Contacts of the helix formed by residues 533 - 550 (chain A) in PDB entry 1PD0
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 ASN 533 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A GLY 4.5 2.8 + - - -
530A SER* 2.8 23.1 + - - +
531A GLY 2.8 3.5 + - - +
532A LYS* 1.3 84.5 - - - +
534A PRO* 1.3 59.5 - - - +
535A ASN* 3.0 3.8 - - + +
536A ASP* 2.6 67.4 + - - +
537A ILE* 3.6 2.4 + - - +
837A LYS* 5.4 2.9 - - + +
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Residues in contact with PRO 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A GLY 3.9 4.9 - - - +
532A LYS 3.3 12.1 - - - +
533A ASN* 1.3 81.1 - - + +
535A ASN* 1.3 67.5 + - - +
537A ILE* 3.2 24.8 + - + +
538A VAL* 3.4 12.5 + - - +
838A GLN* 5.9 3.6 - - - +
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Residues in contact with ASN 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ASN* 2.8 4.3 + - + +
534A PRO* 1.3 78.9 - - - +
536A ASP* 1.3 65.5 + - - +
538A VAL* 3.5 13.6 + - - +
539A LYS* 3.4 21.1 + - - +
837A LYS* 3.3 44.1 + - + +
838A GLN* 3.8 22.4 + - - +
839A GLU* 3.5 30.7 - - - +
868A TYR* 5.2 2.3 + - - -
870A SER* 4.4 6.2 + - - +
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Residues in contact with ASP 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A TYR* 5.8 0.3 - - - -
527A PRO 5.3 0.2 - - - +
528A GLY 3.6 3.1 - - - +
529A PHE* 3.5 27.0 - - + -
530A SER 2.9 30.0 + - - +
533A ASN* 2.6 43.6 + - - +
535A ASN* 1.3 72.0 - - - +
537A ILE* 1.3 61.2 + - - +
539A LYS* 3.3 5.8 + - - +
540A PHE* 3.1 24.4 + - - +
837A LYS* 2.7 36.4 + - - +
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Residues in contact with ILE 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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320A GLY* 4.9 0.9 - - - +
324A THR* 2.8 44.4 - - + +
529A PHE* 3.7 18.6 - - + -
531A GLY* 3.9 22.0 - - - +
533A ASN 4.2 7.0 - - - +
534A PRO* 3.2 15.0 + - + +
535A ASN 3.2 0.2 - - - -
536A ASP* 1.3 78.4 - - - +
538A VAL* 1.3 58.9 + - + +
540A PHE* 4.0 0.3 - - - +
541A SER* 2.9 40.9 + - - +
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A PRO 3.4 15.0 + - - +
535A ASN* 3.8 15.7 - - - +
536A ASP 3.3 0.6 - - - -
537A ILE* 1.3 78.0 - - + +
539A LYS* 1.3 54.7 + - - +
541A SER* 4.6 2.9 - - - -
542A THR* 2.4 43.8 + - - +
868A TYR* 3.5 34.1 - - + +
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Residues in contact with LYS 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A PHE 5.4 3.4 - - - -
526A TYR* 4.2 23.8 - - + +
527A PRO* 6.5 0.7 - - - -
535A ASN 3.4 5.1 + - - +
536A ASP* 3.3 9.0 + - - +
537A ILE 3.3 0.4 - - - -
538A VAL* 1.3 77.9 - - - +
540A PHE* 1.3 67.7 + - - +
542A THR* 3.9 0.3 - - - -
543A GLU* 2.9 47.6 + - - +
806A ASN 4.3 13.0 + - - -
807A GLU* 6.5 0.2 - - - -
837A LYS* 6.0 2.7 - - - +
867A THR* 4.5 3.4 - - - +
868A TYR* 2.7 45.3 + - + +
870A SER* 3.5 26.2 - - - +
872A TYR* 6.0 0.4 - - - +
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Residues in contact with PHE 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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321A LEU* 3.6 24.5 - - + -
324A THR* 3.7 16.8 - - + -
325A THR* 3.5 24.0 - - - -
328A THR* 5.2 0.7 - - - -
445A VAL* 3.7 16.2 - - + -
500A PHE* 3.8 27.1 - + + -
502A ALA* 4.4 5.6 - - + -
526A TYR* 3.7 38.2 + + + -
529A PHE* 4.0 16.6 - + + -
536A ASP 3.1 13.6 + - - +
537A ILE 4.0 1.8 - - - +
539A LYS* 1.3 79.1 - - - +
541A SER* 1.3 61.1 + - - +
543A GLU* 3.4 1.2 + - - +
544A PHE* 2.8 53.4 + + + +
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Residues in contact with SER 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR* 3.3 12.3 + - - +
328A THR* 2.7 31.5 + - - +
537A ILE* 2.9 25.8 + - - +
538A VAL* 4.0 3.8 - - - -
540A PHE* 1.3 76.8 - - - +
542A THR* 1.3 61.0 + - - +
544A PHE* 4.6 0.2 - - - -
545A ALA* 2.9 34.4 + - - +
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Residues in contact with THR 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 VAL* 2.4 33.0 + - - +
541A SER* 1.3 76.3 - - - +
543A GLU* 1.3 58.1 + - - +
545A ALA* 3.8 3.7 - - - +
546A LYS* 3.0 58.1 + - + +
866A ILE 5.0 0.7 - - - +
868A TYR* 3.7 37.5 - - + -
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Residues in contact with GLU 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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500A PHE* 4.4 0.9 - - - -
524A HIS* 4.6 7.3 + - - -
526A TYR* 2.5 40.8 + - - +
539A LYS* 2.9 39.9 + - - +
540A PHE 3.9 0.2 - - - +
542A THR* 1.3 75.5 - - - +
544A PHE* 1.3 60.6 + - - +
546A LYS 3.4 0.5 + - - -
547A HIS* 2.8 32.1 + - - +
866A ILE* 3.6 32.0 - - + +
867A THR* 3.2 12.9 - - - +
868A TYR* 2.8 28.8 + - + +
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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
----------------------------------------------------------
308A PHE* 3.9 26.9 - + - -
325A THR* 4.3 10.1 - - + -
328A THR* 4.0 21.3 - - + -
329A LEU* 4.0 26.9 - - + -
443A ILE* 3.7 7.9 - - + -
445A VAL* 3.7 26.9 - - + -
500A PHE* 3.6 40.7 - + + -
540A PHE* 2.8 36.9 + + + +
541A SER 4.0 2.7 - - - +
543A GLU* 1.3 77.0 - - - +
545A ALA* 1.3 57.3 + - - +
547A HIS* 3.7 1.0 - - - +
548A ILE* 3.0 45.9 + - + +
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Residues in contact with ALA 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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328A THR* 3.9 6.7 - - + +
332A ASN* 3.7 32.4 - - - +
335A SER* 5.1 0.6 - - - -
541A SER 2.9 19.7 + - - +
542A THR* 3.8 4.9 - - - +
544A PHE* 1.3 75.3 - - - +
546A LYS* 1.3 67.7 + - + +
548A ILE* 3.2 13.5 - - - +
549A SER* 3.0 23.4 + - - -
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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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213A LEU* 4.7 12.8 - - + +
214A TYR* 4.7 7.2 + - - +
542A THR* 3.0 40.6 + - + +
545A ALA* 1.3 76.8 - - + +
547A HIS* 1.3 62.3 + - - +
549A SER* 2.8 23.5 + - - +
550A MET* 3.0 11.4 + - - +
860A ARG 4.5 14.3 + - - -
861A ASN* 5.0 3.2 - - - +
862A HIS 3.9 19.0 + - - +
865A VAL 4.3 5.5 + - - +
866A ILE* 3.8 36.5 + - + +
867A THR 5.1 4.6 + - - -
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Residues in contact with HIS 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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441A LYS* 3.9 5.6 + - - -
443A ILE* 4.2 16.5 - - + +
498A ASP* 3.0 42.0 + - + +
500A PHE* 3.6 31.7 - + + -
522A GLN* 5.3 3.8 - - + -
524A HIS* 4.5 12.8 + + - -
543A GLU 2.8 19.3 + - - +
544A PHE 3.7 3.4 - - - +
546A LYS* 1.3 76.7 - - - +
548A ILE* 1.3 65.5 + - + +
550A MET* 3.2 48.2 + - + +
552A PHE* 6.1 0.5 - - - -
591A ASP* 5.1 2.0 + - - -
866A ILE* 3.8 16.9 - - + +
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Residues in contact with ILE 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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306A TYR* 3.8 14.2 + - + -
308A PHE* 4.0 24.7 - - + -
328A THR* 5.1 0.9 - - + +
329A LEU* 4.2 20.9 - - + -
332A ASN* 4.0 24.0 - - + -
336A ILE* 3.7 28.6 - - + +
337A PRO* 3.2 20.4 - - - +
443A ILE* 4.2 11.4 - - + -
544A PHE* 3.0 31.2 + - + +
545A ALA* 3.2 16.2 - - - +
547A HIS* 1.3 80.3 - - + +
549A SER* 1.3 58.3 + - - +
550A MET 3.3 1.5 + - - +
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Residues in contact with SER 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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214A TYR* 3.1 37.0 + - - -
335A SER* 3.3 35.5 - - - +
337A PRO* 3.3 12.8 - - - +
545A ALA 3.0 13.1 + - - -
546A LYS* 2.8 16.6 + - - -
548A ILE* 1.3 76.2 - - - +
550A MET* 1.3 63.6 + - - +
551A ASP* 3.5 2.1 + - - +
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Residues in contact with MET 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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213A LEU* 3.7 26.5 - - + +
214A TYR* 4.6 1.8 - - - -
306A TYR* 4.4 0.7 + - - -
337A PRO* 3.6 8.5 - - - +
441A LYS* 4.0 8.7 - - - +
546A LYS 3.0 11.2 + - - +
547A HIS* 3.2 44.8 + - + +
548A ILE 4.2 1.9 - - - +
549A SER* 1.3 79.7 - - - +
551A ASP* 1.3 76.2 + - - +
552A PHE* 3.9 13.1 - - + -
589A PRO* 4.0 15.5 - - + -
590A ARG* 3.5 20.6 - - + -
591A ASP* 3.3 33.2 - - - +
866A ILE* 5.2 1.8 - - - -
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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
------------------------------------------------------------
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