Contacts of the helix formed by residues 513 - 530 (chain A) in PDB entry 3N00
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 MET 513 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A TRP* 6.1 0.2 - - + -
439A PHE* 4.2 23.1 - - + -
508A LEU* 4.0 8.3 - - + +
511A MET* 3.4 31.7 + - + +
512A GLY* 1.3 77.2 - - - +
514A GLY* 1.3 58.4 + - - +
515A ASP 3.7 0.4 - - - -
516A LEU* 3.8 9.4 - - + -
517A LEU* 2.9 36.4 + - + +
605A LYS* 3.8 6.1 - - + +
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Residues in contact with GLY 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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508A LEU 3.9 0.4 + - - -
509A GLY* 3.6 30.6 + - - -
512A GLY* 3.0 6.7 - - - -
513A MET* 1.3 77.6 - - - +
515A ASP* 1.3 57.7 + - - +
517A LEU* 4.5 0.4 - - - +
518A SER* 3.0 28.1 + - - -
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Residues in contact with ASP 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A GLY* 3.8 4.3 - - - +
514A GLY* 1.3 72.5 + - - -
516A LEU* 1.3 55.4 + - - +
518A SER* 5.0 1.1 - - - +
519A ALA* 3.1 28.7 + - - +
602A HIS* 3.5 16.4 - - + -
605A LYS* 3.2 28.7 + - - -
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Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PHE* 4.4 20.0 - - + -
443A PHE* 5.3 0.7 - - + -
477A PHE* 4.1 10.5 - - + -
481A MET* 4.4 2.2 - - + -
513A MET* 3.5 9.1 + - + +
514A GLY 3.1 0.6 - - - -
515A ASP* 1.3 74.2 - - - +
517A LEU* 1.3 55.9 + - - +
518A SER 3.0 1.3 - - - -
519A ALA* 2.6 25.0 + - + +
520A MET* 2.6 42.4 + - + +
598A LEU* 5.9 0.2 - - + -
602A HIS* 3.3 36.1 - - + +
605A LYS* 3.6 36.6 - - + +
2051B LEU* 4.1 23.3 - - + -
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Residues in contact with LEU 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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439A PHE* 6.0 5.6 - - + -
508A LEU* 5.6 13.0 - - + -
513A MET* 2.9 23.8 + - + +
514A GLY* 4.5 0.7 - - - +
516A LEU* 1.3 75.4 - - + +
518A SER* 1.3 56.8 + - - +
520A MET* 3.6 21.0 - - + +
521A PHE* 2.9 26.9 + - - +
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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
----------------------------------------------------------
514A GLY 3.0 16.8 + - - -
515A ASP* 4.3 1.3 - - - +
516A LEU 3.0 1.0 - - - -
517A LEU* 1.3 75.4 - - - +
519A ALA* 1.3 60.2 + - - +
521A PHE* 3.7 7.6 + - - +
522A ASP* 3.2 28.8 + - - -
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ASP 3.1 20.9 + - - +
516A LEU 2.6 9.9 + - - +
518A SER* 1.3 69.8 - - - +
520A MET* 1.3 58.7 + - - +
522A ASP* 3.2 7.3 + - - +
523A PHE* 3.0 28.9 + - - +
598A LEU* 3.6 20.4 - - + +
602A HIS* 3.5 20.4 - - + +
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Residues in contact with MET 520 (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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439A PHE* 5.3 13.9 - - + -
443A PHE* 6.3 1.8 - - - -
481A MET* 3.3 43.0 - - - +
484A PHE* 3.4 33.2 - - + -
488A PHE* 5.8 0.4 - - - +
516A LEU* 2.6 44.4 + - + +
517A LEU* 3.6 17.5 - - + +
519A ALA* 1.3 73.9 - - - +
521A PHE* 1.3 56.1 + - - +
523A PHE* 4.0 6.2 - - - +
524A SER* 2.5 35.3 + - - +
598A LEU* 5.3 1.1 - - + -
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Residues in contact with PHE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A PHE* 5.4 13.5 - - + -
489A ASN 5.6 7.2 - - - -
490A VAL 5.8 2.9 - - - -
491A LYS 5.3 9.0 - - - -
492A ASP* 5.6 6.7 - - - -
517A LEU 2.9 18.3 + - - +
518A SER* 3.8 8.3 - - - +
519A ALA 3.2 0.4 - - - -
520A MET* 1.3 74.5 - - - +
522A ASP* 1.3 73.3 + - - +
524A SER* 3.4 4.5 + - - -
525A GLU* 3.0 31.9 + - + +
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Residues in contact with ASP 522 (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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518A SER 3.2 17.2 + - - -
519A ALA* 3.2 8.1 + - - +
521A PHE* 1.3 84.0 - - - +
523A PHE* 1.3 66.0 + - - +
525A GLU* 3.4 8.0 - - - +
526A LYS* 3.2 26.0 + - - +
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Residues in contact with PHE 523 (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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481A MET* 4.0 22.7 - - + -
482A VAL* 4.5 4.7 - - + -
519A ALA 3.0 17.6 + - - +
520A MET* 4.0 4.7 - - - +
522A ASP* 1.3 75.5 - - - +
524A SER* 1.3 63.7 + - - +
526A LYS* 3.1 16.6 + - - +
527A LEU* 2.9 46.0 + - + +
540A PHE* 5.1 0.4 - + - -
591A LYS* 4.1 35.7 - - + -
594A ASP* 4.1 14.6 - - + -
595A LEU* 3.6 39.5 - - + -
598A LEU* 3.7 27.1 - - + -
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Residues in contact with SER 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A MET 4.5 1.0 + - - -
484A PHE 4.4 0.7 - - - -
485A ALA* 2.9 42.2 + - - +
488A PHE* 4.5 10.6 - - - +
520A MET* 2.5 24.1 + - - +
521A PHE* 3.8 3.8 - - - -
523A PHE* 1.3 78.4 - - - +
525A GLU* 1.3 62.2 + - - +
527A LEU* 3.1 8.2 + - - -
528A ASN* 2.7 39.6 + - - +
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Residues in contact with GLU 525 (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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521A PHE* 3.0 19.0 + - + +
522A ASP* 3.4 13.0 - - - +
524A SER* 1.3 78.5 - - - +
526A LYS* 1.3 63.1 + - - +
528A ASN* 3.2 12.6 + - - +
529A SER* 3.2 12.5 + - - -
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Residues in contact with LYS 526 (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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522A ASP* 3.2 12.5 + - - +
523A PHE* 3.1 18.9 + - + +
525A GLU* 1.3 78.8 - - - +
527A LEU* 1.3 59.2 + - - +
529A SER* 2.4 31.4 + - - +
530A LEU* 3.9 2.1 + - - +
591A LYS* 4.2 25.6 - - + +
594A ASP* 3.5 32.3 + - - +
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Residues in contact with LEU 527 (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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482A VAL* 4.2 33.4 - - + +
485A ALA* 4.8 8.3 - - - -
486A SER 5.4 0.2 - - - +
523A PHE* 2.9 29.0 + - + +
524A SER* 3.1 9.6 + - - +
526A LYS* 1.3 76.2 - - - +
528A ASN* 1.3 67.5 + - - +
530A LEU* 3.3 31.3 + - + +
531A ALA 4.0 1.6 + - - -
532A LEU* 4.3 21.2 + - + +
537A LEU* 4.4 9.9 - - + -
540A PHE* 4.1 21.8 - - + -
591A LYS* 4.5 15.7 - - + +
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Residues in contact with ASN 528 (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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485A ALA 4.0 21.1 + - - +
486A SER* 5.2 4.7 + - - +
488A PHE* 5.8 1.6 - - - +
489A ASN 5.2 7.9 + - - +
524A SER* 2.7 27.6 + - - +
525A GLU* 3.2 6.8 + - - +
527A LEU* 1.3 83.0 - - - +
529A SER* 1.3 60.2 + - - +
531A ALA* 2.9 24.2 + - - +
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Residues in contact with SER 529 (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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525A GLU 3.2 10.3 + - - -
526A LYS* 2.4 30.3 + - - +
528A ASN* 1.3 77.2 - - - +
530A LEU* 1.3 65.1 + - - +
531A ALA* 3.3 4.2 + - - +
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Residues in contact with LEU 530 (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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526A LYS 4.3 5.6 - - - +
527A LEU* 3.3 18.4 + - + +
529A SER* 1.3 86.1 + - - +
531A ALA* 1.3 65.0 + - - +
532A LEU* 3.9 12.3 - - + -
581A GLU* 4.9 4.5 - - - +
584A ARG* 2.8 36.0 + - + +
587A LYS* 3.5 41.1 - - + +
588A LEU* 3.7 35.9 - - + +
591A LYS* 4.0 23.8 - - - +
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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
------------------------------------------------------------
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