Contacts of the helix formed by residues 508 - 519 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540H TYR* 3.6 11.0 - - - -
504I ARG* 5.0 13.5 + - - +
505I PRO* 4.3 22.9 - - + +
507I PHE* 1.3 80.5 - - - +
509I TYR* 1.3 65.6 + - - +
510I ALA* 3.3 10.3 + - - +
511I THR* 3.0 30.7 + - + +
512I LEU* 3.1 23.6 + - - +
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Residues in contact with TYR 509 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540H TYR* 3.4 21.6 + + - -
544H ASN* 3.1 33.5 + - + +
547H THR* 3.4 11.8 + - - -
548H TRP* 3.7 20.0 - - + -
551H ALA* 3.2 34.4 - - + +
552H VAL* 4.4 4.9 - - + -
555H ASN* 3.6 27.1 + - + +
508I THR* 1.3 74.2 - - - +
510I ALA* 1.3 58.2 + - - +
512I LEU* 3.3 4.9 + - + +
513I ILE* 2.8 41.5 + - + +
534I PHE* 4.0 17.7 - + - -
538I PHE* 4.7 4.9 - + - -
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Residues in contact with ALA 510 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555H ASN* 3.9 12.8 + - - +
559H HIS* 4.8 0.2 - - - +
562H PHE* 3.4 22.3 - - + -
580H TYR* 4.1 4.2 - - + -
583H ARG* 3.8 37.5 - - - +
508I THR* 3.1 9.3 + - - +
509I TYR* 1.3 80.1 - - - +
511I THR* 1.3 63.9 + - + +
513I ILE 3.4 0.2 + - - -
514I ARG* 3.0 22.2 + - - +
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Residues in contact with THR 511 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580H TYR* 3.3 23.8 - - - +
584H ARG* 5.7 6.7 - - - +
504I ARG* 4.8 12.8 - - - +
506I PRO 4.7 2.5 + - - +
507I PHE* 3.7 15.1 - - - +
508I THR* 3.0 38.2 + - + +
510I ALA* 1.3 76.0 - - + +
512I LEU* 1.3 59.1 + - - +
514I ARG* 3.5 4.5 + - - +
515I GLN* 3.0 28.6 + - - +
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Residues in contact with LEU 512 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507H PHE* 4.1 10.5 - - + -
540H TYR* 4.1 17.5 - - + +
541H PHE* 4.0 27.8 - - + -
507I PHE* 3.6 29.2 - - + -
508I THR 3.1 21.4 + - - +
509I TYR* 3.7 0.9 - - + +
511I THR* 1.3 75.1 + - - +
513I ILE* 1.3 67.4 + - - +
515I GLN* 3.3 7.0 + - - +
516I ALA* 3.0 23.9 + - - +
533I TRP* 3.6 27.3 - - + -
534I PHE* 3.6 28.9 - - + -
537I THR* 4.7 1.1 - - + -
538I PHE* 5.0 1.3 - - + -
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Residues in contact with ILE 513 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H VAL* 4.1 24.7 - - + +
555H ASN* 3.9 27.4 - - + -
556H LEU* 3.9 24.0 - - + -
562H PHE* 3.7 25.8 - - + -
509I TYR* 2.8 23.2 + - + +
512I LEU* 1.3 76.1 - - - +
514I ARG* 1.3 63.6 + - - +
516I ALA* 3.3 4.7 + - - +
517I ILE* 3.1 33.8 + - + +
530I ILE* 4.6 7.6 - - + -
534I PHE* 3.9 22.4 - - + -
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Residues in contact with ARG 514 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562H PHE* 4.1 2.2 - - + -
575H VAL* 4.0 21.3 - - + -
577H GLU* 3.0 38.0 + - - -
580H TYR* 3.2 46.6 + - + -
581H GLN* 4.0 6.3 - - - +
510I ALA 3.0 17.9 + - - +
511I THR 3.6 5.5 + - - +
513I ILE* 1.3 77.9 - - - +
515I GLN* 1.3 60.7 + - - +
517I ILE* 3.4 1.0 + - - +
518I MET* 2.8 53.2 + - + +
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Residues in contact with GLN 515 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506H PRO 3.8 10.3 + - - -
507H PHE* 3.3 41.2 - - - -
507I PHE* 4.5 4.7 - - - -
511I THR 3.0 17.5 + - - +
512I LEU* 3.6 10.8 - - - +
514I ARG* 1.3 80.3 - - - +
516I ALA* 1.3 63.1 + - - +
518I MET* 3.2 4.6 + - - -
519I GLU* 2.9 63.8 + - + +
533I TRP* 3.8 8.8 - - + -
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Residues in contact with ALA 516 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512I LEU 3.0 10.3 + - - +
513I ILE* 3.3 10.5 + - - +
515I GLN* 1.3 77.2 - - - +
517I ILE* 1.3 63.4 + - + +
519I GLU* 4.1 2.0 - - - +
520I SER* 3.4 15.1 + - - -
525I LEU* 3.5 21.2 - - + +
530I ILE* 5.2 7.9 - - + -
533I TRP* 3.4 49.9 - - + +
534I PHE* 5.2 0.2 - - + -
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Residues in contact with ILE 517 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562H PHE* 4.8 1.8 - - + -
573H TRP* 3.5 38.6 - - + +
574H THR 4.1 2.9 - - - +
575H VAL* 3.7 25.1 - - + +
513I ILE* 3.1 30.5 + - + +
514I ARG 3.8 2.9 - - - +
516I ALA* 1.3 77.3 - - - +
518I MET* 1.3 73.0 + - + +
520I SER* 2.5 25.9 + - - -
523I ARG* 3.2 31.6 - - - +
524I GLN* 4.1 0.7 - - - +
525I LEU* 4.1 15.7 - - + -
530I ILE* 4.5 4.0 - - + -
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Residues in contact with MET 518 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575H VAL* 3.9 20.4 - - + +
577H GLU* 4.4 17.0 - - - +
514I ARG* 2.8 52.2 + - + +
515I GLN* 3.9 4.5 - - - +
517I ILE* 1.3 92.7 - - + +
519I GLU* 1.3 62.6 + - + +
520I SER 3.2 3.5 + - - +
523I ARG* 2.9 58.4 + - + +
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Residues in contact with GLU 519 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506H PRO* 4.1 17.1 - - - +
515I GLN* 2.9 55.5 + - + +
516I ALA* 4.1 3.4 - - - +
518I MET* 1.3 77.3 - - + +
520I SER* 1.3 61.6 + - - +
533I TRP* 3.9 16.5 + - - +
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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