Contacts of the helix formed by residues 572 - 586 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570G ASP* 3.0 13.6 + - - -
571G LEU* 1.3 76.8 - - - +
573G PRO* 1.3 73.2 - - - +
574G SER* 3.4 19.0 + - - -
575G VAL* 3.5 9.4 + - - +
576G ALA* 3.2 19.6 + - - +
1038G THR* 4.0 2.9 - - - -
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Residues in contact with PRO 573 (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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324G VAL* 3.6 15.7 - - + +
572G SER* 1.3 88.4 - - - +
574G SER* 1.3 56.5 + - - +
576G ALA* 4.3 3.1 - - + +
577G PHE* 2.9 59.0 + - + +
1038G THR* 3.6 32.1 - - - +
1039G ASP* 4.6 1.6 - - - +
1278G ALA* 3.8 23.3 - - + -
1279G GLY* 3.9 11.2 - - - +
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Residues in contact with SER 574 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ILE* 5.5 0.4 - - - -
321G PHE* 3.2 53.2 - - - +
324G VAL* 3.4 24.0 + - - +
325G ASP* 3.8 11.1 + - - +
572G SER* 3.7 13.3 - - - -
573G PRO* 1.3 76.7 - - - +
575G VAL* 1.3 65.8 + - - +
578G ALA* 3.3 16.9 + - - +
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Residues in contact with VAL 575 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321G PHE* 4.7 9.6 - - + -
455G ILE* 3.9 22.3 - - + +
456G LEU* 3.7 27.8 - - + -
570G ASP 4.3 18.2 - - - +
571G LEU* 5.7 2.0 - - - -
572G SER* 3.5 12.5 + - - +
574G SER* 1.3 84.3 + - - +
576G ALA* 1.3 67.0 + - + +
578G ALA* 3.9 0.3 - - - +
579G SER* 3.1 23.4 + - - -
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Residues in contact with ALA 576 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456G LEU* 6.0 0.4 - - - -
571G LEU* 5.5 6.1 - - + -
572G SER 3.2 15.2 + - - +
573G PRO* 3.3 5.4 + - + +
575G VAL* 1.3 81.7 - - + +
577G PHE* 1.3 69.5 + - + +
579G SER* 2.4 24.0 + - - -
580G LEU* 2.9 14.2 + - - +
1034G LEU* 6.6 0.2 - - + -
1038G THR* 5.3 6.1 - - - -
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Residues in contact with PHE 577 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ILE* 4.4 8.3 - - + -
324G VAL* 5.8 0.2 - - + -
573G PRO* 2.9 29.7 + - + +
576G ALA* 1.3 82.1 - - + +
578G ALA* 1.3 61.3 + - - +
580G LEU* 3.2 16.6 + - + +
581G SER* 2.9 32.9 + - - -
1031G ASP* 5.9 0.2 - - - -
1034G LEU* 4.5 15.9 - - + -
1035G ALA* 4.2 17.5 - - - -
1038G THR* 5.5 1.3 - - - -
1279G GLY* 3.0 33.2 - - - -
1282G GLY* 3.4 27.1 - - - +
1283G LEU* 3.3 33.4 - - + -
1286G THR* 4.0 9.1 + - - +
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Residues in contact with ALA 578 (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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317G PRO* 3.5 33.4 - - + +
320G ILE* 4.2 5.6 - - - +
321G PHE* 4.1 8.3 - - + +
455G ILE* 4.0 17.7 - - + -
574G SER 3.3 21.2 + - - +
575G VAL 3.6 2.2 + - - +
576G ALA 3.4 0.2 - - - -
577G PHE* 1.3 77.9 - - - +
579G SER* 1.3 56.4 + - - +
581G SER 3.3 0.7 + - - -
582G LEU* 3.0 34.0 + - - +
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Residues in contact with SER 579 (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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452G LEU* 4.3 4.7 - - - -
455G ILE* 4.5 3.9 - - - +
456G LEU* 3.9 31.8 - - - +
575G VAL 3.1 12.3 + - - -
576G ALA* 2.4 32.6 + - - -
578G ALA* 1.3 76.8 - - - +
580G LEU* 1.3 54.9 + - - +
582G LEU* 3.4 14.4 + - - +
583G PHE* 3.0 41.2 + - - -
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Residues in contact with LEU 580 (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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551G PRO 5.9 1.3 - - - +
555G VAL* 4.8 17.3 - - + -
576G ALA 2.9 14.7 + - - +
577G PHE* 3.2 28.2 + - + +
579G SER* 1.3 78.0 + - - +
581G SER* 1.3 57.3 + - - +
583G PHE* 3.0 14.2 + - + +
584G HIS* 2.9 52.7 + - + +
1031G ASP* 5.6 4.7 - - + -
1283G LEU* 4.7 8.3 - - + -
1286G THR* 3.7 21.3 - - + +
1287G TYR* 5.8 3.4 - - + -
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Residues in contact with SER 581 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G PRO* 4.3 5.2 - - - -
320G ILE* 3.8 11.1 - - - +
577G PHE 2.9 11.3 + - - -
578G ALA 4.1 3.1 - - - -
580G LEU* 1.3 72.4 - - - +
582G LEU* 1.3 61.1 + - - +
584G HIS* 3.2 10.7 + - - +
585G ILE* 2.9 34.2 + - - +
1286G THR* 3.0 37.7 + - - +
1289G LEU* 3.8 21.8 - - - +
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Residues in contact with LEU 582 (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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314G PHE* 4.6 18.8 - - + -
317G PRO* 3.7 22.8 - - + +
448G GLY* 4.4 12.1 - - - +
451G LEU* 4.4 11.9 - - + -
452G LEU* 3.8 40.6 - - + +
455G ILE* 4.1 20.9 - - + -
578G ALA 3.0 18.0 + - - +
579G SER* 3.4 8.5 - - - +
581G SER* 1.3 76.8 - - - +
583G PHE* 1.3 58.9 + - + +
585G ILE* 3.0 8.2 + - + +
586G LEU* 3.0 38.8 + - + +
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Residues in contact with PHE 583 (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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452G LEU* 3.6 42.8 - - + -
456G LEU* 4.7 4.5 - - + -
459G SER 5.9 0.7 - - - -
463G GLY* 4.7 15.3 - - - -
551G PRO* 5.3 11.8 - - + +
554G ALA* 4.7 11.2 - - + -
555G VAL* 4.4 31.4 - - + -
558G THR* 4.5 17.9 - - - -
579G SER* 3.0 29.3 + - - -
580G LEU* 3.0 15.2 + - + +
582G LEU* 1.3 79.0 - - + +
584G HIS* 1.3 61.3 + - + +
586G LEU* 3.6 14.5 + - + +
587G VAL* 3.4 22.9 + - - +
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Residues in contact with HIS 584 (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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551G PRO* 5.8 9.6 - - + +
580G LEU* 2.9 53.3 + - + +
581G SER* 3.6 9.2 - - - +
582G LEU 3.2 0.4 - - - -
583G PHE* 1.3 76.9 - - + +
585G ILE* 1.3 65.2 + - + +
587G VAL* 4.2 9.9 + - - +
588G THR* 4.9 4.0 + - - -
1286G THR* 3.8 18.9 - - + +
1287G TYR* 5.0 10.0 - + - -
1290G MET* 3.4 50.0 - - + +
1294G TYR* 5.1 4.9 - - - -
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Residues in contact with ILE 585 (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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313G GLY* 3.7 30.1 - - - +
314G PHE* 4.2 19.5 - - + -
317G PRO* 4.2 16.8 - - + -
444G GLN* 5.7 4.9 - - + +
581G SER 2.9 19.2 + - - +
582G LEU* 3.0 10.5 + - + +
584G HIS* 1.3 80.0 - - - +
586G LEU* 1.3 74.2 + - + +
587G VAL 3.0 7.8 + - - -
588G THR* 3.7 9.5 + - - -
589G PRO* 3.4 13.3 - - + +
1289G LEU* 6.0 3.6 - - + -
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Residues in contact with LEU 586 (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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314G PHE* 4.5 5.2 - - + -
444G GLN* 3.9 24.2 - - + +
445G ILE* 4.6 10.1 - - + +
448G GLY* 4.1 25.4 - - - +
449G VAL* 5.9 2.0 - - + -
452G LEU* 6.0 3.8 - - + -
467G ILE* 5.4 1.6 - - + +
582G LEU* 3.0 25.1 + - + +
583G PHE* 3.6 13.1 + - + +
584G HIS 3.4 0.6 - - - -
585G ILE* 1.3 92.0 - - + +
587G VAL* 1.3 62.1 + - - +
589G PRO* 3.5 19.1 - - + -
590G LEU* 3.2 24.5 - - + +
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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