Contacts of the helix formed by residues 509 - 532 (chain S) in PDB entry 5L4K
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 GLU 509 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508S ALA* 1.3 86.6 - - + +
510S GLU* 1.3 63.1 + - - +
511S ARG* 3.3 3.8 + - - +
512S ARG* 3.6 55.6 + - + +
513S GLU* 3.7 8.3 + - - +
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Residues in contact with GLU 510 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674N PRO* 5.0 8.8 - - + +
677N ASN* 3.5 44.4 - - + +
678N ASP* 5.3 0.6 - - - -
679N PRO* 5.7 1.0 - - - +
507S SER* 4.3 17.4 + - - +
508S ALA 3.4 1.6 - - - -
509S GLU* 1.3 75.2 - - - +
511S ARG* 1.3 60.3 + - - +
512S ARG 3.3 0.2 - - - -
513S GLU* 3.4 16.7 + - - +
514S ARG* 2.9 51.2 + - - +
517S GLN* 4.7 0.3 + - - -
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Residues in contact with ARG 511 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509S GLU* 3.3 1.3 - - - -
510S GLU* 1.3 76.4 - - - +
512S ARG* 1.3 59.6 + - - +
514S ARG* 3.6 37.5 - - - +
515S GLU* 2.9 60.7 + - - +
518S ASP* 4.0 11.5 + - - -
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Residues in contact with ARG 512 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508S ALA 3.8 11.7 + - - -
509S GLU* 3.6 54.6 + - + +
510S GLU 3.3 0.4 - - - -
511S ARG* 1.3 78.4 - - - +
513S GLU* 1.3 82.8 + - - +
515S GLU* 3.2 10.0 + - - +
516S GLN* 2.9 27.4 + - + +
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Residues in contact with GLU 513 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679N PRO* 5.5 8.8 - - + +
508S ALA 5.5 0.2 - - - +
509S GLU 3.7 14.1 + - - +
510S GLU* 3.4 23.0 + - - +
511S ARG 3.4 0.4 - - - -
512S ARG* 1.3 101.8 + - - +
514S ARG* 1.3 56.9 + - - +
516S GLN* 3.3 11.7 + - - +
517S GLN* 2.9 39.3 + - - +
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Residues in contact with ARG 514 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677N ASN* 4.4 22.1 + - + +
510S GLU* 2.9 46.2 + - - +
511S ARG* 3.6 35.8 - - - +
513S GLU* 1.3 72.8 - - - +
515S GLU* 1.3 60.9 + - - +
517S GLN* 3.3 15.7 + - - +
518S ASP* 2.9 36.0 + - - +
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Residues in contact with GLU 515 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511S ARG* 2.9 40.0 + - - +
512S ARG* 3.2 9.0 + - - +
514S ARG* 1.3 73.9 - - - +
516S GLN* 1.3 65.0 + - - +
518S ASP* 3.2 10.1 + - + +
519S LEU* 3.0 38.9 + - + +
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Residues in contact with GLN 516 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512S ARG* 2.9 14.2 + - + +
513S GLU* 3.5 16.2 - - - +
515S GLU* 1.3 77.1 - - - +
517S GLN* 1.3 58.3 + - + +
519S LEU* 2.8 42.8 + - - +
520S GLU* 2.9 42.6 + - + +
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Residues in contact with GLN 517 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677N ASN* 3.2 26.9 + - - +
678N ASP 5.1 0.3 - - - +
679N PRO* 3.3 37.5 - - + +
684N ARG* 4.4 14.8 + - - -
510S GLU* 4.7 2.6 + - - -
513S GLU* 2.9 27.2 + - - +
514S ARG* 3.6 16.8 - - - +
516S GLN* 1.3 75.3 - - + +
518S ASP* 1.3 65.6 + - - +
520S GLU* 3.3 16.3 + - - +
521S PHE* 3.1 33.2 + - + -
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Residues in contact with ASP 518 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511S ARG* 4.0 15.2 + - - -
514S ARG* 2.9 20.9 + - - +
515S GLU* 3.2 9.1 + - + +
517S GLN* 1.3 80.9 - - - +
519S LEU* 1.3 61.2 + - + +
520S GLU 3.5 0.2 - - - -
521S PHE* 4.0 18.3 + - - +
522S ALA* 3.9 15.6 + - - +
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Residues in contact with LEU 519 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515S GLU* 3.0 28.2 + - + +
516S GLN* 2.8 34.8 + - - +
518S ASP* 1.3 80.3 - - - +
520S GLU* 1.3 57.8 + - - +
521S PHE 3.3 0.9 - - - -
522S ALA* 3.6 10.6 + - + +
523S LYS* 2.9 27.7 + - - +
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Residues in contact with GLU 520 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516S GLN* 2.9 45.8 + - + +
517S GLN* 3.3 10.9 + - - +
519S LEU* 1.3 77.6 - - - +
521S PHE* 1.3 63.2 + - + +
523S LYS* 3.7 18.6 - - - +
524S GLU* 2.9 43.1 + - + +
186V LYS* 4.6 8.0 + - - -
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Residues in contact with PHE 521 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684N ARG* 4.7 13.9 - - - -
721N HIS* 3.1 61.5 - - + +
722N ASP* 4.4 11.4 - - - -
723N ASP* 5.4 6.5 - - - -
517S GLN* 3.1 32.5 + - + -
518S ASP* 4.0 19.7 - - - +
519S LEU 3.3 0.4 - - - -
520S GLU* 1.3 78.8 - - + +
522S ALA* 1.3 61.9 + - - +
524S GLU* 3.3 20.4 - - - +
525S MET* 3.3 33.4 + - - +
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Residues in contact with ALA 522 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518S ASP 3.9 11.0 + - - +
519S LEU* 3.6 15.0 + - + +
520S GLU 3.4 0.4 - - - -
521S PHE* 1.3 79.0 - - - +
523S LYS* 1.3 56.9 + - - +
525S MET* 3.9 7.0 + - - +
526S ALA* 2.9 26.7 + - - +
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Residues in contact with LYS 523 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519S LEU 2.9 19.3 + - - +
520S GLU* 3.8 21.3 - - - +
521S PHE 3.4 0.2 - - - -
522S ALA* 1.3 75.0 - - - +
524S GLU* 1.3 66.7 + - - +
526S ALA* 3.0 11.8 + - + +
527S GLU* 3.0 58.6 + - - +
186V LYS* 3.9 19.8 - - - +
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Residues in contact with GLU 524 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723N ASP* 5.1 6.1 - - - +
520S GLU* 2.9 33.4 + - + +
521S PHE* 3.3 31.2 - - - +
522S ALA 3.6 0.2 - - - -
523S LYS* 1.3 78.6 - - - +
525S MET* 1.3 60.7 + - + +
527S GLU* 3.2 7.1 + - - +
528S ASP* 3.1 30.4 + - - +
184V LEU* 5.2 8.7 - - - +
185V ASN 5.6 1.6 - - - +
186V LYS* 5.1 18.1 - - + +
189V ILE* 5.1 2.7 - - - +
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Residues in contact with MET 525 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720N LYS 5.6 0.7 - - - +
721N HIS* 3.0 40.4 - - + +
521S PHE 3.3 20.7 + - - +
522S ALA* 4.4 7.0 - - - +
523S LYS 3.2 0.2 - - - -
524S GLU* 1.3 74.5 - - + +
526S ALA* 1.3 60.8 + - - +
527S GLU 3.2 1.8 - - - -
528S ASP* 3.4 14.7 + - + +
529S ASP* 2.8 42.2 + - - +
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Residues in contact with ALA 526 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522S ALA 2.9 21.1 + - - +
523S LYS* 3.0 19.5 + - + +
525S MET* 1.3 75.2 - - - +
527S GLU* 1.3 61.1 + - - +
529S ASP* 3.5 6.0 + - - +
530S ASP* 2.9 37.3 + - - +
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Residues in contact with GLU 527 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523S LYS* 3.0 45.8 + - - +
524S GLU* 3.6 7.9 - - - +
526S ALA* 1.3 76.5 - - - +
528S ASP* 1.3 62.1 + - - +
529S ASP 3.2 1.3 - - - -
530S ASP* 3.1 25.3 - - - +
531S ASP* 2.9 38.1 + - - +
186V LYS* 4.1 11.7 - - - -
189V ILE* 3.8 19.0 - - + +
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Residues in contact with ASP 528 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524S GLU* 3.1 16.1 + - - +
525S MET* 3.4 17.4 + - + +
527S GLU* 1.3 76.0 - - - +
529S ASP* 1.3 63.0 + - - +
531S ASP* 4.0 4.7 - - - +
532S SER* 3.1 18.0 + - - -
533S PHE 3.6 12.7 + - - +
189V ILE* 3.0 31.9 - - - +
193V ILE* 3.3 33.4 - - + +
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Residues in contact with ASP 529 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525S MET* 2.8 28.9 + - - +
526S ALA* 3.9 6.6 - - - +
527S GLU 3.2 0.2 - - - -
528S ASP* 1.3 81.5 - - - +
530S ASP* 1.3 62.4 + - - +
531S ASP 3.5 0.2 - - - -
532S SER* 3.4 20.1 + - - +
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Residues in contact with ASP 530 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526S ALA* 2.9 21.3 + - - +
527S GLU* 3.1 33.9 + - - +
529S ASP* 1.3 79.6 - - - +
531S ASP* 1.3 65.6 + - - +
532S SER* 3.3 3.7 + - - -
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Residues in contact with ASP 531 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527S GLU* 2.9 27.0 + - - +
528S ASP* 4.0 5.3 - - - +
530S ASP* 1.3 80.0 - - - +
532S SER* 1.3 66.5 + - - +
533S PHE* 3.3 34.3 - - + +
189V ILE* 2.6 30.6 - - - +
190V GLN* 3.1 28.0 - - - +
193V ILE* 3.8 5.7 - - + +
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Residues in contact with SER 532 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528S ASP 3.1 11.7 + - - -
529S ASP* 3.4 17.9 + - - +
530S ASP 3.3 4.5 + - - -
531S ASP* 1.3 79.5 - - - +
533S PHE* 1.3 65.6 + - - +
534S PRO* 4.0 5.7 - - - +
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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
------------------------------------------------------------
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