Contacts of the helix formed by residues 528 - 545 (chain A) in PDB entry 3S51
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 GLN 528 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A ALA* 3.3 10.7 - - + +
527A SER* 1.3 83.9 + - - +
529A LEU* 1.3 73.0 + - - +
530A ASP* 4.1 15.8 - - + +
531A ALA* 3.5 23.7 + - + +
532A ARG* 3.5 2.4 + - - -
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Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A SER 3.3 2.2 + - - -
528A GLN* 1.3 76.3 + - - +
530A ASP* 1.3 67.5 + - - +
532A ARG* 2.8 26.4 + - - +
533A LYS* 2.9 46.7 + - - +
597A GLN* 3.5 33.4 - - + +
599A ASP* 4.7 7.4 - - + +
600A ILE* 3.5 26.7 - - + +
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Residues in contact with ASP 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A THR 5.7 0.4 - - - -
490A LEU 6.0 1.8 - - - +
491A PRO* 5.3 1.4 - - + +
492A LEU* 3.8 30.0 + - - +
528A GLN* 3.5 11.9 - - + +
529A LEU* 1.3 80.5 - - - +
531A ALA* 1.3 61.9 + - - +
533A LYS* 3.3 22.4 + - - +
534A SER* 3.0 26.4 + - - -
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Residues in contact with ALA 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A THR* 3.8 34.9 + - + +
523A ALA* 4.4 3.3 - - - +
526A ALA* 3.4 28.9 - - + -
528A GLN* 3.5 17.1 + - + +
529A LEU 3.0 0.2 + - - -
530A ASP* 1.3 78.1 - - - +
532A ARG* 1.3 56.1 + - - +
534A SER* 3.1 10.2 + - - -
535A ALA* 3.0 24.9 + - - +
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Residues in contact with ARG 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ALA 4.1 1.3 - - - +
524A MET* 3.2 34.7 - - - +
525A PHE 5.3 0.2 - - - -
526A ALA 3.1 22.7 + - - +
527A SER* 3.1 19.9 + - - +
528A GLN 3.5 1.4 + - - -
529A LEU* 2.8 30.5 + - - +
531A ALA* 1.3 73.4 - - - +
533A LYS* 1.3 60.2 + - - +
535A ALA* 3.1 8.0 + - - +
536A VAL* 2.9 34.9 + - + +
596A GLN* 2.9 50.5 + - - +
597A GLN* 3.1 25.2 + - - +
600A ILE* 3.7 19.0 - - + +
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Residues in contact with LYS 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 3.6 28.7 - - + +
529A LEU* 2.9 43.2 + - + +
530A ASP* 3.5 24.9 + - - +
531A ALA 3.2 0.2 - - - -
532A ARG* 1.3 76.6 - - - +
534A SER* 1.3 59.2 + - - +
537A ALA* 3.3 14.2 + - - +
599A ASP* 2.9 34.5 + - - +
600A ILE* 4.1 7.3 - - + +
603A MET* 3.2 49.9 - - + +
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Residues in contact with SER 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU* 4.1 19.0 + - - -
488A THR* 5.6 0.2 - - - -
490A LEU 4.5 2.6 + - - -
492A LEU* 3.5 24.7 + - - +
495A VAL* 3.8 30.8 - - - +
520A LEU* 4.7 0.9 - - - +
530A ASP 3.0 13.8 + - - -
531A ALA* 3.2 10.2 - - - -
532A ARG 3.1 0.2 - - - -
533A LYS* 1.3 73.2 - - - +
535A ALA* 1.3 66.4 - - - +
536A VAL 3.1 1.8 - - - -
537A ALA* 2.8 15.9 + - - +
538A GLY* 2.9 10.9 + - - -
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Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU* 4.4 0.8 - - - +
520A LEU* 3.9 16.9 - - - +
523A ALA* 3.5 31.0 - - + -
524A MET* 3.7 28.3 - - + +
531A ALA 3.0 8.2 + - - +
532A ARG* 3.1 7.8 + - - +
534A SER* 1.3 74.8 - - - +
536A VAL* 1.3 61.8 + - - +
538A GLY* 3.2 2.6 + - - -
539A PHE* 3.0 26.3 + - - -
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A MET* 4.2 9.9 - - - -
532A ARG* 2.9 20.5 + - + +
535A ALA* 1.3 73.6 - - - +
537A ALA* 1.3 67.0 + - - +
538A GLY 3.0 0.3 + - - -
539A PHE* 3.1 1.9 + - - +
540A LEU* 2.8 47.6 + - + +
590A LEU* 3.8 26.4 - - + +
593A SER* 4.4 18.6 - - - +
600A ILE* 4.6 4.3 - - + -
603A MET* 3.6 30.5 - - + -
604A LEU* 4.5 8.7 - - + -
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Residues in contact with ALA 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 4.4 2.2 - - + -
495A VAL* 5.7 0.4 - - + -
496A GLN* 3.5 38.6 - - + +
499A LEU* 4.3 6.7 - - + +
500A LYS* 5.0 3.9 + - - +
533A LYS 3.3 11.4 + - - +
534A SER* 2.8 14.7 + - - +
536A VAL* 1.3 77.3 - - - +
538A GLY* 1.3 56.6 + - - +
540A LEU* 3.8 7.9 - - - +
541A LEU* 3.0 30.0 + - - +
603A MET* 5.0 3.4 - - - -
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Residues in contact with GLY 538 (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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499A LEU* 3.5 24.0 - - - +
516A LEU* 5.4 1.1 - - - +
520A LEU* 3.5 18.4 - - - -
534A SER 2.9 11.0 + - - -
535A ALA 3.6 3.8 - - - -
536A VAL 3.0 0.4 - - - -
537A ALA* 1.3 73.9 - - - +
539A PHE* 1.3 59.3 + - - +
541A LEU* 3.0 5.5 + - - +
542A LEU* 2.8 29.3 + - - +
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Residues in contact with PHE 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ILE* 4.3 12.6 - - + -
520A LEU* 3.6 17.6 - - + +
521A ARG* 3.6 30.1 - - + -
524A MET* 3.6 34.3 - - + -
535A ALA 3.0 18.5 + - - +
536A VAL 3.8 4.3 - - - +
538A GLY* 1.3 73.1 - - - +
540A LEU* 1.3 64.8 + - - +
542A LEU* 2.9 18.8 + - + +
543A LEU* 2.8 28.6 + - - +
586A ILE* 3.7 44.0 - - + -
589A SER* 4.0 15.7 - - - -
590A LEU* 4.3 10.1 - - + -
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A VAL* 2.8 38.8 + - + +
537A ALA* 3.8 7.6 - - - +
539A PHE* 1.3 72.6 - - - +
541A LEU* 1.3 60.9 + - - +
543A LEU* 3.5 8.0 + - + +
544A LYS* 3.1 34.8 + - - +
590A LEU* 4.4 17.4 - - + +
603A MET* 3.7 17.9 - - + +
604A LEU* 4.6 6.7 - - + -
607A GLY* 3.5 31.9 - - - -
608A PHE* 4.1 4.5 - - + +
611A VAL* 3.5 27.5 - - + +
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Residues in contact with LEU 541 (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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499A LEU* 3.5 32.1 - - + +
500A LYS* 3.5 44.4 - - + +
503A GLN* 3.6 17.5 - - + +
506A LEU* 4.2 17.9 - - + -
516A LEU* 5.8 0.9 - - + -
537A ALA 3.0 19.0 + - - +
538A GLY* 3.0 6.5 + - - +
540A LEU* 1.3 74.6 - - - +
542A LEU* 1.3 67.7 + - + +
544A LYS* 3.1 21.5 + - + +
545A ASN* 3.2 35.5 + - - +
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Residues in contact with LEU 542 (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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506A LEU* 4.5 5.8 - - + -
513A ARG* 4.8 4.3 - - + -
516A LEU* 4.3 20.6 - - + -
517A ILE* 3.6 37.7 - - + -
520A LEU* 3.7 24.0 - - + -
538A GLY 2.8 14.9 + - - +
539A PHE* 3.2 19.1 - - + +
541A LEU* 1.3 74.7 - - - +
543A LEU* 1.3 62.0 + - - +
545A ASN 3.0 11.8 + - - -
546A PHE* 3.0 48.3 + - + +
582A PHE* 4.6 5.6 - - + -
586A ILE* 4.5 10.5 - - + -
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Residues in contact with LEU 543 (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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539A PHE 2.8 18.1 + - - +
540A LEU* 3.7 7.9 - - + +
542A LEU* 1.3 73.0 - - - +
544A LYS* 1.3 61.9 + - - +
546A PHE* 3.7 15.3 + - - +
565A GLN* 3.8 8.8 + - - +
582A PHE* 5.0 1.8 - - + -
583A CYS* 4.0 35.7 - - - +
586A ILE* 3.7 37.9 - - + -
587A ILE* 3.8 19.1 - - + -
590A LEU* 4.1 13.9 - - + -
608A PHE* 5.9 2.0 - - + -
611A VAL* 3.9 29.5 - - + +
614A ARG* 5.6 0.2 - - - +
615A ASN* 4.6 4.0 + - - +
618A LEU* 4.1 8.3 - - + -
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Residues in contact with LYS 544 (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 LYS* 3.5 24.7 - - - +
503A GLN* 5.1 3.8 - - - +
540A LEU* 3.1 26.2 - - - +
541A LEU* 3.4 13.0 - - + +
542A LEU 3.1 0.8 - - - -
543A LEU* 1.3 78.3 - - - +
545A ASN* 1.3 63.6 + - - +
546A PHE 3.6 0.2 - - - -
563A VAL* 4.9 0.7 - - - +
565A GLN* 3.1 10.8 - - - +
607A GLY* 5.3 2.4 - - - -
610A ASP* 3.8 32.2 + - + +
611A VAL* 4.3 17.9 - - + +
614A ARG* 2.9 57.9 - - - +
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Residues in contact with ASN 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A GLN* 2.7 38.8 + - - +
506A LEU* 5.2 1.4 - - + +
507A LYS* 3.4 32.0 + - + +
541A LEU* 3.2 29.7 + - - +
542A LEU 3.0 3.2 + - - +
544A LYS* 1.3 81.9 - - - +
546A PHE* 1.3 83.5 + - + +
563A VAL* 5.7 1.9 - - - +
565A GLN* 3.2 10.3 - - - +
566A VAL* 2.9 23.4 + - - +
614A ARG* 5.7 1.0 - - - -
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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