Contacts of the helix formed by residues 511 - 523 (chain P) in PDB entry 5G04
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 511 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468P MET* 5.6 7.1 - - + +
471P VAL* 5.8 0.2 - - - -
493P TYR* 3.0 24.7 + - - +
512P ALA* 1.3 73.8 + - - +
513P PHE* 3.3 10.5 - - - +
514P ARG* 3.1 49.8 + - - +
515P TYR* 3.1 27.0 + - + -
536P CYS* 6.2 1.6 - - - -
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Residues in contact with ALA 512 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493P TYR* 4.0 18.6 - - + -
494P ILE* 3.5 43.2 - - + +
497P ILE* 4.7 9.9 - - + -
498P TYR* 4.7 11.4 - - + +
511P THR* 1.3 79.8 + - - +
513P PHE* 1.3 58.5 + - + +
515P TYR* 3.2 6.7 + - - +
516P LEU 2.9 24.4 + - - -
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Residues in contact with PHE 513 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498P TYR* 2.8 34.1 - + - -
511P THR 3.3 7.3 - - - +
512P ALA* 1.3 76.0 - - + +
514P ARG* 1.3 66.4 + - - +
516P LEU* 3.2 13.8 + - + +
517P ALA* 3.0 24.7 + - - +
532P CYS* 4.4 23.6 - - + +
535P LYS* 4.6 22.2 - - + -
536P CYS* 4.4 13.9 - - + -
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Residues in contact with ARG 514 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511P THR* 3.1 38.3 + - - +
513P PHE* 1.3 76.8 - - - +
515P TYR* 1.3 101.1 + - + +
517P ALA* 3.3 8.7 + - - +
518P GLN* 3.1 32.0 + - + +
536P CYS* 3.8 29.4 - - - -
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Residues in contact with TYR 515 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471P VAL* 3.5 36.5 - - + +
475P LYS* 6.0 5.6 - - + -
478P GLU* 5.4 0.4 - - - -
490P TYR* 3.3 44.9 - + + -
493P TYR* 4.9 1.6 - + + -
494P ILE* 5.1 0.9 - - + -
511P THR* 3.1 28.4 + - + -
512P ALA* 3.2 10.4 + - - +
514P ARG* 1.3 110.7 + - + +
516P LEU* 1.3 58.2 + - - +
518P GLN* 3.1 33.5 - - - +
519P TYR* 3.0 27.3 + - - +
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Residues in contact with LEU 516 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490P TYR* 5.6 0.4 - - + -
491P ILE* 4.0 14.4 - - + -
494P ILE* 3.7 29.7 - - + +
512P ALA 2.9 13.1 + - - +
513P PHE* 3.2 16.5 + - + +
515P TYR* 1.3 72.1 - - - +
517P ALA* 1.3 59.4 + - - +
519P TYR* 3.3 26.6 + - + +
520P TYR* 2.9 54.3 + - + +
532P CYS* 3.8 21.3 - - - -
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Residues in contact with ALA 517 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513P PHE 3.0 13.0 + - - +
514P ARG* 3.3 11.6 + - - +
516P LEU* 1.3 76.5 - - - +
518P GLN* 1.3 57.2 + - - +
520P TYR 3.4 0.9 + - - -
521P PHE* 2.9 26.6 + - - +
529P ALA* 3.5 31.2 - - + +
532P CYS* 4.0 7.5 - - + +
533P ALA* 3.9 20.9 - - + +
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Residues in contact with GLN 518 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478P GLU* 2.7 40.6 + - - +
490P TYR* 3.0 26.0 + - - -
514P ARG* 3.1 19.4 + - + +
515P TYR* 3.1 28.1 - - - +
517P ALA* 1.3 72.6 - - - +
519P TYR* 1.3 59.4 + - - +
521P PHE* 3.4 14.9 - - + +
522P LYS* 3.1 27.2 + - - +
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Residues in contact with TYR 519 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478P GLU* 5.3 0.6 + - - -
487P ALA* 2.8 48.0 - - + +
490P TYR* 4.9 7.0 - - + -
491P ILE* 4.6 12.5 - - + +
515P TYR 3.0 15.7 + - - +
516P LEU* 3.3 31.2 + - + +
518P GLN* 1.3 77.4 - - - +
520P TYR* 1.3 94.9 + + - +
522P LYS* 3.3 6.7 + - - +
523P CYS* 2.9 52.8 + - + +
525P LEU* 5.7 0.5 - - - +
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Residues in contact with TYR 520 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516P LEU* 2.9 55.7 + - + +
517P ALA 3.4 0.2 + - - -
519P TYR* 1.3 98.9 - + - +
521P PHE* 1.3 55.8 + - - +
523P CYS* 3.4 4.1 + - + -
524P LYS* 3.0 22.9 + - - -
525P LEU* 3.1 38.3 + - + +
528P GLU* 3.2 45.4 + - + -
529P ALA* 3.6 22.0 - - + -
532P CYS* 4.2 8.5 - - - -
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Residues in contact with PHE 521 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517P ALA 2.9 15.4 + - - +
518P GLN* 3.4 18.6 - - + +
520P TYR* 1.3 74.5 - - - +
522P LYS* 1.3 62.7 + - + +
524P LYS* 3.2 15.6 + - - +
526P TRP* 4.4 29.3 + + - -
529P ALA* 4.0 8.2 - - + +
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Residues in contact with LYS 522 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477P HIS 4.5 2.6 + - - -
478P GLU* 4.6 23.0 + - + +
480P LEU 4.4 6.5 + - - -
481P THR* 5.4 0.8 - - - +
482P GLU 2.8 33.7 + - - +
483P SER* 3.3 41.3 + - - +
486P ALA* 5.8 1.3 - - + -
518P GLN 3.1 13.1 + - - +
519P TYR* 3.8 5.4 - - + +
521P PHE* 1.3 78.3 - - + +
523P CYS* 1.3 60.6 + - - +
524P LYS* 3.1 9.0 + - - +
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Residues in contact with CYS 523 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483P SER* 4.4 3.3 + - - -
519P TYR* 2.9 42.8 + - + +
520P TYR* 3.6 11.2 - - + +
521P PHE 3.3 0.2 - - - -
522P LYS* 1.3 74.8 - - - +
524P LYS* 1.3 72.8 + - - +
525P LEU* 3.2 29.4 + - + +
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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