Contacts of the helix formed by residues 508 - 520 (chain G) in PDB entry 2A07
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 THR 508 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B T 4.0 31.7 + - - +
13B G 3.2 20.6 - - - +
540F TYR* 3.4 5.2 - - - -
506G PRO* 5.6 4.5 - - + -
507G PHE* 1.3 81.0 - - - +
509G TYR* 1.3 64.8 + - - +
510G ALA* 3.2 10.4 + - - +
511G THR* 3.0 43.2 + - + +
512G LEU* 3.1 11.9 + - - +
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Residues in contact with TYR 509 (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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13B G 3.2 32.7 + - + +
14B T 4.3 2.1 + - - -
540F TYR* 3.6 15.0 - + - -
543F ARG* 3.3 32.3 + - - -
547F THR 4.4 0.3 - - - -
548F TRP* 3.3 37.9 + - + +
551F ALA* 3.4 32.2 - - + +
552F VAL* 4.1 8.5 - - + -
555F ASN* 3.4 25.1 - - + +
508G THR* 1.3 73.6 - - - +
510G ALA* 1.3 57.8 + - - +
512G LEU* 3.4 5.5 + - + +
513G ILE* 2.9 37.7 + - + +
534G PHE* 3.7 22.4 - + - -
538G PHE* 4.1 5.5 - + - -
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Residues in contact with ALA 510 (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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12B T 5.8 3.1 - - - +
555F ASN* 3.9 12.2 + - - +
559F HIS* 4.3 11.0 - - + +
561F CYS* 5.4 1.6 - - - -
562F PHE* 3.3 29.5 - - + -
580F TYR* 3.5 12.1 - - + +
583F ARG* 6.4 2.0 - - + -
508G THR* 3.1 9.0 + - - +
509G TYR* 1.3 77.4 - - - +
511G THR* 1.3 59.9 + - + +
514G ARG* 2.9 30.8 + - - +
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Residues in contact with THR 511 (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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580F TYR* 2.9 20.4 - - + +
506G PRO 3.8 11.4 + - - +
507G PHE* 3.6 10.6 - - - -
508G THR* 3.0 40.5 + - + +
510G ALA* 1.3 76.2 - - + +
512G LEU* 1.3 62.6 + - - +
514G ARG* 3.7 4.5 + - - +
515G GLN* 2.8 30.3 + - - +
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Residues in contact with LEU 512 (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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507F PHE* 4.0 11.7 - - + -
540F TYR* 4.1 18.6 - - + +
541F PHE* 4.0 25.8 - - + -
507G PHE* 3.9 23.3 - - + -
508G THR 3.1 18.9 + - - +
509G TYR* 3.7 3.6 - - + +
511G THR* 1.3 81.6 + - - +
513G ILE* 1.3 60.9 + - - +
515G GLN* 3.1 7.5 + - - +
516G ALA* 2.9 29.8 + - - +
533G TRP* 3.7 25.2 - - + -
534G PHE* 3.7 31.2 - - + -
538G PHE* 5.0 2.5 - - + -
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Residues in contact with ILE 513 (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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552F VAL* 4.0 24.7 - - + +
555F ASN* 3.8 26.7 - - + -
556F LEU* 4.0 17.5 - - + -
562F PHE* 3.8 27.6 - - + -
509G TYR* 2.9 27.4 + - + +
512G LEU* 1.3 75.1 - - - +
514G ARG* 1.3 62.4 + - - +
516G ALA* 3.4 4.1 + - - +
517G ILE* 3.1 37.9 + - + +
530G ILE* 4.3 10.3 - - + -
534G PHE* 3.8 22.4 - - + -
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Residues in contact with ARG 514 (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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562F PHE* 4.1 3.8 - - + -
575F VAL* 4.0 28.5 - - + -
577F GLU* 3.6 26.8 + - - -
580F TYR* 3.8 38.1 - - + -
510G ALA 2.9 17.6 + - - +
511G THR* 3.7 5.2 - - - +
513G ILE* 1.3 76.7 - - - +
515G GLN* 1.3 64.0 + - - +
517G ILE* 3.8 0.5 - - - +
518G MET* 2.9 56.5 + - + +
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Residues in contact with GLN 515 (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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506F PRO 3.4 13.7 + - - -
507F PHE* 3.2 40.0 - - - -
507G PHE* 4.5 4.2 - - - -
511G THR 2.8 18.5 + - - +
512G LEU* 3.1 12.7 + - - +
514G ARG* 1.3 83.8 - - - +
516G ALA* 1.3 64.0 + - - +
518G MET* 3.7 3.7 - - - +
519G GLU* 3.0 57.8 + - + +
533G TRP* 3.7 12.5 - - + -
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Residues in contact with ALA 516 (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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512G LEU 2.9 14.0 + - - +
513G ILE* 3.6 7.9 - - - +
514G ARG 3.3 0.2 - - - -
515G GLN* 1.3 78.8 - - - +
517G ILE* 1.3 63.7 + - + +
519G GLU* 3.2 9.8 + - - +
520G SER* 3.3 9.9 + - - -
525G LEU* 3.6 18.4 - - + +
530G ILE* 5.2 4.5 - - + -
533G TRP* 3.4 48.8 - - + +
534G PHE* 5.1 2.2 - - + -
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Residues in contact with ILE 517 (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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556F LEU* 5.6 0.2 - - + -
562F PHE* 4.7 2.5 - - + -
573F TRP* 4.4 9.9 - - + -
574F THR* 4.0 24.9 - - - +
575F VAL* 3.7 33.0 - - + +
513G ILE* 3.1 32.1 + - + +
516G ALA* 1.3 75.3 - - - +
518G MET* 1.3 65.0 + - + +
520G SER* 2.7 20.9 + - - -
523G ARG* 3.3 34.7 - - - +
524G GLN* 4.1 2.2 - - - +
525G LEU* 3.6 24.2 - - + -
530G ILE* 4.4 4.3 - - + -
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Residues in contact with MET 518 (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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575F VAL* 4.4 15.7 - - + +
577F GLU* 4.5 14.8 - - - +
514G ARG* 2.9 54.5 + - + +
515G GLN* 3.7 5.6 - - - +
517G ILE* 1.3 85.4 - - + +
519G GLU* 1.3 62.3 + - + +
520G SER 3.3 5.2 - - - +
523G ARG* 3.5 53.9 + - + +
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Residues in contact with GLU 519 (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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504F ARG 5.5 1.4 - - - +
505F PRO 5.0 1.2 - - - +
506F PRO* 4.2 13.1 - - - +
515G GLN* 3.0 52.0 + - + +
516G ALA* 3.2 5.1 + - - +
518G MET* 1.3 79.0 - - + +
520G SER* 1.3 61.4 + - - +
521G SER 4.1 0.2 + - - -
533G TRP* 4.0 16.6 + - + +
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Residues in contact with SER 520 (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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516G ALA 3.3 7.4 + - - -
517G ILE 2.7 23.1 + - - +
518G MET 4.0 4.5 - - - +
519G GLU* 1.3 82.0 - - - +
521G SER* 1.3 63.2 + - - +
522G ASP 3.7 0.2 + - - -
523G ARG* 3.3 11.3 + - - +
524G GLN 3.1 22.3 + - - -
525G LEU* 3.3 27.4 - - - +
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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