Contacts of the helix formed by residues 537 - 543 (chain C) in PDB entry 4MNE
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C SER* 1.3 67.4 - - - +
538C TYR* 1.3 66.7 + - - +
540C HIS* 3.3 4.4 + - + -
541C LEU* 3.1 46.6 + - + +
548C PHE* 4.1 20.9 - - + -
556C ILE* 3.9 25.8 - - + -
579C SER* 3.8 10.1 - - - +
582C ILE* 2.7 31.3 + - + +
583C PHE* 4.6 0.2 - - - +
584C LEU* 4.4 9.7 - - + +
645C VAL* 4.2 18.4 - - + -
649C LEU* 3.7 26.2 - - + -
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Residues in contact with TYR 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C SER* 3.2 5.6 - - - +
537C LEU* 1.3 77.8 - - - +
539C HIS* 1.3 67.5 + - - +
540C HIS 3.1 0.3 + - - -
542C HIS* 2.9 61.0 + + + +
543C ILE* 4.1 4.9 - - + -
579C SER* 3.3 25.6 + - - -
580C ASN* 3.3 40.4 - - - +
619C TRP* 4.7 1.8 - + - -
654C LEU* 4.1 12.4 - - + +
102D GLU* 3.5 42.4 + - + -
103D ILE* 5.9 0.2 - - - +
221D ASN* 3.2 32.0 + - - +
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Residues in contact with HIS 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C SER* 3.6 28.5 + - - -
536C SER* 3.1 19.5 + - - +
538C TYR* 1.3 81.9 - - - +
540C HIS* 1.3 57.4 + - - +
543C ILE* 3.0 44.3 + - + +
544C ILE* 3.0 52.1 + - + +
102D GLU* 4.7 11.0 + - - +
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Residues in contact with HIS 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C SER* 3.8 21.2 + - - -
536C SER 3.2 20.1 + - - -
537C LEU* 3.7 8.5 - - + +
538C TYR 3.1 0.4 - - - -
539C HIS* 1.3 78.3 - - - +
541C LEU* 1.3 58.5 + - - +
544C ILE* 3.7 15.8 - - + +
545C GLU 3.0 10.4 + - - -
546C THR* 2.7 59.2 + - + +
548C PHE* 3.8 25.8 - + + -
584C LEU* 3.8 22.3 - - + +
587C ASP* 3.5 31.4 + - + -
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Residues in contact with LEU 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C LEU* 3.1 40.4 + - + +
540C HIS* 1.3 79.2 - - - +
542C HIS* 1.3 77.2 + - + +
545C GLU* 3.8 18.2 - - - +
546C THR 5.3 3.8 - - - +
548C PHE* 4.2 25.1 - - + -
553C LEU* 4.6 4.0 - - + -
579C SER* 4.3 0.4 - - - +
648C GLU* 3.7 47.6 - - + +
649C LEU* 4.1 13.0 - - + +
652C GLY* 4.0 14.9 - - - +
682C ARG* 5.2 5.8 - - - +
104D LYS* 5.1 0.3 + - - -
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Residues in contact with HIS 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C TYR* 2.9 56.9 + + + +
541C LEU* 1.3 97.8 + - + +
543C ILE* 1.3 64.2 + - + +
545C GLU 4.6 0.7 - - - -
648C GLU* 2.5 32.5 + - + -
652C GLY 3.7 11.1 + - - -
653C GLN* 3.7 29.3 - - - -
654C LEU* 3.4 14.0 + - + +
104D LYS* 2.9 37.1 + - - +
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Residues in contact with ILE 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C TYR* 4.1 12.1 - - + -
539C HIS* 3.0 49.3 + - + +
542C HIS* 1.3 86.4 - - + +
544C ILE* 1.3 65.2 + - + +
545C GLU* 3.2 8.7 + - - +
102D GLU* 3.3 32.8 - - + +
103D ILE* 3.5 30.7 - - - +
104D LYS* 3.9 19.1 - - - +
105D PRO* 4.6 10.6 - - + +
108D ARG* 5.3 3.6 - - - +
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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