Contacts of the helix formed by residues 504 - 518 (chain A) in PDB entry 3F7F
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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493A TRP* 3.8 20.7 + - - +
503A GLY* 1.3 75.7 - - - +
505A GLU* 1.3 66.4 + - - +
506A LEU* 3.8 4.8 + - - +
507A PHE* 3.2 17.3 + - - +
508A LYS* 3.0 23.5 + - - +
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Residues in contact with GLU 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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504A SER* 1.3 73.3 - - - +
506A LEU* 1.3 54.0 + - - +
508A LYS* 3.1 24.2 + - - +
509A TYR* 2.7 36.8 + - - +
576A SER 4.0 8.8 - - - +
577A PHE* 3.5 28.7 - - - -
578A ASP 5.5 0.7 + - - -
582A VAL* 4.4 16.8 - - + +
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Residues in contact with LEU 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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493A TRP* 3.3 37.0 - - + -
504A SER* 3.3 5.1 + - - +
505A GLU* 1.3 75.4 - - - +
507A PHE* 1.3 59.9 + - - +
509A TYR* 3.5 8.9 - - + +
510A LEU* 2.8 39.0 + - + +
582A VAL* 3.3 33.5 - - + +
585A ASP* 3.4 25.4 - - - +
586A LEU* 3.7 41.7 - - + +
590A GLN* 4.4 3.1 - - + +
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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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493A TRP* 3.4 57.1 - + + +
496A ASN 3.9 6.3 - - - -
497A MET* 3.8 26.9 - - - -
500A GLU* 3.2 37.2 - - + -
502A ASP 3.6 16.2 - - - -
503A GLY* 3.9 6.5 - - - -
504A SER* 3.2 19.4 + - - +
505A GLU 3.2 0.6 - - - -
506A LEU* 1.3 79.5 - - - +
508A LYS* 1.3 63.0 + - + +
510A LEU* 3.2 2.2 + - - +
511A ARG* 2.9 58.8 + - - +
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Residues in contact with LYS 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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501A THR 5.4 2.0 - - - -
502A ASP* 3.9 14.3 - - - +
503A GLY 3.2 23.6 + - - -
504A SER 3.0 9.8 + - - +
505A GLU* 3.5 25.7 + - - +
507A PHE* 1.3 88.4 - - + +
509A TYR* 1.3 62.4 + - - +
511A ARG* 3.5 24.4 + - - +
512A THR* 3.1 32.2 + - + +
577A PHE* 3.6 13.9 - - + -
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Residues in contact with TYR 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 GLU 2.7 20.2 + - - +
506A LEU* 3.5 11.4 - - + +
507A PHE 3.2 0.2 - - - -
508A LYS* 1.3 70.3 - - - +
510A LEU* 1.3 71.9 + - + +
512A THR* 3.2 5.0 + - - -
513A LEU* 3.1 59.1 + - + +
574A LEU* 3.9 11.9 - - + -
577A PHE* 3.5 35.4 - + + -
579A ILE* 4.6 17.3 - - + +
582A VAL* 3.5 26.9 - - + -
583A LEU* 3.6 35.9 - - + +
586A LEU* 4.9 0.7 - - + -
633A VAL* 3.9 10.5 - - + +
636A THR* 4.2 7.3 + - - -
637A PHE* 5.4 0.5 - - - -
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Residues in contact with LEU 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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493A TRP* 3.4 44.2 - - + -
497A MET* 3.7 14.7 - - + +
506A LEU* 2.8 25.3 + - + +
507A PHE* 3.7 2.9 - - - +
509A TYR* 1.3 85.4 - - + +
511A ARG* 1.3 57.9 + - - +
513A LEU* 3.0 8.5 + - + +
514A ASN* 2.8 30.5 + - - +
586A LEU* 4.2 17.5 - - + -
629A ILE* 3.9 44.9 - - + -
632A GLN* 4.1 4.8 + - - +
633A VAL* 4.9 3.8 - - + -
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Residues in contact with ARG 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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497A MET* 3.3 44.8 + - + +
498A HIS* 6.1 1.8 - - + +
499A SER 5.7 0.4 - - - +
500A GLU 3.4 23.4 + - - -
501A THR 4.7 4.2 + - - -
502A ASP 4.7 2.0 + - - -
507A PHE* 2.9 36.8 + - + +
508A LYS* 3.7 24.4 + - - +
510A LEU* 1.3 77.2 - - - +
512A THR* 1.3 65.2 + - + +
514A ASN* 3.2 3.2 + - + +
515A GLY* 2.7 26.5 + - - -
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Residues in contact with THR 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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508A LYS* 3.1 17.5 + - + +
509A TYR 3.2 10.9 + - - -
511A ARG* 1.3 85.2 - - + +
513A LEU* 1.3 64.2 + - - +
515A GLY* 3.4 3.5 + - - +
516A PHE* 3.4 14.9 + - - +
570A LEU* 3.8 13.3 - - - +
573A GLU* 3.3 47.7 - - + +
574A LEU* 4.3 9.2 - - - +
577A PHE* 3.8 18.5 - - + -
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Residues in contact with LEU 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 TYR* 3.1 36.5 + - + +
510A LEU* 3.0 13.3 + - + +
512A THR* 1.3 78.6 + - - +
514A ASN* 1.3 62.1 + - - +
516A PHE* 3.4 4.0 + - - +
517A ALA* 3.1 23.2 + - - +
570A LEU* 4.4 5.1 - - + +
574A LEU* 3.7 25.8 - - + -
632A GLN* 3.9 14.7 - - + +
633A VAL* 3.6 46.0 - - + +
635A LEU* 5.8 0.2 - - - +
636A THR* 3.6 26.9 - - + -
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Residues in contact with ASN 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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497A MET* 3.5 38.6 - - + +
498A HIS* 4.6 13.2 + - - -
510A LEU 2.8 4.9 + - - -
511A ARG* 3.5 6.0 - - - +
513A LEU* 1.3 76.0 - - - +
515A GLY* 1.3 67.6 + - - +
518A SER* 2.8 43.8 + - - +
628A ARG* 3.4 30.6 + - - +
632A GLN* 2.9 29.9 + - - +
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Residues in contact with GLY 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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511A ARG 2.7 15.9 + - - -
512A THR* 3.4 5.6 + - - -
513A LEU 3.3 0.4 - - - -
514A ASN* 1.3 78.1 + - - +
516A PHE* 1.3 57.5 + - - +
518A SER* 3.0 17.2 + - - -
519A THR* 3.6 12.6 - - - +
573A GLU* 6.0 0.2 - - - -
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Residues in contact with PHE 516 (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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512A THR 3.4 6.2 + - - +
513A LEU 3.4 6.5 + - - +
514A ASN 3.1 0.6 - - - -
515A GLY* 1.3 73.0 - - - +
517A ALA* 1.3 65.0 + - - +
518A SER 3.2 2.0 - - - -
519A THR* 2.6 28.8 + - - -
520A LEU* 4.0 11.1 + - + +
558A LEU* 5.6 0.7 - - + -
562A PHE* 3.9 39.0 - + + -
566A ASN* 3.7 29.6 - - + +
567A LEU* 3.9 19.7 - - + -
570A LEU* 3.3 34.5 - - + -
635A LEU* 4.1 19.7 - - + -
636A THR* 6.2 0.4 - - + -
639A LEU* 3.5 30.1 - - + -
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Residues in contact with ALA 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 LEU 3.1 10.3 + - - +
516A PHE* 1.3 83.7 - - - +
518A SER* 1.3 61.7 + - - +
519A THR 3.2 1.0 + - - -
520A LEU* 3.2 20.9 + - - +
525A LEU* 4.0 19.7 - - + +
632A GLN* 3.5 37.0 - - + +
635A LEU* 4.1 18.4 - - + -
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Residues in contact with SER 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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498A HIS* 6.2 1.1 - - - -
514A ASN* 2.8 34.0 + - - +
515A GLY* 3.0 14.6 + - - -
517A ALA* 1.3 77.6 - - - +
519A THR* 1.3 62.5 + - - +
520A LEU 3.3 7.8 - - - +
525A LEU* 5.9 0.9 - - - -
628A ARG* 6.0 1.1 - - - -
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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