Contacts of the helix formed by residues 508 - 519 (chain B) in PDB entry 2A1A
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 ASP 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388B LYS* 3.8 13.1 + - - -
506B ILE 4.2 0.2 + - - -
507B PHE* 1.3 78.1 - - - +
509B LYS* 1.3 60.8 + - - +
510B LYS* 2.8 31.3 + - + +
511B GLU* 3.1 43.8 + - + +
512B LYS* 3.0 24.9 + - - +
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Residues in contact with LYS 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ASP* 1.3 75.0 - - - +
510B LYS* 1.3 63.7 + - - +
512B LYS* 3.8 5.1 - - - +
513B THR* 3.3 32.0 + - + +
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Residues in contact with LYS 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ASP* 2.8 33.0 + - + -
509B LYS* 1.3 76.9 - - - +
511B GLU* 1.3 69.8 + - + +
513B THR* 3.3 8.6 + - - -
514B LEU* 3.1 23.9 + - - +
538B VAL* 6.3 0.4 - - + -
539B TRP* 3.5 49.7 + - + +
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Residues in contact with GLU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B LYS* 2.6 38.8 + - - +
392B LEU* 5.0 1.0 - - - +
478B LEU* 5.3 0.2 - - - +
482B LEU* 3.6 31.1 - - + +
506B ILE 4.9 0.5 - - - +
507B PHE* 3.8 11.4 - - + -
508B ASP* 3.1 35.8 + - + +
509B LYS 3.3 0.2 - - - -
510B LYS* 1.3 79.0 + - + +
512B LYS* 1.3 58.4 + - - +
514B LEU* 3.5 2.3 + - - +
515B LEU* 3.0 35.6 + - - +
539B TRP* 3.6 33.2 - - + -
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Residues in contact with LYS 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B ILE* 3.4 37.9 - - + +
504B SER 4.2 10.3 - - - +
505B ASP* 5.0 12.0 + - - +
507B PHE* 4.3 7.4 - - + +
508B ASP 3.0 21.6 + - - +
509B LYS* 3.8 6.3 - - - +
510B LYS 3.2 0.2 - - - -
511B GLU* 1.3 78.0 - - - +
513B THR* 1.3 63.2 + - - +
515B LEU* 3.3 2.3 + - - +
516B GLN* 2.9 55.0 + - - +
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Residues in contact with THR 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B LYS* 3.3 17.9 + - + +
510B LYS* 3.3 14.2 + - - -
512B LYS* 1.3 81.0 - - - +
514B LEU* 1.3 64.1 + - - +
516B GLN* 3.7 22.5 - - - +
517B LYS* 3.3 40.0 + - - +
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B PHE* 5.5 1.3 - - + -
478B LEU* 3.6 23.6 - - + -
510B LYS 3.1 18.1 + - - +
511B GLU 3.7 4.5 - - - +
513B THR* 1.3 77.6 + - - +
515B LEU* 1.3 58.9 + - - +
517B LYS* 3.3 10.6 + - - +
518B LEU* 2.8 47.8 + - + +
527B PRO* 4.2 17.9 - - + -
531B GLU* 5.8 0.7 - - - +
532B ILE* 4.9 15.3 - - + -
535B THR* 4.3 21.5 - - + +
536B LEU* 5.7 2.2 - - + -
539B TRP* 3.7 22.7 - - + -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B GLY* 3.4 30.5 - - - +
478B LEU* 3.6 24.0 - - + -
479B ALA* 3.6 14.4 - - + +
482B LEU* 4.9 4.9 - - + -
498B LEU* 6.0 0.7 - - + -
503B ILE* 4.6 10.3 - - + -
507B PHE* 3.8 50.0 - - + -
511B GLU 3.0 21.9 + - - +
512B LYS* 3.7 4.0 - - - +
514B LEU* 1.3 76.1 - - - +
516B GLN* 1.3 52.5 + - - +
518B LEU* 2.9 6.7 + - + +
519B LEU* 2.7 42.6 + - + +
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Residues in contact with GLN 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B ILE* 3.5 29.5 - - + +
512B LYS* 2.9 42.9 + - - +
513B THR* 3.7 28.7 + - - +
515B LEU* 1.3 72.4 - - - +
517B LYS* 1.3 63.1 + - + +
519B LEU* 3.8 2.1 - - - +
520B SER* 3.0 27.5 + - - -
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Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B THR* 3.3 37.9 + - - +
514B LEU* 3.6 14.8 - - - +
515B LEU 3.1 0.6 - - - -
516B GLN* 1.3 82.1 - - + +
518B LEU* 1.3 64.1 + - - +
519B LEU 3.3 0.3 + - - -
520B SER* 3.4 12.3 + - - -
525B ASP* 3.6 20.2 - - + +
526B ARG* 3.4 19.1 - - - +
527B PRO* 4.1 14.2 - - + +
531B GLU* 5.8 0.6 + - - -
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Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B PHE* 5.2 1.6 - - + -
471B LEU* 3.4 25.5 - - + +
472B TYR* 3.7 13.2 - - - -
474B LEU* 4.9 2.5 - - + -
475B GLY* 4.1 22.9 - - - +
478B LEU* 4.3 10.3 - - + -
514B LEU* 2.8 44.1 + - + +
515B LEU* 3.5 3.8 - - - +
517B LYS* 1.3 75.7 - - - +
519B LEU* 1.3 59.1 + - - +
526B ARG* 3.2 24.1 - - + -
527B PRO* 3.9 25.1 - - + +
532B ILE* 3.7 31.0 - - + -
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B TYR* 3.6 36.6 + - + +
475B GLY* 3.7 36.1 - - - +
476B LEU* 3.8 16.4 - - + +
479B ALA* 5.5 0.9 - - + -
498B LEU* 3.1 49.8 - - + +
499B ARG 4.8 2.0 - - - +
501B GLY* 5.1 6.1 + - - +
503B ILE* 5.0 6.5 - - + -
515B LEU* 2.7 25.1 + - + +
516B GLN* 3.8 4.7 - - - +
518B LEU* 1.3 72.0 - - - +
520B SER* 1.3 66.8 + - - +
521B LYS* 3.5 1.6 + - - -
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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