Contacts of the helix formed by residues 540 - 549 (chain D) in PDB entry 5MG3
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 GLN 540 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537D THR* 3.1 25.7 + - + +
539D GLN* 1.4 101.8 + - + +
541D ALA* 1.4 63.3 + - - +
542D ILE 3.4 2.3 + - - -
543D ASP* 3.4 15.6 + - + +
544D GLU* 3.1 29.5 + - + +
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Residues in contact with ALA 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D THR* 3.7 14.1 - - - +
538D VAL 3.2 19.5 - - - +
539D GLN 3.4 1.6 + - - -
540D GLN* 1.4 63.0 - - - +
542D ILE* 1.3 62.3 + - + +
544D GLU* 3.5 1.4 - - - +
545D GLY* 2.6 32.9 + - - -
601D VAL* 4.3 0.2 - - - +
605D TYR* 3.7 43.9 + - + -
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Residues in contact with ILE 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ARG* 3.9 10.8 - - - +
540D GLN 3.5 0.8 - - - -
541D ALA* 1.3 85.3 - - + +
543D ASP* 1.4 57.0 + - - +
545D GLY* 3.3 0.9 + - - -
546D TYR* 2.8 53.2 + - + -
601D VAL* 4.0 18.3 - - + +
602D ASN* 3.3 57.4 - - - +
605D TYR* 4.2 7.0 - - + -
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Residues in contact with ASP 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D GLN* 3.4 15.2 + - + +
541D ALA 3.3 0.2 - - - -
542D ILE* 1.4 78.2 - - - +
544D GLU* 1.3 60.7 + - + +
546D TYR* 3.3 14.1 + - - +
547D ARG* 2.9 26.9 + - - +
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Residues in contact with GLU 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D ARG* 5.0 2.8 + - - -
536D ARG* 5.7 9.7 + - + -
537D THR* 4.1 22.0 - - + +
540D GLN* 3.1 25.0 + - + +
541D ALA 3.8 2.5 - - - +
543D ASP* 1.3 73.0 - - + +
545D GLY* 1.4 60.2 + - - +
547D ARG* 2.8 51.2 + - - +
548D GLY* 2.8 27.5 + - - -
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Residues in contact with GLY 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D ARG* 6.1 0.7 - - - -
528D ILE* 4.5 3.6 - - - -
541D ALA 2.6 21.0 + - - -
542D ILE 3.3 2.2 + - - -
544D GLU* 1.4 72.5 - - - +
546D TYR* 1.3 59.4 + - - +
549D ALA* 2.9 43.9 + - - +
550D PHE* 3.4 7.3 - - - -
601D VAL* 4.0 12.3 - - - -
605D TYR* 5.8 1.1 - - - -
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Residues in contact with TYR 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ARG* 3.5 24.5 + - - +
542D ILE* 2.8 40.1 + - + +
543D ASP* 3.3 12.3 + - - +
545D GLY* 1.3 73.7 - - - +
547D ARG* 1.4 59.8 + - - +
550D PHE* 3.8 27.6 - + + +
598D ARG* 3.5 74.0 + - + +
601D VAL* 4.6 3.6 - - + -
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Residues in contact with ARG 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536D ARG* 5.2 6.3 - - - +
543D ASP 2.9 18.7 + - - +
544D GLU* 2.8 47.0 + - - +
546D TYR* 1.4 73.1 - - - +
548D GLY* 1.4 58.7 + - - +
550D PHE 5.3 0.6 + - - -
551D SER* 5.6 3.1 + - - -
223F GLU* 5.1 9.9 + - - -
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Residues in contact with GLY 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D ARG* 3.2 29.6 + - - -
544D GLU 2.8 18.4 + - - -
547D ARG* 1.4 77.7 - - - +
549D ALA* 1.3 61.3 + - - +
550D PHE 3.3 3.3 + - - -
551D SER* 3.6 19.5 + - - -
223F GLU* 6.2 0.2 - - - -
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Residues in contact with ALA 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D ILE* 3.4 26.9 - - + +
527D ARG* 3.8 21.3 - - + +
528D ILE* 3.5 22.9 - - + -
544D GLU 4.2 0.2 + - - -
545D GLY* 2.9 28.2 + - - +
548D GLY* 1.3 72.0 - - - +
550D PHE* 1.3 60.4 + - + +
551D SER 3.6 0.7 - - - -
552D SER 5.2 1.1 + - - -
553D ILE* 3.2 19.4 - - - +
601D VAL* 4.4 0.2 - - + -
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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