Contacts of the helix formed by residues 504 - 515 (chain A) in PDB entry 6FD3
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 SER 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A GLU* 2.6 36.0 + - - -
502A ARG 4.3 0.2 + - - -
503A LEU* 1.3 75.6 - - - +
505A ALA* 1.3 64.6 - - - +
506A VAL* 3.4 12.8 - - - +
507A PHE* 3.1 16.3 + - - +
508A ARG* 3.0 21.3 + - - +
536A LEU* 5.2 1.8 - - - -
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Residues in contact with ALA 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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503A LEU 3.8 0.8 + - - -
504A SER* 1.3 72.8 - - - +
506A VAL* 1.3 57.8 + - - +
508A ARG* 3.3 26.9 + - - +
509A ASP* 2.9 29.2 + - - +
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Residues in contact with VAL 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SER* 3.4 14.8 - - - +
505A ALA* 1.3 78.6 - - - +
507A PHE* 1.3 65.1 + - - +
509A ASP* 3.3 4.6 + - - +
510A PHE* 3.0 18.9 + - - +
531A HIS* 3.4 8.2 - - + -
532A PRO* 3.8 22.7 - - + +
533A PHE* 3.5 28.0 - - + +
536A LEU* 3.7 26.7 - - + -
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Residues in contact with PHE 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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376A GLU* 3.5 27.6 - - + +
379A ILE* 3.8 28.7 - - + -
467A ALA* 4.5 3.8 - - + -
471A VAL* 3.6 31.6 - - + -
503A LEU* 3.9 19.3 - - + -
504A SER* 3.1 23.9 + - - +
506A VAL* 1.3 76.0 - - - +
508A ARG* 1.3 64.9 + - - +
510A PHE* 3.2 6.1 + + - +
511A LEU* 3.0 47.5 + - + +
533A PHE* 3.3 38.1 - + + -
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Residues in contact with ARG 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 5.1 4.3 - - + -
500A PRO* 3.4 34.8 + - - -
501A GLU* 4.7 4.2 + - - +
503A LEU* 2.3 51.1 + - + -
504A SER 3.0 14.1 + - - +
505A ALA* 3.6 26.7 - - - +
507A PHE* 1.3 76.5 - - - +
509A ASP* 1.3 57.0 + - - +
511A LEU* 3.4 10.4 + - - +
512A ASN* 2.9 39.0 + - - +
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Residues in contact with ASP 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 ALA 2.9 17.1 + - - +
506A VAL* 3.6 7.9 - - + +
507A PHE 3.2 0.4 - - - -
508A ARG* 1.3 73.3 - - - +
510A PHE* 1.3 64.4 + - - +
512A ASN* 3.2 12.4 + - - +
513A ARG* 3.0 39.3 + - - +
531A HIS* 2.7 26.7 + - + +
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Residues in contact with PHE 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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383A CYS* 3.9 31.0 - - + -
387A LEU* 4.0 29.8 - - + -
463A LEU* 4.7 4.0 - - + -
467A ALA* 5.0 6.7 - - + -
506A VAL 3.0 13.2 + - - +
507A PHE* 3.4 14.8 - + - +
509A ASP* 1.3 76.1 - - - +
511A LEU* 1.3 66.8 + - + +
513A ARG* 3.2 4.4 + - - +
514A CYS* 3.0 42.7 + - - -
528A LEU* 4.1 19.7 - - + -
531A HIS* 3.5 33.8 + + + -
533A PHE* 3.7 24.7 - + + -
534A LEU* 4.3 7.0 - - + -
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Residues in contact with LEU 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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464A GLY* 4.0 13.0 - - - +
467A ALA* 3.6 34.1 - - + -
468A ILE* 4.6 6.1 - - + +
471A VAL* 5.3 1.6 - - + -
497A LEU* 4.0 20.4 - - + -
503A LEU* 4.0 26.7 - - + -
507A PHE* 3.0 34.8 + - + +
508A ARG* 3.6 9.6 - - - +
510A PHE* 1.3 78.8 - - + +
512A ASN* 1.3 66.3 + - - +
514A CYS* 3.2 4.4 + - + +
515A LEU* 3.0 36.9 + - + +
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Residues in contact with ASN 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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494A THR* 4.5 14.9 + - - +
508A ARG* 2.9 27.0 + - - +
509A ASP* 3.2 14.2 + - - +
511A LEU* 1.3 77.7 - - - +
513A ARG* 1.3 63.4 + - + +
515A LEU* 3.6 4.5 - - - -
516A GLU* 3.2 31.1 + - - +
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Residues in contact with ARG 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 ASP* 3.0 33.3 + - - +
510A PHE 3.2 6.0 + - - +
512A ASN* 1.3 76.7 - - + +
514A CYS* 1.3 62.6 + - - +
515A LEU 3.5 0.2 + - - -
516A GLU* 3.9 9.7 + - - +
521A ARG 2.6 30.3 + - - -
522A ARG* 3.4 8.7 + - - +
523A GLY* 3.2 47.4 + - - +
527A GLU* 4.7 15.6 + - - +
528A LEU* 3.9 19.8 - - + +
531A HIS* 4.4 9.5 - - + -
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Residues in contact with CYS 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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460A ILE* 3.7 16.4 - - - +
461A TRP* 3.5 12.1 + - - -
463A LEU* 4.6 6.3 - - - -
464A GLY* 3.7 26.0 - - - -
510A PHE* 3.0 48.3 + - - -
511A LEU* 3.2 7.8 + - - +
513A ARG* 1.3 77.2 - - - +
515A LEU* 1.3 57.7 + - - +
516A GLU 3.4 1.3 - - - -
522A ARG* 3.1 23.6 - - - -
528A LEU* 3.9 16.6 - - - -
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Residues in contact with LEU 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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461A TRP* 3.3 55.8 - - + +
464A GLY* 3.9 13.0 - - - +
465A ILE* 3.7 17.9 - - + +
468A ILE* 3.9 27.8 - - + -
494A THR* 2.6 44.0 + - + -
495A PRO* 4.2 9.6 - - + +
511A LEU* 3.0 27.4 + - + +
512A ASN 3.6 3.8 - - - -
513A ARG 3.3 0.2 - - - -
514A CYS* 1.3 78.0 - - - +
516A GLU* 1.3 59.1 + - - +
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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