Contacts of the helix formed by residues 527 - 545 (chain A) in PDB entry 4BWM
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 PRO 527 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A LEU* 4.0 18.4 - - + -
523A ARG 5.3 1.1 - - - +
526A HIS* 1.3 103.2 - - + +
528A ILE* 1.3 61.7 + - - +
529A VAL 3.2 0.9 + - - -
530A GLU* 3.8 9.6 + - + +
531A LYS* 3.6 24.7 + - - +
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Residues in contact with ILE 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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474A VAL* 3.8 40.4 - - + +
477A LEU* 3.6 23.2 - - + +
478A ALA* 4.2 9.4 - - + +
482A PHE* 5.3 0.4 - - + -
490A LEU* 6.3 0.2 - - + -
493A VAL* 4.5 7.6 - - + -
494A LEU* 3.9 18.4 - - + -
498A LEU* 3.7 27.6 - - + -
500A LEU* 4.7 0.2 - - + -
526A HIS* 3.0 26.9 + - + +
527A PRO* 1.3 78.7 - - - +
529A VAL* 1.3 69.7 + - + +
531A LYS* 3.3 5.1 + - - +
532A ILE* 3.1 26.0 + - + +
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Residues in contact with VAL 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LEU* 4.6 6.3 - - + -
500A LEU* 3.8 28.7 - - + -
519A LEU* 3.2 46.0 - - + +
522A LEU* 3.5 26.9 - - + +
523A ARG* 4.1 4.3 - - - -
526A HIS* 3.6 12.8 - - + +
527A PRO 3.1 1.2 - - - -
528A ILE* 1.3 83.2 - - + +
530A GLU* 1.3 63.9 + - - +
532A ILE* 3.1 10.4 + - - +
533A LEU* 3.1 23.0 + - + +
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Residues in contact with GLU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ARG* 3.4 38.5 + - + +
526A HIS 4.6 1.0 + - - +
527A PRO* 3.8 8.1 + - + +
529A VAL* 1.3 80.3 - - - +
531A LYS* 1.3 70.8 + - + +
533A LEU* 3.4 11.0 + - + +
534A GLN* 3.1 50.1 + - + +
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Residues in contact with LYS 531 (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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470A LEU* 3.6 30.7 - - + +
473A GLU* 3.8 36.8 + - + +
474A VAL* 3.7 19.7 - - + -
477A LEU* 4.7 3.0 - - + +
527A PRO* 3.6 24.3 + - - +
528A ILE* 3.4 10.5 - - - +
529A VAL 3.1 0.2 - - - -
530A GLU* 1.3 82.6 + - - +
532A ILE* 1.3 59.7 + - - +
534A GLN* 3.4 7.9 + - - +
535A TYR* 2.8 30.5 + - - +
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Residues in contact with ILE 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A VAL* 3.6 24.9 - - + -
484A LEU* 3.5 29.8 - - + +
490A LEU* 4.0 25.6 - - + -
494A LEU* 4.9 5.8 - - + -
519A LEU* 3.8 22.2 - - + -
528A ILE* 3.1 24.9 + - + +
529A VAL* 3.4 8.7 - - - +
531A LYS* 1.3 74.3 - - - +
533A LEU* 1.3 64.9 + - - +
535A TYR* 3.3 5.1 + - + +
536A ARG* 2.9 39.7 + - + +
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Residues in contact with LEU 533 (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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516A ALA* 4.0 25.6 - - + +
519A LEU* 3.7 43.7 - - + +
520A GLU* 3.9 33.4 - - - +
523A ARG* 4.2 20.9 - - + +
529A VAL* 3.1 11.5 + - + +
530A GLU* 3.6 9.6 - - - +
531A LYS 3.3 0.2 - - - -
532A ILE* 1.3 80.4 - - - +
534A GLN* 1.3 64.1 + - + +
536A ARG* 3.4 8.4 + - + +
537A GLU* 3.3 22.5 + - - +
110B G 5.9 0.2 - - - +
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Residues in contact with GLN 534 (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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466A GLU* 4.7 4.6 - - - +
470A LEU* 3.6 31.9 - - + +
523A ARG* 5.2 3.8 - - - +
530A GLU* 3.1 47.9 + - + +
531A LYS* 3.8 7.2 - - - +
533A LEU* 1.3 77.2 - - + +
535A TYR* 1.3 65.4 + - - +
537A GLU* 3.4 3.2 + - - -
538A LEU* 3.0 38.2 + - + +
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Residues in contact with TYR 535 (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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467A ILE* 4.0 29.2 - - + -
470A LEU* 3.7 14.7 - - + +
471A GLU* 4.0 22.2 + - + -
474A VAL* 5.4 1.3 - - + -
484A LEU* 3.7 47.6 - - + +
485A ASN* 3.0 40.2 + - - -
531A LYS 2.8 18.9 + - - +
532A ILE* 3.6 6.5 - - + +
534A GLN* 1.3 76.6 - - - +
536A ARG* 1.3 75.6 + - + +
538A LEU* 4.1 1.9 - - - +
539A THR* 2.8 53.9 + - - +
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Residues in contact with ARG 536 (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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484A LEU 5.1 6.5 + - - +
485A ASN* 6.0 0.2 - - - +
486A SER 5.8 0.2 - - - -
487A ARG* 4.3 13.7 - - - +
490A LEU* 4.4 14.7 - - - +
514A THR* 2.7 49.3 + - - -
515A ARG* 4.5 1.4 - - - +
516A ALA* 4.5 0.4 - - - +
519A LEU* 3.6 15.5 - - - +
532A ILE* 2.9 31.7 + - + +
533A LEU* 3.7 7.4 - - - +
534A GLN 3.2 0.2 - - - -
535A TYR* 1.3 90.5 - - + +
537A GLU* 1.3 62.6 + - - +
539A THR* 3.7 2.4 - - - -
540A LYS* 3.0 25.2 + - - +
109B C 4.2 8.3 + - - -
110B G 3.4 28.5 + - - +
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Residues in contact with GLU 537 (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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533A LEU 3.3 13.5 + - - +
534A GLN* 4.0 3.8 - - - +
536A ARG* 1.3 80.3 - - - +
538A LEU* 1.3 71.3 + - + +
540A LYS* 3.3 5.2 + - - +
541A LEU* 3.0 44.1 + - + +
585A PRO* 3.7 8.0 - - - +
588A THR* 2.7 47.1 + - - +
589A PRO* 5.6 0.3 - - - +
590A LEU* 5.1 3.8 - - + -
111B C 4.5 15.4 + - - +
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Residues in contact with LEU 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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463A VAL* 4.0 12.8 - - + +
466A GLU* 3.5 36.8 - - + -
467A ILE* 3.7 20.9 - - + -
470A LEU* 3.9 14.6 - - + -
534A GLN* 3.0 26.2 + - + +
535A TYR 4.1 0.9 - - - +
537A GLU* 1.3 86.2 - - + +
539A THR* 1.3 62.6 + - - +
541A LEU* 4.3 0.2 - - - +
542A LYS* 2.9 28.4 + - - +
590A LEU* 4.0 27.1 - - + +
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Residues in contact with THR 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ILE* 3.8 16.7 - - + +
485A ASN* 4.2 18.8 - - - +
535A TYR* 2.8 48.4 + - - +
536A ARG* 3.7 3.8 - - - -
538A LEU* 1.3 77.3 - - - +
540A LYS* 1.3 59.3 + - - +
542A LYS* 3.9 1.8 - - - +
543A SER* 3.0 29.0 + - - +
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Residues in contact with LYS 540 (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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536A ARG 3.0 17.5 + - - +
537A GLU* 3.6 6.7 - - - +
538A LEU 3.2 0.2 - - - -
539A THR* 1.3 77.4 - - - +
541A LEU* 1.3 67.5 + - + +
543A SER* 2.9 19.6 + - - +
544A THR* 3.0 43.1 + - + +
545A TYR* 6.3 0.7 - - + -
583A ASN* 5.9 4.0 - - - +
1839A FMT 4.6 8.5 + - - -
110B G 5.7 11.9 - - - +
111B C 5.5 6.1 - - - +
8G G 6.3 0.2 - - - +
9G C 2.8 49.4 + - - +
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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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537A GLU* 3.0 45.0 + - + +
540A LYS* 1.3 82.5 - - + +
542A LYS* 1.3 60.7 + - - +
544A THR* 3.9 2.7 - - - +
545A TYR* 3.0 32.9 + - + +
546A ILE* 2.9 26.0 + - + +
583A ASN 4.3 2.7 - - - +
585A PRO* 3.7 31.2 - - + -
590A LEU* 3.9 31.0 - - + -
591A GLY 4.2 4.3 - - - +
594A ILE* 4.0 11.0 - - + -
111B C 5.8 2.7 - - - +
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Residues in contact with LYS 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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460A SER* 3.8 16.7 + - - -
463A VAL* 3.9 15.3 - - + -
464A ALA* 3.6 28.0 - - - +
467A ILE* 3.9 21.3 - - + -
538A LEU 2.9 19.5 + - - +
539A THR 3.9 3.6 - - - +
541A LEU* 1.3 77.4 - - - +
543A SER* 1.3 63.1 + - - +
544A THR 3.5 0.2 + - - -
546A ILE* 3.6 15.5 + - + +
547A ASP* 2.6 63.0 + - - +
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Residues in contact with SER 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 THR* 3.0 15.2 + - - +
540A LYS* 2.9 19.1 + - - +
542A LYS* 1.3 81.8 - - - +
544A THR* 1.3 64.0 + - - +
547A ASP* 5.0 3.1 - - - +
548A PRO* 3.2 17.8 - - - +
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Residues in contact with THR 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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540A LYS* 3.0 51.9 + - - +
541A LEU* 3.9 1.2 - - - +
543A SER* 1.3 87.5 - - - +
545A TYR* 1.3 90.3 + - - +
548A PRO* 3.4 15.5 - - - +
549A LEU* 5.5 0.2 - - - +
579A PRO* 5.6 1.6 - - - +
1839A FMT 4.2 19.5 + - - +
9G C 5.7 2.5 - - - +
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Residues in contact with TYR 545 (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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540A LYS* 6.3 0.7 - - - -
541A LEU* 3.0 27.5 + - + +
544A THR* 1.3 106.6 + - - +
546A ILE* 1.3 66.7 + - - +
547A ASP 3.4 1.8 - - - -
548A PRO* 3.5 1.5 - - - +
549A LEU* 3.0 45.6 + - + +
579A PRO* 3.9 22.9 - - + -
580A ASN 2.6 30.0 + - - -
583A ASN* 3.1 39.1 - - + +
584A ILE* 3.5 27.6 - - + -
594A ILE* 4.0 16.2 - - + -
1839A FMT 3.4 14.3 - - - -
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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