Contacts of the helix formed by residues 572 - 586 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570F ASP* 3.0 13.0 + - - -
571F LEU* 1.3 76.6 - - - +
573F PRO* 1.3 76.1 - - - +
574F SER* 3.4 19.2 + - - -
575F VAL* 3.5 9.1 + - - +
576F ALA* 3.2 19.6 + - - +
1038F THR* 4.0 2.2 - - - -
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Residues in contact with PRO 573 (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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324F VAL* 3.6 16.3 - - + +
572F SER* 1.3 87.4 - - - +
574F SER* 1.3 56.6 + - - +
576F ALA* 4.3 3.8 - - + +
577F PHE* 2.9 57.1 + - + +
1038F THR* 3.6 33.0 - - - +
1039F ASP* 4.6 1.6 - - - +
1278F ALA* 3.8 22.7 - - + -
1279F GLY* 3.9 10.8 - - - +
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Residues in contact with SER 574 (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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320F ILE* 5.0 0.8 - - - -
321F PHE* 3.2 52.5 - - - +
324F VAL* 3.4 23.7 - - - +
325F ASP* 3.8 10.6 - - - +
572F SER* 3.7 12.9 - - - -
573F PRO* 1.3 76.2 - - - +
575F VAL* 1.3 67.9 + - - +
578F ALA* 3.3 17.0 + - - +
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Residues in contact with VAL 575 (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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321F PHE* 4.7 10.1 - - + -
455F ILE* 3.9 22.4 - - + +
456F LEU* 3.7 26.9 - - + -
570F ASP 4.3 18.6 - - - +
571F LEU* 5.7 2.5 - - - -
572F SER* 3.5 12.3 + - - +
574F SER* 1.3 82.5 + - - +
576F ALA* 1.3 66.9 + - + +
578F ALA* 3.9 0.2 - - - +
579F SER* 3.1 23.2 + - - -
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Residues in contact with ALA 576 (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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571F LEU* 5.5 6.5 - - + -
572F SER 3.2 15.8 + - - +
573F PRO* 3.3 5.6 + - + +
575F VAL* 1.3 82.0 - - + +
577F PHE* 1.3 71.4 + - + +
579F SER* 2.4 24.0 + - - -
580F LEU* 2.9 13.9 + - - +
1038F THR* 5.3 5.8 - - - -
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Residues in contact with PHE 577 (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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320F ILE* 4.4 9.0 - - + -
324F VAL* 5.8 0.2 - - + -
573F PRO* 2.9 30.6 + - + +
576F ALA* 1.3 84.4 - - + +
578F ALA* 1.3 60.1 + - - +
580F LEU* 3.4 15.9 - - + +
581F SER* 2.9 33.1 + - - -
1034F LEU* 4.5 16.2 - - + -
1035F ALA* 4.2 17.5 - - - -
1038F THR* 5.5 1.8 - - - -
1279F GLY* 3.0 32.8 - - - -
1282F GLY* 3.4 26.9 - - - +
1283F LEU* 3.3 33.9 - - + -
1286F THR* 4.0 9.4 + - - +
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Residues in contact with ALA 578 (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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317F PRO* 3.5 34.1 - - + +
320F ILE* 4.2 5.8 - - - +
321F PHE* 4.1 7.4 - - + +
455F ILE* 4.0 17.0 - - + -
574F SER 3.3 21.5 + - - +
575F VAL 3.6 2.6 + - - +
576F ALA 3.4 0.2 - - - -
577F PHE* 1.3 79.5 - - - +
579F SER* 1.3 57.3 + - - +
581F SER* 3.3 1.1 + - - -
582F LEU* 3.0 32.9 + - - +
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Residues in contact with SER 579 (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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452F LEU* 4.3 4.5 - - - -
455F ILE* 4.5 3.9 - - - +
456F LEU* 3.9 32.9 - - - +
575F VAL 3.1 12.8 + - - -
576F ALA* 2.4 32.2 + - - -
578F ALA* 1.3 77.5 - - - +
580F LEU* 1.3 55.0 + - - +
582F LEU* 3.4 13.4 + - - +
583F PHE* 3.0 41.8 + - - -
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Residues in contact with LEU 580 (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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551F PRO 5.9 1.1 - - - +
555F VAL* 4.8 17.7 - - + -
576F ALA 2.9 13.9 + - - +
577F PHE* 3.2 29.3 + - + +
579F SER* 1.3 77.0 + - - +
581F SER* 1.3 56.6 + - - +
583F PHE* 3.0 14.6 + - + +
584F HIS* 2.9 52.6 + - + +
1031F ASP* 5.6 5.6 - - + -
1283F LEU* 4.7 8.1 - - + -
1286F THR* 3.7 22.2 - - + +
1287F TYR* 5.8 3.1 - - + -
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Residues in contact with SER 581 (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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317F PRO* 4.3 6.1 - - - -
320F ILE* 3.8 10.1 - - - +
577F PHE 2.9 11.2 + - - -
578F ALA 4.1 2.9 - - - -
580F LEU* 1.3 72.6 - - - +
582F LEU* 1.3 61.6 + - - +
584F HIS* 3.2 11.1 + - - +
585F ILE* 2.9 33.2 + - - +
1286F THR* 3.0 38.0 + - - +
1289F LEU* 3.8 21.4 - - - +
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Residues in contact with LEU 582 (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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314F PHE* 4.6 19.7 - - + -
317F PRO* 3.7 21.2 - - + +
448F GLY* 4.4 13.0 - - - +
451F LEU* 4.4 11.0 - - + -
452F LEU* 3.8 41.1 - - + +
455F ILE* 4.1 20.6 - - + -
578F ALA 3.0 18.6 + - - +
579F SER* 3.4 8.3 - - - +
581F SER* 1.3 75.9 - - - +
583F PHE* 1.3 60.2 + - + +
585F ILE* 3.0 7.5 + - + +
586F LEU* 3.0 38.0 + - + +
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Residues in contact with PHE 583 (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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452F LEU* 3.6 43.3 - - + -
456F LEU* 4.7 5.2 - - + -
459F SER 5.9 0.4 - - - -
463F GLY* 4.7 15.3 - - - -
551F PRO* 5.3 11.0 - - + +
554F ALA* 4.7 11.0 - - + -
555F VAL* 4.4 32.1 - - + -
558F THR* 4.5 16.8 - - - -
579F SER* 3.0 29.2 + - - -
580F LEU* 3.0 15.0 + - + +
582F LEU* 1.3 78.8 - - + +
584F HIS* 1.3 61.5 + - - +
585F ILE 3.6 0.2 + - - -
586F LEU* 3.6 14.6 + - + +
587F VAL* 3.4 22.3 + - - +
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Residues in contact with HIS 584 (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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551F PRO* 5.8 9.2 - - + +
580F LEU* 2.9 53.2 + - + +
581F SER* 3.6 9.2 - - - +
582F LEU 3.2 0.2 - - - -
583F PHE* 1.3 76.4 - - - +
585F ILE* 1.3 64.8 + - + +
587F VAL* 4.2 9.8 + - - +
588F THR* 4.9 3.8 + - - -
1286F THR* 3.8 19.3 - - + +
1287F TYR* 5.0 9.8 - + - -
1290F MET* 3.4 49.0 - - + +
1294F TYR* 5.1 4.7 - - - -
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Residues in contact with ILE 585 (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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313F GLY* 3.7 30.3 - - - +
314F PHE* 4.2 19.3 - - + -
317F PRO* 4.2 17.0 - - + -
444F GLN* 5.7 5.4 - - + +
581F SER* 2.9 19.3 + - - +
582F LEU* 3.0 10.3 + - + +
584F HIS* 1.3 80.5 - - + +
586F LEU* 1.3 75.3 + - + +
587F VAL 3.0 8.3 + - - -
588F THR* 3.7 9.4 + - - -
589F PRO* 3.4 12.2 - - + +
1289F LEU* 6.0 3.8 - - + -
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Residues in contact with LEU 586 (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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314F PHE* 4.5 5.4 - - + -
444F GLN* 3.9 24.0 - - + +
445F ILE* 4.6 9.6 - - + +
448F GLY* 4.1 25.4 - - - +
449F VAL* 5.0 1.8 - - + +
452F LEU* 6.0 3.8 - - + -
467F ILE* 5.4 1.5 - - + +
582F LEU* 3.0 25.1 + - + +
583F PHE* 3.6 13.4 + - + +
584F HIS 3.4 1.0 - - - -
585F ILE* 1.3 91.2 - - + +
587F VAL* 1.3 60.3 + - - +
589F PRO* 3.5 19.2 - - + +
590F LEU* 3.2 25.1 - - + +
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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