Contacts of the helix formed by residues 537 - 542 (chain A) in PDB entry 3C4C
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 LEU 537 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 1.3 71.5 - - - +
538A TYR* 1.3 58.3 + - - +
540A HIS* 3.0 3.1 + - - -
541A LEU* 2.8 61.2 + - + +
548A PHE* 4.6 3.6 - - + -
556A ILE* 3.8 27.6 - - + -
560A THR* 5.2 0.9 - - - +
579A SER* 3.7 20.4 - - - +
582A ILE* 2.9 31.9 + - + +
584A LEU* 3.9 21.6 - - + +
645A VAL* 4.5 13.0 - - + -
648A GLU* 6.2 0.2 - - + -
649A LEU* 4.0 16.2 - - + -
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Residues in contact with TYR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 3.8 7.9 - - - +
537A LEU* 1.3 72.4 - - - +
539A HIS* 1.3 71.5 + - - +
542A HIS* 3.0 56.5 + + + +
543A ALA* 5.8 3.1 - - + -
579A SER* 3.1 36.5 + - - +
580A ASN* 3.1 41.3 - - + -
619A TRP* 4.0 5.3 - + - -
654A LEU* 3.4 32.2 - - + +
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Residues in contact with HIS 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A SER* 3.2 36.0 + - - +
536A SER* 3.1 9.9 + - - +
538A TYR* 1.3 84.0 - - - +
540A HIS* 1.3 64.0 + + - +
543A ALA* 3.1 30.8 + - + +
544A SER* 3.0 50.2 + - - -
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Residues in contact with HIS 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A GLY 5.7 0.2 - - - -
535A SER* 3.6 18.8 + - - -
536A SER 3.2 5.0 + - - +
537A LEU 3.0 8.5 + - - +
539A HIS* 1.3 96.3 + + - +
541A LEU* 1.3 65.7 + - - +
542A HIS 3.1 2.8 + - - -
544A SER* 4.4 2.9 - - - -
545A GLU* 4.1 4.9 + - - -
546A THR* 3.8 42.2 + - + +
548A PHE* 3.3 32.3 - + + -
584A LEU* 3.1 26.8 - - + +
587A ASP* 3.6 31.3 + - + -
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Residues in contact with LEU 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A LEU* 2.8 48.5 + - + +
538A TYR 3.3 0.2 + - - -
540A HIS* 1.3 78.9 - - - +
542A HIS* 1.3 84.9 + - + +
545A GLU* 5.7 0.4 - - - -
546A THR 5.8 0.9 - - - +
548A PHE* 3.7 25.8 - - + -
553A LEU* 4.2 9.2 - - + -
648A GLU* 3.8 20.2 - - + +
649A LEU* 3.8 32.8 - - + +
652A GLY* 3.7 18.3 - - - +
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Residues in contact with HIS 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A TYR* 3.0 54.5 + + + +
540A HIS 3.1 2.6 + - - -
541A LEU* 1.3 104.2 + - + +
543A ALA* 1.3 58.9 + - + +
544A SER 3.4 5.7 + - - -
545A GLU* 4.2 11.9 + - - +
579A SER* 4.3 0.4 + - - -
648A GLU* 2.3 32.4 + - + -
652A GLY 4.3 3.8 + - - -
653A GLN* 4.1 9.1 - - - -
654A LEU* 3.6 32.9 + - + +
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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
------------------------------------------------------------
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