Contacts of the helix formed by residues 501 - 518 (chain A) in PDB entry 3ODX
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 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A LEU* 2.9 49.7 + - + +
498A ALA* 4.7 0.7 - - - +
500A PHE* 1.3 79.7 - - - +
502A GLY* 1.3 75.3 + - - +
503A ALA 3.6 0.9 + - - -
504A GLU* 3.8 4.5 + - - +
505A GLY* 2.9 13.9 + - - -
590A LEU* 3.8 11.4 - - - +
594A CYS* 3.8 21.8 - - - -
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Residues in contact with GLY 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ASP* 1.3 85.0 + - - +
503A ALA* 1.3 52.9 + - - -
505A GLY* 3.2 0.3 + - - -
506A SER* 2.8 35.3 + - - -
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Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ASP 3.6 0.2 + - - -
502A GLY* 1.3 68.4 - - - -
504A GLU* 1.3 65.2 + - + +
506A SER* 3.1 8.7 + - - -
507A TRP* 2.9 27.0 + - - +
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Residues in contact with GLU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A LEU* 3.9 22.7 - - - +
477A ARG* 4.8 8.3 - - - +
498A ALA 3.1 28.7 - - - +
499A ARG* 3.2 13.3 - - + +
501A ASP 3.8 2.2 + - - +
502A GLY 3.5 0.2 - - - -
503A ALA* 1.3 76.1 - - + +
505A GLY* 1.3 69.8 + - - +
507A TRP* 3.7 13.6 - - - +
508A PHE* 3.0 18.4 + - - +
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Residues in contact with GLY 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A ARG 3.3 3.9 + - - -
500A PHE 3.1 37.0 - - - -
501A ASP 2.9 13.1 + - - -
502A GLY 3.4 3.8 - - - -
504A GLU* 1.3 80.9 - - - +
506A SER* 1.3 62.2 + - - +
508A PHE* 3.2 9.7 + - - +
509A GLN* 3.2 13.1 + - - +
598A ILE* 4.3 4.7 - - - +
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Residues in contact with SER 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A GLY 2.8 17.5 + - - -
503A ALA* 3.1 11.4 + - - -
505A GLY* 1.3 72.3 - - - +
507A TRP* 1.3 55.4 + - - +
509A GLN* 3.4 16.8 + - - +
510A LYS* 3.0 27.1 + - - +
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Residues in contact with TRP 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A GLU* 3.0 32.5 + - + +
470A VAL* 3.5 23.8 - - + -
503A ALA 2.9 13.0 + - - +
504A GLU* 3.7 20.6 - - - +
505A GLY 3.2 0.2 - - - -
506A SER* 1.3 72.1 - - - +
508A PHE* 1.3 59.5 + - - +
510A LYS* 3.0 38.8 + - + +
511A ILE* 2.8 61.0 + - + +
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Residues in contact with PHE 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A VAL* 3.3 38.6 - - + -
471A HIS* 3.5 30.3 - + - -
499A ARG* 3.2 49.6 - - + +
500A PHE* 3.9 7.9 - + - -
504A GLU 3.0 10.4 + - - +
505A GLY 3.5 8.3 - - - +
507A TRP* 1.3 84.0 - - - +
509A GLN* 1.3 58.0 + - - +
511A ILE* 3.9 0.2 - - - +
512A SER* 2.8 44.4 + - - -
565A LEU* 4.1 22.7 - - + -
568A TYR* 4.2 1.3 - + - -
598A ILE* 4.0 21.5 - - + -
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Residues in contact with GLN 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A GLY 3.2 8.5 + - - +
506A SER* 3.4 17.7 + - - +
507A TRP 3.2 0.2 - - - -
508A PHE* 1.3 83.7 - - - +
510A LYS* 1.3 56.9 + - - +
512A SER* 5.0 0.7 - - - -
513A SER* 2.8 38.4 + - - +
597A GLU 4.1 2.0 + - - -
598A ILE* 4.0 35.7 - - + +
601A HIS* 2.8 56.6 - - + +
602A VAL* 4.9 1.6 - - + -
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Residues in contact with LYS 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A SER 3.0 10.5 + - - +
507A TRP* 3.3 41.0 - - + +
509A GLN* 1.3 79.2 - - - +
511A ILE* 1.3 71.8 + - + +
513A SER* 3.9 4.5 + - - -
514A ARG* 3.3 35.0 + - + +
601A HIS* 6.0 1.3 - - - -
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Residues in contact with ILE 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A SER* 4.1 21.8 - - - +
466A GLU* 4.0 8.5 - - + +
467A LEU* 3.7 37.0 - - + +
470A VAL* 4.5 6.5 - - + -
507A TRP* 2.8 63.2 + - + +
508A PHE 3.9 1.6 - - - +
510A LYS* 1.3 86.1 - - + +
512A SER* 1.3 66.8 + - - +
514A ARG* 3.5 11.2 + - - +
515A PHE* 3.3 20.8 + - - +
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Residues in contact with SER 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A LEU* 3.9 12.5 - - - +
470A VAL* 5.6 0.2 - - - +
508A PHE* 2.8 29.9 + - - -
509A GLN* 4.2 1.3 - - - -
511A ILE* 1.3 75.6 - - - +
513A SER* 1.3 56.9 + - - -
515A PHE* 3.4 2.5 + - - +
516A CYS* 2.9 28.7 + - - -
561A GLU* 2.8 32.5 + - - +
565A LEU* 3.5 24.4 - - - +
598A ILE* 6.0 0.2 - - - -
602A VAL* 4.8 0.4 - - - -
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Residues in contact with SER 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A GLN 2.8 23.2 + - - -
510A LYS* 3.9 4.5 + - - -
512A SER* 1.3 70.0 - - - +
514A ARG* 1.3 70.0 + - - +
516A CYS* 3.7 3.7 - - - +
517A SER* 2.9 30.0 + - - -
601A HIS* 3.8 22.7 - - - -
602A VAL* 3.3 32.0 - - - +
605A ALA* 4.3 8.6 - - - +
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Residues in contact with ARG 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A GLN* 5.0 3.6 + - - +
459A ASN* 5.7 2.8 + - - -
462A PRO* 2.7 39.3 + - + +
463A SER* 2.7 35.0 + - - -
510A LYS* 3.3 33.2 + - + +
511A ILE* 3.6 15.9 - - - +
513A SER* 1.3 80.1 + - - +
515A PHE* 1.3 66.1 + - - +
517A SER* 3.2 14.4 + - - -
518A ARG* 3.7 5.9 + - - +
609A MET* 5.7 0.5 - - - +
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Residues in contact with PHE 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A LEU* 5.2 2.7 - - + -
438A LEU* 4.3 16.4 - - + -
460A ILE 4.9 1.1 - - - -
461A PHE* 4.2 21.1 - + - -
462A PRO* 3.8 31.0 - - + +
463A SER* 4.0 12.1 - - - +
464A LEU* 3.8 23.1 - - + -
467A LEU* 3.8 22.0 - - + -
511A ILE 3.3 9.4 + - - +
512A SER 3.8 5.6 - - - +
514A ARG* 1.3 81.8 - - - +
516A CYS* 1.3 64.6 + - - +
518A ARG 3.6 5.9 + - - -
519A GLN* 3.8 7.2 + - + -
558A ILE* 3.7 35.7 - - + -
561A GLU* 3.9 24.0 - - + -
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Residues in contact with CYS 516 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A SER* 2.9 28.3 + - - +
513A SER 3.7 3.4 - - - +
515A PHE* 1.3 73.4 - - - +
517A SER* 1.3 65.0 + - - +
519A GLN* 3.2 28.1 - - - +
561A GLU* 3.6 27.1 - - - -
562A MET* 3.7 38.8 - - + -
565A LEU* 4.5 2.0 - - - -
602A VAL* 3.8 15.9 - - + -
606A VAL* 3.8 8.0 - - + +
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Residues in contact with SER 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A SER* 2.9 22.0 + - - -
514A ARG* 3.2 7.1 + - - -
516A CYS* 1.3 77.8 - - - +
518A ARG* 1.3 61.4 + - - +
519A GLN* 3.6 0.9 + - - +
520A SER* 4.6 3.6 + - - -
521A PHE* 5.2 0.9 + - - +
602A VAL 4.9 0.2 + - - -
605A ALA* 2.9 36.7 + - - +
606A VAL* 3.6 17.1 + - - +
609A MET* 3.6 34.5 - - - +
610A GLU* 4.8 7.6 - - - +
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Residues in contact with ARG 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A ASN* 2.9 58.4 + - - +
460A ILE 5.6 0.2 - - - -
462A PRO* 3.7 21.7 - - + +
514A ARG 3.7 2.6 + - - +
515A PHE 3.6 2.7 + - - +
516A CYS 3.1 0.4 - - - -
517A SER* 1.3 80.9 - - - +
519A GLN* 1.3 53.6 + - - +
520A SER 3.4 1.3 - - - -
521A PHE* 2.7 32.4 + - + +
522A ALA* 2.5 36.9 + - + -
609A MET* 3.7 33.6 - - + +
613A LEU* 3.9 23.2 - - - +
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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