - +
575H VAL 3.4 0.2 - - - -
576H ALA* 4.3 3.4 - - + +
577H PHE* 2.9 58.3 + - + +
1038H THR* 3.6 33.4 - - - +
1039H ASP* 4.6 1.8 - - - +
1278H ALA* 3.8 23.1 - - + -
1279H GLY* 3.9 11.0 - - - +
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Residues in contact with SER 574 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H ILE* 5.2 0.6 - - - -
321H PHE* 3.2 53.0 - - - +
324H VAL* 3.4 23.9 - - - +
325H ASP* 3.8 11.3 + - - +
572H SER* 3.7 13.4 - - - -
573H PRO* 1.3 76.4 - - - +
575H VAL* 1.3 66.3 + - - +
578H ALA* 3.3 16.2 + - - +
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Residues in contact with VAL 575 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H PHE* 4.7 10.5 - - + -
455H ILE* 3.9 22.1 - - + +
456H LEU* 3.7 27.8 - - + -
570H ASP 4.3 18.2 - - - +
571H LEU* 5.7 2.5 - - - -
572H SER* 3.5 11.6 + - - +
573H PRO 3.4 0.2 - - - -
574H SER* 1.3 84.4 + - - +
576H ALA* 1.3 66.3 + - + +
578H ALA* 3.9 0.2 - - - +
579H SER* 3.1 23.6 + - - -
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Residues in contact with ALA 576 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456H LEU* 6.0 0.2 - - - -
571H LEU* 5.5 6.3 - - + -
572H SER 3.2 15.4 + - - +
573H PRO* 4.1 5.6 - - + +
575H VAL* 1.3 83.1 - - + +
577H PHE* 1.3 69.2 + - + +
579H SER* 2.4 23.0 + - - -
580H LEU* 2.9 14.2 + - - +
1038H THR* 5.3 6.1 - - - -
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Residues in contact with PHE 577 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H ILE* 4.4 9.2 - - + -
324H VAL* 5.5 0.4 - - + -
573H PRO* 2.9 28.2 + - + +
576H ALA* 1.3 83.1 - - + +
578H ALA* 1.3 60.6 + - - +
580H LEU* 3.2 17.1 + - + +
581H SER* 2.9 33.8 + - - -
1034H LEU* 4.5 16.4 - - + -
1035H ALA* 4.2 17.5 - - - -
1038H THR* 5.5 1.6 - - - -
1279H GLY* 3.0 33.2 - - - -
1282H GLY* 3.4 27.1 - - - +
1283H LEU* 3.3 35.0 - - + -
1286H THR* 4.0 8.2 + - - +
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Residues in contact with ALA 578 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H PRO* 3.5 35.0 - - + +
320H ILE* 4.2 6.0 - - + +
321H PHE* 4.1 8.3 - - + +
455H ILE* 4.0 17.5 - - + -
574H SER 3.3 21.4 + - - +
575H VAL 3.6 1.5 + - - +
576H ALA 3.4 0.4 - - - -
577H PHE* 1.3 78.2 - - - +
579H SER* 1.3 56.4 + - - +
581H SER 3.3 0.5 + - - -
582H LEU* 3.0 33.3 + - - +
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Residues in contact with SER 579 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452H LEU* 4.3 4.7 - - - -
455H ILE* 4.5 3.9 - - - +
456H LEU* 3.9 32.2 - - - +
575H VAL 3.1 12.0 + - - -
576H ALA* 2.4 32.9 + - - -
578H ALA* 1.3 77.3 - - - +
580H LEU* 1.3 55.2 + - - +
582H LEU* 3.4 13.4 + - - +
583H PHE* 3.0 40.7 + - - -
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Residues in contact with LEU 580 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551H PRO 5.9 1.1 - - - +
555H VAL* 4.8 18.2 - - + -
576H ALA 2.9 14.7 + - - +
577H PHE* 3.2 29.1 + - + +
579H SER* 1.3 77.0 + - - +
581H SER* 1.3 58.3 + - - +
583H PHE* 3.0 14.4 + - + +
584H HIS* 2.9 51.8 + - + +
1031H ASP* 5.6 6.1 - - + -
1283H LEU* 4.7 7.9 - - + -
1286H THR* 3.7 22.7 - - + +
1287H TYR* 5.8 3.1 - - + -
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Residues in contact with SER 581 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H PRO* 4.3 5.6 - - - -
320H ILE* 3.8 10.9 - - - +
577H PHE 2.9 12.2 + - - -
578H ALA 4.1 2.9 - - - -
580H LEU* 1.3 73.1 - - - +
582H LEU* 1.3 60.7 + - - +
584H HIS* 3.2 11.3 + - - +
585H ILE* 2.9 33.5 + - - +
1286H THR* 3.0 38.2 + - - +
1289H LEU* 3.8 21.2 - - - +
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Residues in contact with LEU 582 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314H PHE* 4.6 19.7 - - + -
317H PRO* 3.7 22.8 - - + +
448H GLY* 4.4 13.2 - - - +
451H LEU* 4.4 12.6 - - + -
452H LEU* 3.8 40.8 - - + +
455H ILE* 4.1 20.4 - - + -
578H ALA 3.0 18.3 + - - +
579H SER* 3.4 7.9 - - - +
581H SER* 1.3 76.8 - - - +
583H PHE* 1.3 59.0 + - + +
585H ILE* 3.0 7.5 + - + +
586H LEU* 3.0 38.8 + - + +
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Residues in contact with PHE 583 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H LEU* 3.6 42.8 - - + -
456H LEU* 4.7 3.8 - - + -
459H SER 5.8 0.4 - - - -
463H GLY* 4.7 16.2 - - - -
551H PRO* 5.3 10.6 - - + +
554H ALA* 5.0 9.4 - - + -
555H VAL* 4.4 31.0 - - + -
558H THR* 4.5 18.2 - - - -
579H SER* 3.0 29.3 + - - -
580H LEU* 3.0 15.9 + - + +
582H LEU* 1.3 78.8 - - + +
584H HIS* 1.3 61.8 + - - +
585H ILE 3.6 0.2 + - - -
586H LEU* 3.6 14.2 + - + +
587H VAL* 3.4 22.0 + - - +
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Residues in contact with HIS 584 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551H PRO* 5.8 8.7 - - + +
580H LEU* 2.9 53.1 + - + +
581H SER* 3.6 8.7 - - - +
582H LEU 3.2 0.4 - - - -
583H PHE* 1.3 77.2 - - + +
585H ILE* 1.3 65.5 + - + +
587H VAL* 4.2 9.9 + - - +
588H THR* 4.9 4.0 + - - -
1286H THR* 3.8 18.9 - - + +
1287H TYR* 5.0 10.0 - + - -
1290H MET* 3.4 49.4 - - + +
1294H TYR* 5.1 4.9 - - - -
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Residues in contact with ILE 585 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313H GLY* 3.7 29.4 - - - +
314H PHE* 4.2 20.9 - - + -
317H PRO* 4.2 17.0 - - + -
444H GLN* 5.7 4.7 - - + +
581H SER* 2.9 19.6 + - - +
582H LEU* 3.0 9.6 + - - +
584H HIS* 1.3 79.7 - - - +
586H LEU* 1.3 75.1 + - + +
587H VAL 3.0 7.6 + - - -
588H THR* 3.7 9.0 + - - -
589H PRO* 3.4 12.0 - - + +
1289H LEU* 6.0 3.8 - - + -
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Residues in contact with LEU 586 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314H PHE* 4.5 4.7 - - + -
444H GLN* 3.9 25.1 - - + +
445H ILE* 4.6 9.6 - - + +
448H GLY* 4.1 25.6 - - - +
449H VAL* 5.9 1.8 - - + -
452H LEU* 6.0 3.4 - - + -
467H ILE* 5.4 1.8 - - + +
582H LEU* 3.0 25.1 + - + +
583H PHE* 3.6 12.9 + - + +
584H HIS 3.4 0.8 - - - -
585H ILE* 1.3 91.4 - - + +
587H VAL* 1.3 61.5 + - - +
589H PRO* 3.5 19.7 - - + -
590H LEU* 3.2 24.9 - - + +
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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
------------------------------------------------------------
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