Contacts of the helix formed by residues 535 - 549 (chain A) in PDB entry 5ULM
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 LYS 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A HIS* 4.8 12.1 - - + -
492A MET* 3.8 42.6 - - + +
495A ILE* 4.0 14.3 - - + +
533A VAL* 2.8 7.4 + - + +
534A ALA* 1.3 80.1 - - + +
536A GLN* 1.3 64.9 + - - +
537A GLU 3.1 2.9 - - - -
538A LEU* 3.0 33.3 + - + +
539A VAL* 3.2 14.5 + - - +
592A LEU* 4.1 12.6 - - + -
594A ASP* 3.9 19.0 + - - -
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Residues in contact with GLN 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A HIS* 3.1 28.2 + - - -
522A LYS* 4.6 7.9 - - - +
532A PRO* 4.7 11.2 - - + -
533A VAL* 2.7 34.6 + - - +
534A ALA 3.4 0.6 - - - -
535A LYS* 1.3 69.9 - - - +
537A GLU* 1.3 53.1 + - + +
539A VAL* 3.1 17.3 + - - +
540A ASP* 2.8 67.1 + - - +
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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
----------------------------------------------------------
534A ALA 4.9 2.4 + - - +
535A LYS 3.1 0.4 - - - -
536A GLN* 1.3 79.0 - - + +
538A LEU* 1.3 57.0 + - - +
540A ASP* 3.5 10.2 + - - +
541A PHE* 3.0 26.3 + - - +
591A VAL* 3.7 17.1 - - + +
592A LEU* 3.8 40.0 + - + +
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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
----------------------------------------------------------
495A ILE* 3.8 28.7 - - + -
535A LYS* 3.0 30.3 + - - +
537A GLU* 1.3 75.8 - - - +
539A VAL* 1.3 66.2 + - - +
541A PHE* 3.7 3.0 - - + +
542A TRP* 3.1 33.1 + - + +
572A PRO* 3.6 38.1 - - + -
591A VAL* 3.8 21.1 - - + +
592A LEU* 4.1 30.7 - - + +
594A ASP* 5.5 1.8 - - - +
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Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A HIS* 3.5 38.4 - - + +
494A VAL* 4.4 15.0 - - + -
495A ILE* 3.9 20.6 - - + -
522A LYS* 4.2 21.5 - - - +
535A LYS 3.2 9.2 + - - +
536A GLN* 3.1 18.2 + - - +
538A LEU* 1.3 73.8 - - - +
540A ASP* 1.3 64.7 + - - +
542A TRP* 3.4 3.7 + - - +
543A MET* 3.0 29.5 + - + +
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Residues in contact with ASP 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LYS* 4.9 5.0 + - - -
536A GLN* 2.8 53.4 + - - +
537A GLU* 3.7 10.1 - - - +
538A LEU 3.3 0.2 - - - -
539A VAL* 1.3 72.6 - - - +
541A PHE* 1.3 64.4 + - - +
543A MET* 3.4 5.8 + - - +
544A ASP* 2.9 25.7 + - - +
574A TYR* 4.7 1.6 - - - +
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Residues in contact with PHE 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 17.9 + - - +
538A LEU* 3.7 7.0 - - - +
539A VAL 3.3 0.2 - - - -
540A ASP* 1.3 74.6 - - - +
542A TRP* 1.3 87.0 + + - +
544A ASP* 3.1 4.7 + - - +
545A PHE* 2.7 51.7 + + + +
560A PRO* 3.6 14.4 - - + -
561A VAL 3.3 18.8 - - - -
562A LEU* 3.9 6.7 - - + -
572A PRO* 3.7 26.5 - - + -
573A SER 3.3 25.4 - - - -
574A TYR* 3.7 29.8 + + + +
591A VAL* 4.3 11.2 - - + -
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Residues in contact with TRP 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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494A VAL* 5.4 0.4 - - + -
495A ILE* 3.7 39.2 - - + +
498A SER* 3.6 34.1 - - - +
499A GLU* 3.6 38.4 - - + -
502A PHE* 4.1 6.5 - - + -
538A LEU* 3.1 26.7 + - + +
539A VAL* 4.1 3.8 - - - +
540A ASP 3.3 0.2 - - - -
541A PHE* 1.3 90.4 - + - +
543A MET* 1.3 66.9 + - + +
545A PHE* 3.7 28.2 - + + +
546A LEU* 2.9 36.3 + - + +
562A LEU* 3.6 39.0 - - + -
570A TYR 5.9 0.4 - - - -
572A PRO* 4.1 12.6 - - + +
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Residues in contact with MET 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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482A LEU* 4.5 5.6 - - + -
486A VAL* 4.5 9.0 - - + -
494A VAL* 3.6 29.4 - - + -
498A SER* 3.7 14.6 - - - +
518A ILE* 3.7 35.0 - - + -
522A LYS* 3.8 29.4 - - - +
539A VAL* 3.0 24.1 + - + +
540A ASP* 3.8 5.4 - - - +
542A TRP* 1.3 78.9 - - + +
544A ASP* 1.3 61.6 + - - +
546A LEU* 4.1 10.0 - - + +
547A VAL* 3.0 35.3 + - + +
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Residues in contact with ASP 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 ASP 2.9 18.9 + - - +
541A PHE 3.3 4.7 - - - +
543A MET* 1.3 74.7 - - - +
545A PHE* 1.3 59.4 + - - +
547A VAL* 4.1 4.1 - - - +
548A GLU* 2.9 36.6 + - - +
558A ARG* 4.8 2.8 + - - -
560A PRO* 3.9 10.3 - - - +
574A TYR* 2.8 35.8 + - - +
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Residues in contact with PHE 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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502A PHE* 3.6 39.0 - + + -
541A PHE* 2.7 36.7 + + + +
542A TRP* 3.7 26.9 - + + +
544A ASP* 1.3 74.6 - - - +
546A LEU* 1.3 69.2 + - + +
548A GLU* 3.3 0.7 + - - +
549A ALA* 3.0 30.4 + - + +
560A PRO* 3.5 35.2 - - + +
561A VAL* 4.3 2.0 - - - -
562A LEU* 4.0 16.2 - - + -
636A TYR 4.4 0.7 - - - -
637A PHE 3.9 5.2 - - - -
638A CYS* 3.4 37.8 - - + +
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Residues in contact with LEU 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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482A LEU* 3.7 22.9 - - + -
498A SER* 3.6 43.3 - - - +
501A LEU* 4.4 9.6 - - + -
502A PHE* 5.0 3.4 - - + +
511A LEU* 3.9 24.1 - - + +
514A ILE* 6.0 0.2 - - + -
515A VAL* 3.5 22.0 - - + +
518A ILE* 5.2 4.7 - - + -
542A TRP* 2.9 19.1 + - + +
543A MET* 4.3 9.4 - - + +
545A PHE* 1.3 92.0 - - + +
547A VAL* 1.3 63.2 + - + +
549A ALA* 3.3 18.8 + - + +
550A THR* 3.6 5.0 + - - +
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Residues in contact with VAL 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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515A VAL* 4.1 24.5 - - + +
518A ILE* 5.7 7.4 - - + -
519A LEU* 4.1 27.8 - - + -
543A MET* 3.0 26.4 + - + +
544A ASP* 4.1 4.3 - - - +
546A LEU* 1.3 73.3 - - + +
548A GLU* 1.3 65.3 + - - +
550A THR* 2.8 25.9 + - - +
551A LYS* 3.7 25.5 + - - +
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Residues in contact with GLU 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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544A ASP* 2.9 26.3 + - - +
545A PHE 3.7 4.0 - - - +
547A VAL* 1.3 76.0 - - - +
549A ALA* 1.3 56.0 + - - +
551A LYS* 3.0 44.5 + - - +
553A ASP 5.0 0.3 - - - +
554A VAL* 4.8 4.3 - - - +
555A THR 4.9 0.7 + - - -
556A VAL* 3.3 35.4 - - + +
560A PRO* 4.3 17.9 - - + +
638A CYS* 3.6 12.1 - - - -
642A HIS* 2.8 38.8 + - + +
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Residues in contact with ALA 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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508A ALA* 5.5 6.2 - - - +
511A LEU* 3.7 19.7 - - + +
545A PHE* 3.0 16.4 + - + +
546A LEU* 3.3 15.5 - - + +
547A VAL 3.1 0.6 - - - -
548A GLU* 1.3 75.6 - - - +
550A THR* 1.3 58.2 + - - +
551A LYS 3.3 1.7 - - - +
638A CYS* 3.7 22.4 - - + +
639A THR* 3.2 25.6 - - - +
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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
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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