Contacts of the helix formed by residues 536 - 543 (chain A) in PDB entry 5MJ6
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 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ILE* 3.8 12.2 - - - +
239A TYR* 5.4 7.2 - - - -
240A HIS* 6.0 1.6 - - - -
534A VAL 3.7 0.4 - - - -
535A GLN* 1.3 79.1 - - - +
537A SER* 1.3 65.8 - - - +
538A GLU* 3.5 19.8 + - - +
539A GLN* 3.2 27.5 + - - +
540A ILE* 3.0 23.2 + - - +
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Residues in contact with SER 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 4.3 3.4 - - - +
297A LEU* 3.7 27.3 - - - +
536A SER* 1.3 74.3 - - - +
538A GLU* 1.3 74.3 + - - +
540A ILE* 3.1 5.4 + - - +
541A GLU* 2.9 36.7 + - - +
958A LEU 4.9 2.2 + - - -
1147A BR 4.3 8.5 - - - -
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Residues in contact with GLU 538 (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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239A TYR* 5.6 1.0 + - - -
536A SER* 3.2 20.4 + - - +
537A SER* 1.3 93.5 + - - +
539A GLN* 1.3 58.5 + - + +
541A GLU* 3.4 2.8 + - - +
542A GLU* 2.9 35.6 + - - +
958A LEU* 3.8 38.6 - - + +
959A GLY 3.9 3.2 - - - +
993A ALA* 6.2 1.9 - - - +
997A LEU* 3.6 30.7 - - + -
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Residues in contact with GLN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A SER* 3.8 15.8 + - - -
534A VAL* 3.8 16.2 - - + +
535A GLN* 3.0 30.7 + - - +
536A SER* 3.2 23.0 + - - +
538A GLU* 1.3 75.5 - - + +
540A ILE* 1.3 67.2 + - - +
542A GLU* 3.3 18.8 + - - +
543A MET* 3.3 23.2 + - - +
997A LEU* 6.2 0.7 - - + -
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Residues in contact with ILE 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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166A ILE* 4.2 11.2 - - + -
296A PRO* 3.8 27.1 - - + -
297A LEU* 3.9 25.6 - - + -
479A TRP* 4.1 14.1 - - + -
480A TRP* 3.7 42.6 - - + +
534A VAL* 4.0 16.8 - - + -
536A SER 3.0 20.1 + - - +
537A SER* 3.1 8.9 + - - +
539A GLN* 1.3 75.7 - - - +
541A GLU* 1.3 64.1 + - - +
543A MET* 3.1 22.7 + - - +
544A PHE* 3.8 5.9 - - - -
1147A BR 4.4 2.2 - - + -
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Residues in contact with GLU 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.0 33.9 + - - -
296A PRO* 3.8 17.3 - - + +
297A LEU* 4.7 6.0 - - + +
537A SER* 2.9 21.1 + - - +
538A GLU 3.6 3.1 - - - +
540A ILE* 1.3 76.9 - - + +
542A GLU* 1.3 61.4 + - - +
544A PHE* 3.1 27.6 + - - +
957A PRO* 4.1 9.2 - - + +
958A LEU 4.0 13.7 - - - +
959A GLY 3.3 21.3 - - - +
960A SER* 3.4 25.7 - - - +
961A TYR 4.8 0.9 + - - -
1137A 7O2 4.8 8.0 - - - -
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Residues in contact with GLU 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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528A HIS* 4.6 4.8 - - + -
538A GLU 2.9 23.3 + - - +
539A GLN* 3.5 23.0 + - - +
540A ILE 3.2 0.6 - - - -
541A GLU* 1.3 72.4 - - - +
543A MET* 1.3 65.1 + - - +
544A PHE* 3.1 1.2 + - - -
545A ASP* 3.5 8.8 - - - +
959A GLY* 3.4 14.5 - - - +
960A SER 6.0 0.2 - - - -
997A LEU* 3.4 18.2 - - - +
998A ARG* 3.2 78.1 + - - +
999A CYS* 3.7 10.1 - - - -
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Residues in contact with MET 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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480A TRP* 3.6 27.8 - - + +
481A ASN* 3.8 9.6 - - - +
483A LEU* 3.7 22.0 - - + +
484A TRP 5.2 0.9 - - - +
528A HIS* 4.0 23.8 - - + +
530A ILE 3.8 20.2 - - - +
532A SER* 4.6 8.3 - - - +
534A VAL* 3.6 19.1 - - + -
539A GLN 3.3 13.8 + - - +
540A ILE* 3.1 15.0 + - - +
542A GLU* 1.3 78.4 - - - +
544A PHE* 1.3 56.6 + - - +
545A ASP* 2.8 11.0 + - - +
548A SER* 2.8 43.0 + - - +
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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