Contacts of the helix formed by residues 530 - 548 (chain A) in PDB entry 1W6J
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 TYR 530 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TRP* 5.7 3.9 + - - -
500A PHE 2.9 7.2 + - - +
502A THR* 3.7 25.1 - - + -
523A ASP* 4.6 7.4 + - - +
526A ILE 5.2 0.2 + - - -
527A ASP* 4.6 0.8 + - - -
528A TYR* 3.0 57.0 + + + +
529A THR* 1.3 76.0 - - - +
531A VAL* 1.3 61.3 + - - +
532A GLU* 3.6 11.7 - - - +
533A CYS* 4.0 16.4 - - - -
534A THR* 2.7 34.0 + - - -
566A PHE* 3.7 4.5 - - - -
580A SER* 3.3 39.3 - - - -
581A TRP* 3.7 23.7 - + - +
697A ASN* 5.3 2.8 + - - -
698A LYS* 6.0 2.7 - - - -
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Residues in contact with VAL 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A TYR* 1.3 73.1 - - - +
532A GLU* 1.3 70.7 + - + +
534A THR* 3.6 1.3 - - - -
535A SER* 2.7 33.6 + - - -
566A PHE* 3.9 10.0 - - + -
567A CYS* 3.8 22.2 - - + -
570A GLN* 4.9 7.9 - - + +
577A TRP* 3.7 37.2 - - + +
578A GLU 4.3 8.7 - - - +
588A GLY* 4.0 16.2 - - - +
591A PHE 4.6 0.2 - - - -
592A GLY* 4.1 17.7 - - - +
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Residues in contact with GLU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASP* 5.3 4.0 - - - +
530A TYR* 3.6 17.3 - - - +
531A VAL* 1.3 87.3 + - + +
533A CYS* 1.3 62.6 + - - +
536A ALA* 3.0 30.3 + - - +
578A GLU 4.4 1.4 - - - +
579A GLY* 3.5 8.9 - - - -
580A SER* 2.8 31.7 + - - -
581A TRP* 3.3 23.7 + - + -
587A TYR* 3.5 14.8 - - + +
588A GLY* 4.7 1.8 - - - -
591A PHE* 3.5 46.4 - - + -
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Residues in contact with CYS 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A SER* 3.6 8.1 - - - +
455A ASP* 3.7 29.2 - - - -
500A PHE* 3.4 20.0 - - - +
501A ALA 3.5 18.4 - - - +
502A THR* 4.2 0.2 - - - -
530A TYR* 3.5 24.1 + - - +
531A VAL 3.4 0.2 - - - -
532A GLU* 1.3 79.8 - - - +
534A THR* 1.3 56.6 + - - +
536A ALA* 3.4 1.6 + - - +
537A VAL* 3.0 35.2 + - - +
581A TRP* 4.6 4.7 - - - -
1733A R71 3.8 16.6 - - - -
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Residues in contact with THR 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLY 4.0 13.7 - - - +
499A GLY* 3.3 5.5 - - - -
500A PHE* 2.9 30.9 + - + +
530A TYR 2.7 22.7 + - - -
531A VAL* 3.6 4.5 - - - -
533A CYS* 1.3 76.3 - - - +
535A SER* 1.3 63.7 + - - +
537A VAL* 3.3 3.1 + - - +
538A MET* 2.9 34.0 + - + +
563A GLY* 3.8 24.0 - - - +
566A PHE* 3.3 17.1 - - + -
567A CYS* 4.0 5.4 - - - -
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Residues in contact with SER 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A VAL* 2.7 23.0 + - - -
532A GLU 3.9 3.1 - - - -
534A THR* 1.3 74.8 - - - +
536A ALA* 1.3 56.0 + - - +
538A MET* 3.4 4.2 + - - +
539A GLN* 2.8 49.1 + - - +
567A CYS* 4.6 0.6 - - - -
591A PHE* 2.7 35.4 + - - -
595A ALA* 3.7 21.7 + - - +
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Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASP* 4.1 19.1 - - + -
458A ALA* 3.4 14.0 - - + +
459A GLU* 3.4 26.1 - - - +
462A LYS* 5.1 2.3 - - - +
532A GLU 3.0 18.3 + - - +
533A CYS 3.7 3.8 - - - +
535A SER* 1.3 73.5 - - - +
537A VAL* 1.3 66.2 + - - +
539A GLN* 3.5 11.8 + - - +
540A ALA* 3.1 18.5 + - - +
591A PHE* 4.4 6.0 - - + -
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Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A SER* 4.0 25.4 - - - +
455A ASP 4.9 0.2 - - - +
458A ALA* 3.9 6.5 - - + -
490A LEU* 4.0 18.8 - - + -
500A PHE* 3.6 48.7 - - + -
533A CYS 3.0 21.3 + - - +
534A THR 3.7 4.0 - - - +
536A ALA* 1.3 72.7 - - - +
538A MET* 1.3 62.9 + - + +
540A ALA* 3.2 2.5 + - - +
541A LEU* 2.9 46.9 + - + +
559A THR* 5.1 0.2 - - + -
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Residues in contact with MET 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A PHE* 5.8 2.5 - - + -
534A THR* 2.9 27.3 + - + +
535A SER 3.6 4.7 - - - +
537A VAL* 1.3 78.7 - - + +
539A GLN* 1.3 56.6 + - - +
541A LEU* 5.2 0.2 - - - -
542A LYS* 2.8 33.2 + - - +
559A THR* 4.9 2.5 - - + +
560A LEU* 3.3 28.6 - - + +
563A GLY* 3.5 30.7 - - - +
564A LEU* 3.5 20.4 - - - +
567A CYS* 4.3 1.3 - - - -
595A ALA* 4.0 25.6 - - + +
598A CYS* 4.3 6.5 - - - -
599A MET* 3.5 31.9 - - + -
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Residues in contact with GLN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLU* 5.4 1.5 + - - -
462A LYS* 3.1 34.1 + - + +
535A SER* 2.8 38.5 + - - +
536A ALA* 3.8 10.0 - - - +
538A MET* 1.3 78.5 - - - +
540A ALA* 1.3 61.5 + - - +
542A LYS* 3.6 3.5 + - - +
543A TYR* 3.1 24.4 + - - +
591A PHE* 4.5 7.5 - - - -
594A GLU* 3.5 31.9 - - - +
598A CYS* 4.1 26.4 - - + -
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Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ALA* 3.3 37.7 - - + +
461A LEU* 4.4 15.4 - - + +
462A LYS* 3.7 13.2 - - + +
465A LEU* 4.5 2.1 - - - +
490A LEU* 4.7 2.5 - - + -
536A ALA 3.1 17.0 + - - +
537A VAL* 3.7 2.5 - - - +
539A GLN* 1.3 77.7 - - - +
541A LEU* 1.3 59.0 + - - +
543A TYR* 3.4 3.1 + - - +
544A PHE* 3.0 28.3 + - - +
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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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461A LEU* 5.4 0.4 - - + -
487A VAL* 4.0 33.2 - - + -
490A LEU* 4.2 21.8 - - + -
491A LEU* 4.2 13.9 - - + -
500A PHE* 5.2 0.4 - - + -
537A VAL* 2.9 38.7 + - + +
538A MET 4.1 1.8 - - - +
540A ALA* 1.3 72.6 - - - +
542A LYS* 1.3 61.2 + - - +
544A PHE* 3.7 4.4 - - - +
545A HIS* 2.8 33.4 + - - +
556A ILE* 4.1 22.6 - - + +
559A THR* 3.8 26.5 - - + -
560A LEU* 4.3 6.7 - - + -
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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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538A MET 2.8 20.1 + - - +
539A GLN* 3.7 7.4 - - - +
541A LEU* 1.3 76.3 - - - +
543A TYR* 1.3 58.7 + - - +
545A HIS* 3.5 7.9 + - + +
546A LYS* 3.1 27.0 + - - +
560A LEU* 4.0 25.2 - - + +
598A CYS* 3.1 36.2 + - + +
599A MET* 4.6 16.9 - - - +
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Residues in contact with TYR 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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462A LYS* 4.7 13.2 - - + -
465A LEU* 3.5 38.3 - - + +
466A LEU* 3.5 37.3 - - + +
469A GLU* 2.6 41.2 + - + +
470A LYS* 5.4 0.3 - - - -
539A GLN 3.1 15.2 + - - +
540A ALA* 3.8 5.6 - - - +
541A LEU 3.2 0.2 - - - -
542A LYS* 1.3 77.2 - - - +
544A PHE* 1.3 66.3 + - - +
546A LYS* 3.4 32.3 + - + +
547A ARG* 3.5 17.8 + - + +
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Residues in contact with PHE 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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461A LEU* 4.7 2.5 - - + -
465A LEU* 3.9 22.3 - - + +
483A LEU* 4.3 18.8 - - + -
484A CYS* 4.2 10.8 - - - -
487A VAL* 3.7 32.3 - - + -
540A ALA 3.0 18.5 + - - +
541A LEU* 3.7 5.6 - - - +
543A TYR* 1.3 76.8 - - - +
545A HIS* 1.3 54.2 + - - +
547A ARG* 3.1 2.9 + - - -
548A PHE* 2.8 78.5 + + + -
551A HIS* 3.6 33.4 - - + -
556A ILE* 4.0 19.7 - - + -
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Residues in contact with HIS 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU 2.8 21.7 + - - +
542A LYS* 3.6 9.6 - - + +
544A PHE* 1.3 76.5 - - - +
546A LYS* 1.3 66.0 + - - +
548A PHE 4.4 4.5 + - - -
549A PRO* 3.3 40.2 - - + +
553A ALA* 3.6 40.5 - - + -
556A ILE* 4.0 21.8 - - + +
557A ARG* 3.0 38.2 + - + +
560A LEU* 5.2 6.7 - - + -
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Residues in contact with LYS 546 (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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469A GLU* 4.3 22.2 + - - -
542A LYS 3.1 14.4 + - - +
543A TYR* 3.6 28.3 - - + +
544A PHE 3.3 0.2 - - - -
545A HIS* 1.3 79.3 - - - +
547A ARG* 1.3 65.1 + - - +
549A PRO* 3.7 12.0 - - - +
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Residues in contact with ARG 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 5.3 9.8 + - + +
468A GLN* 4.3 12.9 + - - +
469A GLU* 3.9 52.7 + - - +
543A TYR* 3.5 16.1 + - + +
544A PHE* 3.1 4.4 + - - +
546A LYS* 1.3 84.2 - - + +
548A PHE* 1.3 93.7 + - + +
549A PRO* 3.6 5.9 - - - +
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Residues in contact with PHE 548 (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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465A LEU* 4.1 22.4 - - + -
480A ARG* 3.9 39.9 - - + -
483A LEU* 4.1 17.9 - - + -
484A CYS* 5.9 0.2 - - - -
544A PHE* 2.8 50.7 + + + +
545A HIS* 3.5 7.4 + - - +
547A ARG* 1.3 106.4 - - + +
549A PRO* 1.3 65.9 - - - +
550A GLU* 3.1 17.3 + - - +
551A HIS* 3.1 17.5 + - + +
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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