Contacts of the helix formed by residues 528 - 547 (chain A) in PDB entry 5TQW
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 GLY 528 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A ILE* 1.3 81.0 - - - +
529A TYR* 1.3 58.8 + - - +
530A LEU 3.5 0.7 - - - -
531A GLU* 3.2 24.0 - - - +
532A ASP* 2.9 37.7 + - - +
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Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ILE 3.1 10.5 - - - +
528A GLY* 1.3 76.2 - - - +
530A LEU* 1.3 77.0 + - + +
532A ASP* 3.0 28.7 + - + +
533A GLN* 3.1 39.0 + - + +
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Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ILE 4.1 7.4 + - - +
529A TYR* 1.3 95.0 - - + +
531A GLU* 1.3 56.8 + - - +
533A GLN* 3.1 29.4 + - - +
534A ILE* 2.8 35.0 + - + +
621A LEU* 4.6 10.6 - - + +
624A LYS* 3.8 49.1 - - + +
625A VAL* 4.7 10.1 - - + +
628A ALA* 5.7 4.3 - - + -
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Residues in contact with GLU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LYS* 4.5 17.1 - - + +
470A ILE* 4.5 22.1 - - - +
527A ILE 4.2 4.4 + - - +
528A GLY* 3.2 27.4 - - - +
530A LEU* 1.3 75.5 - - - +
532A ASP* 1.3 62.0 + - - +
534A ILE* 3.0 14.3 + - + +
535A MET* 2.9 51.1 + - + +
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Residues in contact with ASP 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A GLY* 2.9 18.0 + - - +
529A TYR* 3.0 16.0 + - + +
531A GLU* 1.3 75.6 - - - +
533A GLN* 1.3 57.5 + - + +
535A MET* 3.4 21.3 - - + +
536A SER* 2.7 39.6 + - - +
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Residues in contact with GLN 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A TYR* 3.1 47.3 + - + +
530A LEU* 3.1 31.5 + - - +
532A ASP* 1.3 77.3 - - + +
534A ILE* 1.3 54.5 + - - +
536A SER* 4.0 4.6 - - - -
537A LEU* 2.9 31.9 + - - +
621A LEU* 3.3 23.8 - - + +
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Residues in contact with ILE 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ASN* 5.7 1.8 - - - +
462A LEU* 4.1 36.6 - - + +
463A THR* 5.3 8.7 - - + -
466A LYS* 4.0 39.0 - - + -
469A LEU* 5.7 2.7 - - + -
530A LEU* 2.8 20.5 + - + +
531A GLU* 3.0 17.7 + - + +
533A GLN* 1.3 75.0 - - - +
535A MET* 1.3 66.0 + - + +
537A LEU* 3.4 4.0 + - - +
538A HIS* 2.8 31.4 + - + +
621A LEU* 4.3 11.0 - - + -
625A VAL* 4.7 13.7 - - + -
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Residues in contact with MET 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LYS* 5.7 8.1 - - - +
531A GLU* 2.9 45.3 + - + +
532A ASP* 3.4 25.4 - - - +
534A ILE* 1.3 81.3 - - + +
536A SER* 1.3 58.0 + - - +
538A HIS* 3.3 12.5 - - + +
539A ALA* 2.9 26.5 + - - +
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Residues in contact with SER 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ASP* 2.7 24.8 + - - +
533A GLN* 4.0 5.2 - - - -
535A MET* 1.3 75.5 - - - +
537A LEU* 1.3 59.2 + - - +
539A ALA* 3.0 11.3 + - - +
540A GLU* 3.0 34.0 + - - +
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Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 5.3 2.9 - - + -
533A GLN 2.9 18.8 + - - +
534A ILE 3.9 3.1 - - - +
536A SER* 1.3 75.6 - - - +
538A HIS* 1.3 57.1 + - - +
540A GLU* 3.1 28.5 + - - +
541A ILE* 2.8 40.0 + - + +
614A CYS* 4.0 22.0 - - + +
617A LYS* 3.8 35.4 - - + +
618A ILE* 3.7 26.7 - - + -
621A LEU* 3.8 18.6 - - + -
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Residues in contact with HIS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ASN* 3.4 25.2 + - - +
463A THR* 5.6 5.3 - - + +
534A ILE* 2.8 20.4 + - + +
535A MET* 3.3 12.3 - - + +
537A LEU* 1.3 75.1 - - - +
539A ALA* 1.3 63.1 + - + +
541A ILE* 3.0 12.7 + - - +
542A MET* 2.9 66.5 + - + +
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Residues in contact with ALA 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 MET 2.9 13.7 + - - +
536A SER* 3.0 11.9 + - - +
538A HIS* 1.3 80.1 - - + +
540A GLU* 1.3 58.4 + - + +
542A MET* 3.3 8.8 + - - +
543A GLU* 3.0 39.8 + - - +
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Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 3.0 16.9 + - - +
537A LEU* 3.2 33.3 - - + +
539A ALA* 1.3 75.7 - - + +
541A ILE* 1.3 56.3 + - - +
543A GLU* 3.2 21.4 + - - +
544A LEU* 2.9 34.1 + - + +
614A CYS* 4.3 11.1 - - - -
617A LYS* 3.4 21.3 + - - -
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Residues in contact with ILE 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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455A LEU* 4.7 22.7 - - + +
456A LEU* 4.8 8.3 - - + -
459A ASN* 3.9 28.9 - - + +
462A LEU* 6.4 0.9 - - + -
537A LEU* 2.8 34.8 + - + +
538A HIS* 3.0 16.4 + - - +
540A GLU* 1.3 75.0 - - - +
542A MET* 1.3 76.6 + - + +
544A LEU* 3.0 11.4 + - - +
545A GLN* 2.9 33.1 + - + +
614A CYS* 5.0 7.9 - - + -
618A ILE* 4.5 14.8 - - + -
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Residues in contact with MET 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 5.3 1.1 - - + -
459A ASN* 4.5 4.0 - - - +
538A HIS* 2.9 53.7 + - + +
539A ALA* 3.6 9.0 - - - +
541A ILE* 1.3 86.9 - - + +
543A GLU* 1.3 57.0 + - + +
545A GLN* 3.2 47.8 + - - +
546A LYS* 2.9 41.2 + - - +
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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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539A ALA* 3.0 26.7 + - - +
540A GLU* 3.2 26.9 - - - +
541A ILE 3.2 0.2 - - - -
542A MET* 1.3 74.6 - - + +
544A LEU* 1.3 63.0 + - + +
546A LYS* 3.1 8.9 + - + +
547A SER* 3.0 28.4 + - - -
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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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455A LEU* 5.0 4.0 - - + -
540A GLU* 2.9 18.2 + - + +
541A ILE* 3.0 11.6 + - - +
543A GLU* 1.3 78.1 - - + +
545A GLN* 1.3 61.2 + - - +
547A SER* 3.7 19.9 + - - +
549A TYR* 4.0 12.3 + - - -
607A HIS* 5.1 6.9 - - + +
610A LYS* 3.7 41.1 - - + +
611A LEU* 3.8 31.9 - - + +
614A CYS* 3.7 32.8 - - + -
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Residues in contact with GLN 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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452A MET* 6.2 6.1 - - + -
456A LEU* 3.6 27.6 - - + +
541A ILE* 2.9 15.8 + - + +
542A MET* 3.3 47.9 - - - +
543A GLU 3.1 0.2 - - - -
544A LEU* 1.3 79.7 - - - +
546A LYS* 1.3 63.2 + - + +
547A SER 3.4 5.5 + - - +
549A TYR* 4.2 13.0 + - - -
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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 MET* 2.9 27.6 + - - +
543A GLU* 3.1 8.9 + - + +
545A GLN* 1.3 78.1 - - + +
547A SER* 1.3 64.8 + - - +
548A PRO* 3.6 4.9 - - - +
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Residues in contact with SER 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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543A GLU 3.0 13.5 + - - -
544A LEU* 3.9 13.7 - - - -
545A GLN 3.2 5.8 - - - +
546A LYS* 1.3 79.9 - - - +
548A PRO* 1.3 75.4 - - - +
549A TYR* 3.5 16.3 - - - -
607A HIS* 2.6 37.3 + - - -
610A LYS* 5.7 3.3 + - - -
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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