Contacts of the helix formed by residues 532 - 550 (chain A) in PDB entry 40ER
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 SER 532 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A GLY* 1.3 70.6 - - - -
533A HIS* 1.3 58.9 + - - +
534A THR* 3.5 3.1 + - - -
535A ILE* 3.5 23.1 + - - +
536A GLU* 3.0 33.7 + - - +
75G TRP* 3.6 26.2 - - - -
82G PHE* 3.9 6.1 - - - -
161G GLY 3.2 18.8 + - - -
162G ASN* 3.1 17.7 + - - -
163G THR 4.6 0.3 + - - -
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Residues in contact with HIS 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A TYR 5.9 0.2 - - - -
447A SER* 4.5 19.9 - - - -
448A LYS 5.1 1.8 - - - -
467A SER* 5.1 6.3 - - - -
468A ILE* 2.7 49.6 + - + -
469A ASP* 4.5 8.3 - - - -
470A ASP 5.6 1.1 - - - -
529A ARG* 4.1 15.6 + - - +
531A GLY 3.9 0.4 + - - -
532A SER* 1.3 72.7 - - - +
534A THR* 1.3 63.2 + - - +
536A GLU* 3.7 10.4 + - - +
537A PHE* 3.4 22.5 + - + +
257B HIS* 5.8 4.7 - + - -
160G SER* 3.3 14.5 + - - +
162G ASN* 2.8 20.9 + - - +
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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
----------------------------------------------------------
532A SER* 3.2 4.7 - - - -
533A HIS* 1.3 76.7 - - - +
535A ILE* 1.3 65.3 + - + +
537A PHE* 3.5 13.9 + - - +
538A PHE* 3.2 27.7 - - + -
257B HIS* 3.4 45.7 + - + +
266B THR* 3.9 20.8 + - + +
162G ASN* 2.9 31.4 + - - +
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Residues in contact with ILE 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A SER* 3.4 25.4 + - - +
534A THR* 1.3 73.2 - - - +
536A GLU* 1.3 68.0 + - - +
537A PHE 3.1 2.2 - - - -
538A PHE* 2.9 23.6 + - + +
539A GLU* 2.9 18.1 + - + +
266B THR* 5.1 5.8 - - + -
268B LEU* 3.9 18.8 - - + -
50G VAL* 3.7 32.3 - - + -
75G TRP* 3.4 42.0 - - + +
82G PHE* 4.0 16.4 - - + -
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Residues in contact with GLU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ARG* 5.4 5.7 + - - +
440A ASN* 4.6 16.2 + - - +
445A THR* 4.8 11.3 + - - -
446A TYR 5.5 0.5 - - - -
447A SER* 3.5 29.1 + - - +
529A ARG* 5.5 6.4 + - - -
531A GLY* 3.9 9.7 - - - -
532A SER 3.0 36.1 + - - +
533A HIS* 3.9 10.9 + - - +
534A THR 3.4 0.2 - - - -
535A ILE* 1.3 76.2 - - - +
537A PHE* 1.3 60.6 + - - +
539A GLU* 3.9 6.9 - - - +
540A MET* 3.0 30.2 + - + +
75G TRP* 5.2 0.7 - - + -
80G GLN* 3.7 25.8 + - + +
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Residues in contact with PHE 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A SER* 5.4 1.5 - - - -
448A LYS 4.6 4.0 - - - +
449A MET* 3.9 15.3 - - + -
465A PHE 3.9 14.4 - - - -
466A ARG* 3.4 13.0 - - - -
467A SER* 3.4 48.0 - - - -
533A HIS* 3.4 13.9 + - + +
534A THR* 3.5 11.0 - - - +
535A ILE 3.1 0.2 - - - -
536A GLU* 1.3 79.4 - - - +
538A PHE* 1.3 79.2 + + - +
540A MET* 3.3 9.2 + - - +
541A CYS* 3.0 47.4 + - - -
239B ASN 4.3 1.8 - - - -
241B LEU* 3.7 24.5 - - + -
255B ALA* 4.4 7.9 - - + -
257B HIS* 4.4 5.4 - - + -
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Residues in contact with PHE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A THR* 3.2 36.8 + - + -
535A ILE* 2.9 9.0 + - + +
537A PHE* 1.3 88.6 - + - +
539A GLU* 1.3 55.1 - - - +
541A CYS* 3.3 2.9 + - - +
542A ALA* 2.7 38.0 + - - +
241B LEU* 4.4 1.6 - - + -
253B LEU* 3.8 29.0 - - + +
254B SER* 3.4 24.9 - - - -
255B ALA* 3.3 23.3 - - + -
257B HIS* 4.2 5.2 - - - -
266B THR* 3.2 32.1 - - + -
268B LEU* 3.6 31.0 - - + -
270B LYS* 5.4 0.2 - - - -
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Residues in contact with GLU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ARG* 4.2 12.5 + - - +
535A ILE* 2.9 21.8 + - + +
536A GLU* 3.9 4.4 - - - +
538A PHE* 1.3 76.7 - - - +
540A MET* 1.3 62.2 + - - +
542A ALA* 4.1 5.8 - - - -
543A ASN* 3.0 35.3 + - - +
268B LEU* 5.0 0.9 - - + -
270B LYS* 3.9 26.0 - - + +
75G TRP* 3.0 29.8 + - - -
77G SER* 3.2 23.6 + - - -
80G GLN* 2.9 29.6 + - - +
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Residues in contact with MET 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 4.9 2.9 - - - +
424A TYR* 3.9 25.6 - - + -
436A VAL* 5.0 3.1 - - + -
437A ARG* 4.7 2.2 - - - -
438A ARG* 3.5 26.9 - - + +
447A SER* 3.1 51.4 - - - +
448A LYS* 4.4 3.6 - - - +
449A MET* 3.7 32.0 - - - +
536A GLU 3.0 18.2 + - - +
537A PHE* 3.5 8.3 - - - +
538A PHE 3.2 0.2 - - - -
539A GLU* 1.3 75.4 - - - +
541A CYS* 1.3 64.2 + - - +
543A ASN* 3.9 4.9 - - - +
544A LEU* 3.4 19.9 + - - +
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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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449A MET* 3.9 9.2 - - - -
465A PHE* 3.5 31.9 - - + -
537A PHE* 3.0 46.3 + - - +
538A PHE 3.7 2.9 - - - +
540A MET* 1.3 74.9 - - - +
542A ALA* 1.3 54.9 + - - +
544A LEU* 3.0 6.2 + - - +
545A ILE* 2.8 43.7 + - + +
241B LEU* 3.5 31.2 - - + -
253B LEU* 4.3 0.2 - - + -
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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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538A PHE 2.7 22.6 + - - +
539A GLU 3.6 4.9 - - - +
540A MET 3.3 0.2 - - - -
541A CYS* 1.3 73.0 - - - +
543A ASN* 1.3 63.8 + - - +
545A ILE* 3.3 3.2 + - - +
546A LYS* 3.0 25.6 + - - +
251B MET* 3.5 36.1 - - + +
253B LEU* 4.4 5.1 - - + +
270B LYS* 3.8 23.3 - - - +
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Residues in contact with ASN 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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422A LEU* 3.8 23.8 - - + +
424A TYR* 3.3 23.2 + - - -
438A ARG* 4.7 6.1 - - - +
539A GLU* 3.0 22.4 + - - +
540A MET* 3.9 2.9 - - - +
542A ALA* 1.3 77.4 - - - +
544A LEU* 1.3 62.7 + - - +
546A LYS* 3.5 9.2 + - - +
547A ILE* 3.4 22.2 + - - +
270B LYS* 4.0 15.9 + - - -
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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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415A VAL* 4.7 6.7 - - + -
418A ALA* 4.1 15.9 - - + +
419A ILE* 4.2 23.3 - - + +
422A LEU* 4.0 10.5 - - + +
436A VAL* 6.3 0.9 - - + -
449A MET* 5.2 4.3 - - + -
451A LEU* 3.7 24.0 - - + -
465A PHE* 3.6 28.7 - - + -
540A MET 3.4 11.8 + - - +
541A CYS* 3.0 7.9 + - - +
543A ASN* 1.3 79.8 - - - +
545A ILE* 1.3 61.3 + - - +
547A ILE* 3.2 12.5 + - + +
548A LEU* 3.1 45.9 + - + +
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Residues in contact with ILE 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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402A ILE* 4.2 23.3 - - + +
465A PHE* 4.1 23.1 - - + -
541A CYS* 2.8 40.6 + - + +
542A ALA* 3.8 9.0 - - - +
544A LEU* 1.3 72.7 - - - +
546A LYS* 1.3 64.1 + - - +
548A LEU* 3.2 7.5 + - - +
549A ALA* 2.9 27.8 + - + +
241B LEU* 5.1 7.4 - - + -
243B ALA* 5.5 6.3 - - + -
246B ILE* 5.9 6.1 - - + -
251B MET* 4.5 13.2 - - + -
253B LEU* 4.5 11.2 - - + -
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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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542A ALA 3.0 16.9 + - - +
543A ASN* 3.7 8.7 - - - +
544A LEU 3.2 0.2 - - - -
545A ILE* 1.3 77.7 - - - +
547A ILE* 1.3 64.9 + - + +
549A ALA* 4.1 4.2 - - + +
550A GLN* 3.1 48.0 + - + +
251B MET* 4.7 10.5 - - + +
272B ILE* 4.0 46.8 - - + +
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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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417A ARG* 5.1 7.2 - - - +
418A ALA* 4.1 22.7 - - + +
421A GLN* 4.3 27.6 - - + +
422A LEU* 4.5 18.6 - - + -
543A ASN 3.4 18.2 - - - +
544A LEU* 3.2 7.5 + - - +
546A LYS* 1.3 84.0 - - + +
548A LEU* 1.3 65.4 + - - +
549A ALA 3.2 0.4 + - - -
550A GLN 3.7 17.6 - - - +
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Residues in contact with LEU 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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402A ILE* 3.5 34.5 - - + -
414A GLU* 5.5 1.8 - - + +
415A VAL* 3.8 32.1 - - + -
418A ALA* 3.6 17.5 - - + -
463A LEU* 4.4 12.6 - - + -
465A PHE* 5.4 0.7 - - + -
544A LEU* 3.1 45.3 - - + +
545A ILE* 3.2 4.6 + - - +
547A ILE* 1.3 77.5 - - - +
549A ALA* 1.3 62.2 + - - +
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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
----------------------------------------------------------
402A ILE* 5.0 2.4 - - + +
545A ILE* 2.9 22.5 + - + +
546A LYS* 4.1 4.5 - - + +
548A LEU* 1.3 81.8 - - - +
550A GLN* 1.3 65.1 + - + +
246B ILE* 5.1 14.4 - - + -
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Residues in contact with GLN 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A LYS* 3.1 36.8 + - + +
547A ILE* 3.7 18.5 - - - +
549A ALA* 1.3 83.4 + - + +
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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