Contacts of the helix formed by residues 508 - 526 (chain A) in PDB entry 4E9F
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 LEU 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A ASN* 3.9 20.6 - - + +
468A ARG* 4.0 8.5 - - + -
507A GLY* 1.4 68.0 - - - +
509A TYR* 1.3 58.0 + - - +
510A ASP 3.6 0.2 - - - -
511A LEU* 4.5 5.6 - - + -
512A ARG* 3.1 46.6 + - + +
8C G 4.1 18.2 - - + +
5D C 3.6 39.7 - - + +
6D G 2.8 77.3 + - + +
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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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500A SER* 3.2 35.1 + - - +
503A LEU* 3.7 21.0 - - - +
504A LYS* 3.6 44.2 - - + -
507A GLY* 3.0 9.6 + - - -
508A LEU* 1.3 74.8 - - - +
510A ASP* 1.3 88.5 + - - +
513A ALA* 3.1 26.7 + - - +
6D G 3.3 33.3 + - - -
7D C 2.9 35.2 + - - -
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A TRP* 3.3 31.5 - - + -
500A SER* 2.7 26.5 + - - -
504A LYS* 4.5 3.7 + - - -
509A TYR* 1.3 86.8 - - - +
511A LEU* 1.3 66.7 + - - +
513A ALA* 3.4 1.0 + - - +
514A LYS* 3.1 34.1 + - - +
6D G 2.8 18.7 + - - +
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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
----------------------------------------------------------
508A LEU* 4.1 14.6 - - + +
510A ASP* 1.3 78.0 - - - +
512A ARG* 1.3 62.9 + - + +
514A LYS* 3.4 7.2 + - - +
515A THR* 3.0 34.7 + - - +
8C G 3.4 15.9 - - - +
9C C 5.1 1.3 - - - +
10C A 6.1 1.6 - - - +
4D G 4.3 10.5 - - - +
5D C 3.3 39.7 - - - +
6D G 2.9 14.0 + - - +
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Residues in contact with ARG 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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464A ILE* 2.9 37.3 + - + -
465A PHE* 2.8 31.7 + - - +
467A ASN* 3.3 19.0 + - + +
469A THR* 3.0 23.6 + - - -
503A LEU* 3.9 17.4 - - + +
506A LEU* 3.4 21.1 + - - +
507A GLY 3.0 22.8 + - - -
508A LEU* 3.1 29.4 + - + +
511A LEU* 1.3 82.2 - - + +
513A ALA* 1.3 60.0 + - - +
515A THR* 3.5 7.5 - - - +
516A ILE* 2.9 33.8 + - + +
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Residues in contact with ALA 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A TRP* 3.2 31.0 - - + +
499A VAL* 3.8 18.1 - - + +
500A SER* 3.5 13.0 - - - +
503A LEU* 3.7 1.9 - - + +
509A TYR 3.1 23.0 + - - +
510A ASP 3.8 3.4 - - - +
511A LEU 3.3 0.2 - - - -
512A ARG* 1.3 76.9 - - - +
514A LYS* 1.3 61.8 + - - +
516A ILE* 3.4 1.9 + - - +
517A VAL* 3.2 28.1 + - - +
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Residues in contact with LYS 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A TRP* 3.5 59.7 - - + +
510A ASP* 3.1 22.7 + - - +
511A LEU* 3.6 5.8 - - - +
513A ALA* 1.3 76.6 - - - +
515A THR* 1.4 62.3 + - - +
517A VAL* 3.5 3.0 + - - +
518A LYS* 3.1 24.1 + - - +
535A HIS* 5.3 1.6 - - - -
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Residues in contact with THR 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ILE* 4.3 21.5 - - + -
511A LEU* 3.0 24.5 + - - +
512A ARG* 3.3 14.9 + - + +
514A LYS* 1.4 77.0 - - - +
516A ILE* 1.3 52.6 + - - +
518A LYS* 3.3 1.0 + - - +
519A PHE* 2.8 37.6 + - - +
535A HIS* 4.0 18.7 + - - +
536A GLY* 3.5 32.9 - - - +
10C A 5.9 0.7 - - - -
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Residues in contact with ILE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ILE* 3.9 19.7 - - + -
464A ILE* 4.1 20.9 - - + -
465A PHE* 3.8 28.3 - - + -
481A PHE* 3.6 29.4 - - + -
491A ALA* 4.5 5.2 - - + -
499A VAL* 4.3 11.7 - - + -
503A LEU* 4.0 18.8 - - + -
512A ARG* 2.9 23.4 + - + +
513A ALA* 3.4 4.7 + - - +
515A THR* 1.3 71.3 - - - +
517A VAL* 1.3 62.2 + - + +
519A PHE* 4.0 4.9 - - - +
520A SER* 2.7 37.5 + - - +
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Residues in contact with VAL 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ALA 3.7 18.8 - - - +
492A ARG* 3.8 23.0 - - - +
494A ALA* 3.7 26.2 - - + +
496A TRP* 4.3 16.6 - - + +
499A VAL* 4.5 6.3 - - + -
513A ALA 3.2 15.9 + - - +
514A LYS* 3.9 5.4 - - - +
516A ILE* 1.3 78.2 - - + +
518A LYS* 1.3 61.9 + - - +
520A SER* 3.4 2.1 + - - -
521A ASP* 3.1 23.5 + - + +
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Residues in contact with LYS 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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514A LYS 3.1 17.5 + - - +
515A THR 3.9 2.0 - - - +
517A VAL* 1.3 75.8 - - - +
519A PHE* 1.3 65.3 + - - +
521A ASP* 3.2 7.5 + - + +
522A GLU* 3.0 47.2 + - + +
535A HIS* 3.6 40.6 + - + +
11C G 4.2 9.1 + - - -
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Residues in contact with PHE 519 (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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457A TRP* 3.4 23.8 - + - -
460A LEU* 3.5 34.1 - - + -
461A ILE* 3.9 23.3 - - + -
464A ILE* 4.0 15.0 - - + -
515A THR* 2.8 23.3 + - + +
516A ILE* 4.0 1.1 - - - +
518A LYS* 1.3 74.0 - - - +
520A SER* 1.3 54.9 + - - +
522A GLU* 3.2 5.5 + - - +
523A TYR* 2.7 45.2 + + + +
534A LEU* 3.7 26.7 - - + -
535A HIS 3.2 23.7 + - - +
537A ILE* 3.5 23.8 - - + -
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Residues in contact with SER 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A TRP* 2.9 33.0 + - - +
461A ILE* 4.1 3.3 - - - +
488A ALA* 3.7 18.3 - - - +
491A ALA* 3.3 18.0 - - - +
492A ARG* 3.9 5.4 - - - -
516A ILE 2.7 22.8 + - - -
517A VAL 3.8 3.8 - - - -
519A PHE* 1.3 76.9 - - - +
521A ASP* 1.3 63.7 + - - +
523A TYR* 3.4 4.6 + - - +
524A LEU* 3.4 24.4 + - - +
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Residues in contact with ASP 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ARG* 2.8 47.6 + - + +
517A VAL* 3.1 14.8 + - + +
518A LYS* 3.5 12.2 - - - +
519A PHE 3.2 0.2 - - - -
520A SER* 1.3 78.6 - - - +
522A GLU* 1.4 60.9 + - - +
524A LEU* 3.3 0.7 + - - +
525A THR* 2.9 42.0 + - - +
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Residues in contact with GLU 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 LYS* 3.0 43.9 + - + +
519A PHE* 3.7 4.0 - - - +
521A ASP* 1.4 76.3 - - + +
523A TYR* 1.3 68.1 + - - +
525A THR* 4.0 7.2 - - - +
526A LYS* 2.9 44.4 + - + +
533A GLU 4.3 3.6 - - - +
534A LEU* 3.6 20.7 - - + +
535A HIS* 2.9 33.7 + - - +
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Residues in contact with TYR 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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455A ASP* 4.7 1.0 + - - -
456A PRO* 3.5 18.0 - - - +
457A TRP* 3.2 44.3 + + + +
460A LEU* 4.2 6.7 - - + -
488A ALA* 4.1 9.0 - - + -
519A PHE* 2.7 38.9 + + + +
520A SER* 3.5 10.5 - - - +
521A ASP 3.4 0.2 - - - -
522A GLU* 1.3 71.5 - - - +
524A LEU* 1.3 77.9 + - + +
526A LYS 4.2 1.0 - - - +
528A TRP* 2.9 52.5 + + - -
534A LEU* 3.8 15.1 - - + +
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ALA* 3.6 18.6 - - + +
489A GLU* 3.5 58.6 - - + +
492A ARG* 4.0 15.7 - - - +
520A SER 3.4 1.8 + - - +
521A ASP 3.3 6.6 + - - +
522A GLU 3.2 0.4 - - - -
523A TYR* 1.3 96.1 - - + +
525A THR* 1.3 65.1 + - + +
526A LYS 3.8 1.7 - - - +
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Residues in contact with THR 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ARG* 3.7 16.4 - - - +
521A ASP* 2.9 43.4 + - - +
522A GLU* 4.0 2.6 - - - +
524A LEU* 1.3 83.5 - - + +
526A LYS* 1.4 64.3 + - - +
527A GLN 4.1 0.3 + - - -
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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
----------------------------------------------------------
522A GLU* 2.9 36.5 + - + +
523A TYR 4.2 2.8 - - - +
524A LEU 4.6 1.4 - - - +
525A THR* 1.4 81.9 + - - +
527A GLN* 1.3 77.1 + - + +
528A TRP* 3.3 18.2 + - - -
533A GLU* 3.8 31.3 + - + +
534A LEU* 3.9 20.4 - - + -
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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
------------------------------------------------------------
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