Contacts of the helix formed by residues 534 - 551 (chain A) in PDB entry 2W3C
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 534 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A ILE* 3.5 12.4 - - - +
491A ARG* 3.4 30.4 + - - +
525A GLN* 4.6 10.3 - - - +
530A LEU* 3.5 31.6 + - + +
532A GLU 3.3 0.2 - - - -
533A GLU* 1.3 78.1 - - + +
535A GLN* 1.3 63.1 + - - +
536A LEU 3.2 1.8 - - - -
537A VAL* 3.3 33.0 + - + +
538A GLN* 3.1 26.7 + - + +
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Residues in contact with GLN 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ASN* 6.1 0.4 - - - +
530A LEU 4.2 1.4 + - - -
531A GLY 3.5 25.3 + - - +
532A GLU* 3.4 21.4 - - - +
533A GLU 3.2 0.4 - - - -
534A GLU* 1.3 79.2 - - - +
536A LEU* 1.3 62.5 + - - +
538A GLN* 3.5 12.5 + - - +
539A GLY 3.0 18.0 + - - -
583A PHE* 3.3 62.0 - - + +
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Residues in contact with LEU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ILE* 4.7 6.5 - - + -
492A VAL* 3.7 21.1 - - + -
532A GLU 4.6 1.0 + - - +
533A GLU 3.8 10.1 + - - +
534A GLU 3.2 0.8 - - - -
535A GLN* 1.3 77.8 - - - +
537A VAL* 1.3 64.0 + - - +
539A GLY* 3.1 3.8 + - - -
540A LEU* 3.1 30.6 + - + +
583A PHE* 4.8 5.4 - - - +
584A ILE* 4.3 16.4 - - - -
587A HIS* 4.0 27.6 - - + +
608A ILE* 3.6 35.2 - - + -
609A PHE* 3.8 26.2 - - + -
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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
----------------------------------------------------------
482A LEU* 5.9 0.9 - - + -
488A ILE* 4.0 27.4 - - + +
491A ARG* 3.9 29.4 - - + +
492A VAL* 4.1 15.0 - - + +
495A LEU* 3.8 20.4 - - + -
521A PHE* 6.4 1.1 - - + -
525A GLN* 4.3 9.2 - - - +
533A GLU 5.6 0.2 - - - +
534A GLU* 3.3 28.2 + - - +
536A LEU* 1.3 75.0 - - - +
538A GLN* 1.3 61.8 + - - +
540A LEU* 3.2 5.0 + - - +
541A CYS* 3.1 27.8 + - - -
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Residues in contact with GLN 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLN* 2.7 33.5 + - - +
526A ILE* 3.4 22.1 + - - +
528A GLU 2.6 30.8 + - - +
530A LEU* 4.2 15.6 + - + +
534A GLU* 3.1 22.2 + - + +
535A GLN* 3.6 22.7 + - - +
537A VAL* 1.3 75.0 - - - +
539A GLY* 1.3 62.4 - - - +
541A CYS* 3.4 9.5 + - - +
542A ALA* 3.1 20.3 + - - +
580A LYS* 3.6 29.5 + - + +
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Residues in contact with GLY 539 (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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535A GLN 3.0 13.5 + - - -
536A LEU 3.5 3.8 - - - -
538A GLN* 1.3 75.6 - - - +
540A LEU* 1.3 57.9 + - - +
542A ALA* 3.4 4.7 + - - +
543A LEU 3.0 21.8 + - - -
580A LYS 2.9 29.1 + - - -
581A LEU* 4.1 1.9 - - - -
583A PHE* 4.7 0.7 - - - -
584A ILE* 3.4 19.5 - - - +
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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
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492A VAL* 3.7 44.2 - - + +
495A LEU* 3.7 27.5 - - + +
496A MET* 4.7 2.5 - - + -
499A CYS* 3.9 6.6 - - - -
536A LEU* 3.1 26.9 + - + +
537A VAL* 3.2 6.2 + - - +
539A GLY* 1.3 73.4 - - - +
541A CYS* 1.3 60.5 + - - +
543A LEU* 3.3 5.7 + - + +
544A LEU* 2.9 27.7 + - - +
584A ILE* 4.0 13.5 - - + -
609A PHE* 5.7 1.6 - - + -
613A PHE* 3.2 42.4 - - + -
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Residues in contact with CYS 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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482A LEU* 5.5 0.4 - - - -
495A LEU* 4.2 16.4 - - - +
521A PHE* 4.6 8.7 - - - -
522A LEU* 3.9 26.7 - - + +
525A GLN* 4.2 19.5 - - + -
526A ILE* 3.6 18.4 - - + +
537A VAL* 3.1 22.9 + - - -
538A GLN* 3.4 9.9 - - - +
540A LEU* 1.3 74.2 - - - +
542A ALA* 1.3 54.3 + - - +
544A LEU* 3.2 4.6 + - - +
545A LEU* 2.7 36.0 + - - +
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Residues in contact with ALA 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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526A ILE* 3.5 17.3 - - + +
538A GLN 3.1 9.7 + - - +
539A GLY 3.4 9.4 + - - +
541A CYS* 1.3 75.1 - - - +
543A LEU* 1.3 55.1 + - - +
546A GLY* 2.7 32.7 + - - -
577A PHE* 3.4 30.2 - - + +
580A LYS 4.5 0.2 - - - -
581A LEU* 4.0 27.0 - - + +
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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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499A CYS* 3.9 9.2 - - - -
539A GLY 3.0 14.3 + - - +
540A LEU* 3.4 8.5 - - + +
542A ALA* 1.3 73.7 - - - +
544A LEU* 1.3 56.9 + - - +
546A GLY* 3.4 1.5 + - - -
547A ILE* 2.8 43.2 + - + +
581A LEU* 3.7 18.2 - - + +
584A ILE* 3.7 15.9 - - + -
613A PHE* 3.6 35.2 - - + -
616A LEU* 4.5 3.8 - - + -
617A VAL* 3.9 17.5 - - + -
620A LEU* 4.6 11.9 - - + -
621A GLU* 5.1 4.3 - - + +
624A ILE* 3.8 21.5 - - + -
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Residues in contact with LEU 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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482A LEU* 5.2 0.7 - - + -
495A LEU* 3.9 17.0 - - + -
498A LEU* 3.6 45.8 - - + +
499A CYS* 3.9 12.5 - - - +
502A LEU* 3.9 25.8 - - + -
512A PHE* 3.9 21.8 - - + -
522A LEU* 4.2 15.3 - - + -
540A LEU 2.9 13.9 + - - +
541A CYS* 3.2 10.0 + - - +
543A LEU* 1.3 73.2 - - - +
545A LEU* 1.3 66.4 + - - +
547A ILE* 3.1 6.9 + - + +
548A SER* 2.9 24.2 + - - -
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Residues in contact with LEU 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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519A VAL* 4.5 22.7 - - + -
522A LEU* 3.9 18.7 - - + +
523A THR* 4.3 19.3 - - - +
526A ILE* 3.8 21.3 - - + -
541A CYS 2.7 19.8 + - - +
542A ALA 3.8 3.1 - - - +
544A LEU* 1.3 72.4 - - - +
546A GLY* 1.3 58.5 + - - +
548A SER* 3.0 34.1 - - - -
549A ILE* 3.2 10.7 + - + +
564A LEU* 4.6 14.6 - - + +
567A LEU* 6.5 0.7 - - + -
568A ILE* 3.9 31.0 - - + -
572A ILE* 4.5 2.9 - - + -
577A PHE* 4.2 4.0 - - + -
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Residues in contact with GLY 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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542A ALA 2.7 21.9 + - - -
543A LEU 3.6 1.8 - - - -
545A LEU* 1.3 73.8 - - - +
547A ILE* 1.3 55.2 + - - +
549A ILE* 3.2 11.4 + - - +
550A TYR* 2.9 29.3 + - - +
577A PHE* 4.1 8.0 - - - -
624A ILE* 3.9 26.8 - - - +
628A ILE* 5.3 1.4 - - - +
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Residues in contact with ILE 547 (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 CYS* 3.6 40.2 - - + +
502A LEU* 3.9 16.6 - - + +
503A SER* 3.8 18.2 - - - +
509A VAL* 4.3 1.5 - - + +
543A LEU* 2.8 31.2 + - + +
544A LEU* 3.1 6.5 + - + +
546A GLY* 1.3 70.4 - - - +
548A SER* 1.3 60.7 + - - +
550A TYR* 4.4 0.4 - - - +
551A PHE* 2.9 50.4 + - + +
616A LEU* 4.7 1.3 - - + -
620A LEU* 4.0 29.6 - - + -
624A ILE* 4.1 8.3 - - + -
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Residues in contact with SER 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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502A LEU* 4.2 5.2 - - - +
509A VAL* 3.4 17.1 - - - +
512A PHE* 4.2 12.8 - - - -
513A LEU* 3.8 28.2 - - - +
544A LEU 2.9 14.6 + - - -
545A LEU* 3.0 24.5 + - - +
547A ILE* 1.3 75.7 - - - +
549A ILE* 1.3 55.5 + - - +
552A ASN* 3.0 31.3 + - - +
564A LEU* 4.5 3.4 - - - -
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Residues in contact with ILE 549 (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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545A LEU* 3.2 15.1 + - + +
546A GLY* 3.6 7.9 - - - +
547A ILE 3.1 0.6 - - - -
548A SER* 1.3 77.2 - - - +
550A TYR* 1.3 65.1 - - - +
552A ASN* 3.2 19.5 + - - +
561A LYS* 3.3 34.2 + - + +
564A LEU* 3.6 35.2 - - + -
565A LYS* 4.2 17.3 - - + +
568A ILE* 3.4 33.2 - - + -
627A ALA* 5.1 5.8 - - + +
628A ILE* 3.8 17.7 - - + -
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Residues in contact with TYR 550 (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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546A GLY 2.9 16.4 + - - +
547A ILE* 3.4 2.2 + - - +
549A ILE* 1.3 78.6 - - - +
551A PHE* 1.3 97.7 + + + +
552A ASN 3.5 0.3 + - - +
561A LYS* 3.2 19.7 + - - +
620A LEU* 4.8 2.2 - - + -
623A VAL* 3.6 48.1 - - + +
624A ILE* 4.2 12.6 - - + -
627A ALA* 3.8 25.4 - - + -
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Residues in contact with PHE 551 (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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502A LEU 4.3 3.4 - - - +
503A SER* 4.1 6.5 - - - -
504A ASN* 3.4 59.5 - - - +
505A CYS 4.6 3.8 - - - +
506A PRO* 3.4 32.5 - - + +
509A VAL* 4.1 15.1 - - + +
547A ILE* 2.9 35.1 + - + +
550A TYR* 1.3 108.3 - + + +
552A ASN* 1.3 61.3 + - - +
620A LEU* 3.8 26.0 - - + -
624A ILE* 5.9 0.4 - - + -
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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
------------------------------------------------------------
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