Contacts of the helix formed by residues 508 - 520 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A A 3.6 37.9 - - - +
10A A 3.2 13.9 - - - +
507J PHE* 1.3 78.3 - - - +
509J TYR* 1.3 66.1 + - - +
510J ALA* 3.6 9.3 + - - +
511J THR* 3.0 30.3 + - - +
512J LEU* 3.0 22.6 + - - +
584J ARG* 5.3 1.0 + - - -
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Residues in contact with TYR 509 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A A 3.1 28.6 + - + +
11A C 3.5 10.5 + - - -
504J ARG* 3.5 28.2 + - - -
508J THR* 1.3 74.3 - - - +
510J ALA* 1.3 58.2 + - - +
512J LEU* 3.2 7.3 + - + +
513J ILE* 2.8 37.5 + - + +
534J PHE* 3.9 29.8 - + - -
540J TYR* 4.4 1.9 + - - -
541J PHE* 3.4 14.9 - + - -
547J THR* 5.7 0.7 - - - +
548J TRP* 3.2 32.1 - - - +
551J ALA* 3.5 29.3 - - + +
552J VAL* 4.1 11.4 - - + -
555J ASN* 3.4 28.0 - - + +
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Residues in contact with ALA 510 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508J THR* 3.1 8.6 + - - +
509J TYR* 1.3 78.8 - - - +
511J THR* 1.3 62.9 + - - +
514J ARG* 3.0 22.5 + - - +
555J ASN* 3.8 12.6 - - - +
559J HIS* 4.5 3.6 - - + +
562J PHE* 3.3 33.0 - - + -
580J TYR* 4.2 5.1 - - + -
584J ARG* 3.3 30.1 - - - +
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Residues in contact with THR 511 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507J PHE* 4.0 26.2 - - + -
508J THR* 3.0 28.7 + - - +
510J ALA* 1.3 77.8 - - - +
512J LEU* 1.3 55.7 + - + +
514J ARG* 3.4 8.0 + - - +
515J GLN* 2.9 30.8 + - + +
580J TYR* 2.9 28.3 + - - +
584J ARG* 5.8 0.5 + - - -
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Residues in contact with LEU 512 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505J PRO* 4.5 12.8 - - + -
507J PHE* 3.4 47.1 - - + +
508J THR 3.0 13.8 + - - +
509J TYR* 3.6 11.4 - - + +
511J THR* 1.3 77.1 - - + +
513J ILE* 1.3 66.3 + - - +
515J GLN* 3.2 8.1 + - + +
516J ALA* 3.0 18.4 + - - +
533J TRP* 3.5 22.5 - - + -
534J PHE* 3.6 28.9 - - + -
538J PHE* 4.5 10.3 - - + -
541J PHE* 4.0 18.8 - - + -
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Residues in contact with ILE 513 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509J TYR* 2.8 27.3 + - + +
510J ALA 3.8 3.1 - - - +
512J LEU* 1.3 72.9 - - - +
514J ARG* 1.3 64.1 + - - +
516J ALA* 3.2 6.0 + - - +
517J ILE* 3.1 29.3 + - + +
530J ILE* 4.5 9.0 - - + -
534J PHE* 3.9 22.9 - - + -
552J VAL* 3.9 23.1 - - + +
555J ASN* 3.6 29.8 - - + -
556J LEU* 3.6 29.2 - - + -
562J PHE* 3.7 18.8 - - + -
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Residues in contact with ARG 514 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510J ALA 3.0 17.7 + - - +
511J THR* 3.6 8.3 + - - +
513J ILE* 1.3 76.2 - - - +
515J GLN* 1.3 67.8 + - - +
517J ILE* 3.3 1.4 + - - +
518J MET* 2.8 60.2 + - + +
562J PHE* 4.0 7.8 - - + -
575J VAL* 4.0 19.5 - - + -
577J GLU* 2.8 40.7 + - - -
580J TYR* 3.4 46.6 + - + -
581J GLN* 4.2 2.8 - - - +
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Residues in contact with GLN 515 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511J THR* 2.9 17.8 + - + +
512J LEU* 3.3 11.7 - - + +
513J ILE 3.2 0.4 - - - -
514J ARG* 1.3 88.0 + - - +
516J ALA* 1.3 62.2 + - - +
518J MET* 3.8 7.0 - - - +
519J GLU* 2.6 66.8 + - - +
533J TRP* 3.7 18.2 - - + -
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Residues in contact with ALA 516 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512J LEU 3.0 8.2 + - - +
513J ILE* 3.4 11.4 - - - +
515J GLN* 1.3 78.5 - - - +
517J ILE* 1.3 62.6 + - + +
519J GLU* 3.3 9.7 + - - +
520J SER* 3.4 8.3 + - - -
525J LEU* 3.6 22.2 - - + +
530J ILE* 4.8 9.0 - - + -
533J TRP* 3.5 48.0 - - + +
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Residues in contact with ILE 517 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513J ILE* 3.1 27.9 + - + +
514J ARG 3.8 3.1 - - - +
516J ALA* 1.3 73.6 - - - +
518J MET* 1.3 66.1 + - - +
520J SER* 2.5 26.8 + - - -
523J ARG* 3.4 34.3 - - + +
524J GLN 3.9 1.3 - - - +
525J LEU* 4.2 8.5 - - + -
530J ILE* 4.5 13.0 - - + -
562J PHE* 4.4 2.2 - - + -
573J TRP* 3.8 35.2 - - + +
574J THR* 4.1 6.3 - - - +
575J VAL* 3.5 31.9 - - + +
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Residues in contact with MET 518 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514J ARG* 2.8 56.2 + - + +
515J GLN* 3.8 9.9 - - - +
517J ILE* 1.3 73.6 - - + +
519J GLU* 1.3 62.0 + - + +
520J SER 3.5 5.5 + - - +
523J ARG* 3.8 44.9 - - - +
575J VAL* 5.0 7.2 - - + -
577J GLU* 4.0 22.4 - - + +
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Residues in contact with GLU 519 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515J GLN* 2.6 51.0 + - - +
516J ALA 3.8 5.4 - - - +
517J ILE 3.1 0.6 - - - -
518J MET* 1.3 76.6 - - + +
520J SER* 1.3 63.5 + - - +
521J SER* 3.7 1.2 + - - -
533J TRP* 3.0 28.2 + - + +
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Residues in contact with SER 520 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516J ALA 3.4 4.0 + - - -
517J ILE 2.5 22.5 + - - -
518J MET 3.8 7.1 - - - +
519J GLU* 1.3 81.6 - - - +
521J SER* 1.3 65.3 + - - +
522J ASP 4.4 0.7 - - - -
523J ARG* 3.2 8.5 + - - +
524J GLN 3.0 35.6 + - - -
525J LEU* 3.8 20.2 - - - -
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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