Contacts of the helix formed by residues 542 - 552 (chain A) in PDB entry 2Z82
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 ILE 542 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A LYS 5.2 1.8 - - - +
513A SER* 6.0 2.5 - - - -
535A TRP* 4.4 8.1 - - + -
536A ASP 3.5 25.8 + - - +
537A CYS* 3.3 32.8 - - - +
538A SER 3.2 7.1 + - - +
541A ARG* 1.3 75.3 - - - +
543A ASP* 1.3 66.7 + - - +
544A TYR 3.7 0.7 - - - -
545A LEU* 3.6 34.8 - - + -
546A SER* 3.1 13.1 + - - +
569A VAL* 3.7 22.9 - - + -
572A ILE* 3.6 24.5 - - + -
574A CYS* 4.3 6.1 - - - -
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Residues in contact with ASP 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 CYS 4.1 1.4 + - - +
540A PRO 3.8 14.5 + - - +
541A ARG 2.6 10.8 + - - +
542A ILE* 1.3 72.8 - - - +
544A TYR* 1.3 64.8 + - - +
546A SER* 2.8 22.6 + - - -
547A ARG* 2.8 43.4 + - - +
574A CYS* 3.3 37.2 + - - +
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Residues in contact with TYR 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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514A VAL* 4.3 17.0 - - + +
515A PRO 3.9 4.3 - - - -
516A ASP* 3.5 27.1 + - + +
517A GLY* 3.2 31.9 - - - -
518A ILE* 3.9 5.4 - - + -
519A PHE* 2.9 38.8 + + - +
520A ASP* 3.3 30.4 + - - -
541A ARG 4.1 2.9 + - - +
542A ILE 3.7 0.2 - - - -
543A ASP* 1.3 77.8 - - - +
545A LEU* 1.3 64.0 + - - +
547A ARG* 3.1 10.3 + - + +
548A TRP* 2.8 41.7 + + + +
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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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513A SER* 5.5 0.2 - - - -
514A VAL* 3.8 15.9 + - + +
519A PHE* 3.8 29.2 - - + -
530A LEU* 4.7 5.4 - - + -
535A TRP* 3.5 42.2 - - + -
541A ARG 5.1 0.8 + - - -
542A ILE* 3.6 25.2 + - + +
543A ASP 3.3 0.8 - - - -
544A TYR* 1.3 85.0 - - - +
546A SER* 1.3 61.0 + - - +
548A TRP* 3.3 2.6 + - + +
549A LEU* 3.1 47.9 + - + +
569A VAL* 4.1 12.1 - - + -
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Residues in contact with SER 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ILE* 3.1 15.7 + - - +
543A ASP* 2.8 22.3 + - - -
545A LEU* 1.3 72.2 - - - +
547A ARG* 1.3 69.4 + - - +
548A TRP 3.1 1.8 + - - -
549A LEU* 3.3 2.8 + - - +
550A ASN* 3.3 28.3 + - - +
569A VAL* 3.4 33.0 - - - -
570A ARG* 4.2 2.6 - - - +
572A ILE* 3.3 25.4 + - - -
573A ILE* 5.1 1.0 - - - -
574A CYS* 5.3 0.3 - - - -
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Residues in contact with ARG 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 ASP* 2.8 47.6 + - - +
544A TYR* 3.7 8.3 - - + +
546A SER* 1.3 79.5 + - - +
548A TRP* 1.3 62.5 + - - +
550A ASN* 3.6 6.8 + - - +
551A LYS* 3.3 43.5 + - - +
573A ILE* 5.8 5.1 - - - +
574A CYS 4.3 14.3 + - - +
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Residues in contact with TRP 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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519A PHE* 3.4 42.8 + + + +
520A ASP* 3.7 18.3 + - - +
525A LEU* 4.1 17.9 - - + -
528A ILE* 4.0 27.8 - - + -
530A LEU* 4.8 1.6 - - + -
544A TYR* 2.8 43.5 + + + +
545A LEU* 3.6 6.1 - - - +
546A SER 3.1 0.2 - - - -
547A ARG* 1.3 75.3 - - - +
549A LEU* 1.3 84.3 + - + +
550A ASN 3.1 2.0 - - - -
551A LYS* 3.3 4.7 + - + -
552A ASN* 2.9 67.6 + - + +
555A LYS* 4.6 12.3 - - + -
556A GLU* 5.4 1.3 - - + -
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Residues in contact with LEU 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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530A LEU* 4.0 20.2 - - + -
545A LEU* 3.1 20.8 + - + +
546A SER 3.3 4.7 + - - +
548A TRP* 1.3 103.9 - - + +
550A ASN* 1.3 56.6 + - - +
552A ASN 3.8 2.2 - - - +
553A SER* 3.2 30.0 + - - -
556A GLU* 4.0 28.0 - - + +
560A ALA* 4.8 8.5 - - + +
569A VAL* 3.7 38.6 - - + -
570A ARG* 4.0 20.5 - - + +
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Residues in contact with ASN 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 SER 3.3 15.3 + - - +
547A ARG* 3.8 7.4 - - - +
548A TRP 3.1 0.4 - - - -
549A LEU* 1.3 80.2 - - - +
551A LYS* 1.3 61.8 + - + +
552A ASN 3.2 0.8 + - - -
553A SER* 4.2 10.5 + - - -
570A ARG* 2.8 47.1 + - - +
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Residues in contact with LYS 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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547A ARG* 3.3 32.0 + - - +
548A TRP* 3.3 4.8 + - + +
550A ASN* 1.3 77.7 - - + +
552A ASN* 1.3 78.4 + - - +
553A SER 3.8 0.7 - - - -
554A GLN* 5.0 5.0 + - - -
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Residues in contact with ASN 552 (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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520A ASP* 5.1 2.4 + - - -
548A TRP* 2.9 68.9 + - + +
549A LEU* 3.6 5.0 - - - +
550A ASN 3.2 0.2 - - - -
551A LYS* 1.3 92.9 - - - +
553A SER* 1.3 63.1 + - - +
554A GLN* 3.2 12.6 + - - +
555A LYS* 3.2 38.0 + - + +
556A GLU* 3.5 10.9 + - - +
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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