Contacts of the helix formed by residues 536 - 543 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B ILE* 5.3 8.7 - - - -
535B GLN* 1.3 85.4 - - - +
537B SER* 1.3 63.8 + - - +
538B GLU* 3.2 21.4 + - - +
539B GLN* 3.3 29.9 + - - +
540B ILE* 3.2 22.7 + - - +
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Residues in contact with SER 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 5.9 1.5 - - - +
297B LEU* 3.6 26.3 - - - +
300B ARG* 5.3 4.9 + - - -
536B SER* 1.3 73.0 - - - +
538B GLU* 1.3 72.0 + - - +
540B ILE* 3.2 5.8 + - - +
541B GLU* 3.0 29.8 + - - +
958B LEU 4.8 1.8 - - - -
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Residues in contact with GLU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B SER* 3.2 21.1 + - - +
537B SER* 1.3 83.7 + - - +
539B GLN* 1.3 57.5 + - + +
541B GLU* 3.3 5.0 + - - +
542B GLU* 2.9 33.5 + - - +
958B LEU* 3.9 42.7 + - + +
959B GLY 3.9 2.3 + - - +
993B ALA* 5.3 3.8 - - - +
997B LEU* 3.8 31.0 - - + -
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Residues in contact with GLN 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B SER 3.8 5.5 - - - +
534B VAL* 3.2 22.1 - - + +
535B GLN* 2.8 26.6 + - - +
536B SER* 3.3 23.8 + - - +
537B SER 3.2 0.6 - - - -
538B GLU* 1.3 73.9 - - + +
540B ILE* 1.3 65.5 + - - +
542B GLU* 3.3 21.0 + - - +
543B MET* 3.3 25.8 + - - +
998B ARG* 4.3 8.9 + - - +
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Residues in contact with ILE 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 6.2 1.1 - - + -
296B PRO* 3.7 29.4 - - + -
297B LEU* 3.6 27.8 - - + -
479B TRP* 4.0 17.5 - - + -
480B TRP* 3.6 41.1 - - + +
534B VAL* 4.6 8.5 - - + -
535B GLN 4.7 2.0 - - - +
536B SER 3.2 16.9 + - - +
537B SER* 3.2 10.0 + - - +
539B GLN* 1.3 77.2 - - - +
541B GLU* 1.3 61.9 + - - +
543B MET* 3.1 24.5 + - - +
544B PHE* 3.7 8.0 - - - -
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Residues in contact with GLU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B TYR* 3.1 33.1 + - - -
296B PRO* 3.4 19.5 - - + +
297B LEU* 5.0 4.8 - - + +
537B SER* 3.0 16.8 + - - +
538B GLU 3.5 6.3 - - - +
540B ILE* 1.3 77.4 - - - +
542B GLU* 1.3 60.9 + - - +
544B PHE* 3.1 26.3 + - - +
957B PRO* 4.1 7.4 - - + +
958B LEU 4.0 12.3 - - - +
959B GLY 3.3 23.4 - - - +
960B SER* 3.6 25.7 - - - +
961B TYR 4.8 1.2 + - - -
1127B 7O2 4.4 11.3 - - - -
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Residues in contact with GLU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B HIS* 4.6 2.8 - - - -
538B GLU* 2.9 21.2 + - - +
539B GLN* 3.6 17.2 - - - +
540B ILE 3.3 0.4 - - - -
541B GLU* 1.3 75.4 - - - +
543B MET* 1.3 63.0 + - - +
544B PHE 3.2 0.9 + - - -
545B ASP* 3.5 22.7 - - - +
959B GLY* 3.8 12.6 - - - +
964B GLN* 5.3 3.0 + - - +
997B LEU* 3.3 24.9 - - - +
998B ARG* 2.9 76.1 + - + +
999B CYS* 4.5 11.0 - - - -
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Residues in contact with MET 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B TRP* 3.6 21.1 - - + +
481B ASN* 3.6 28.0 - - - +
483B LEU* 3.4 22.5 - - + +
484B TRP 5.9 0.2 - - - +
528B HIS* 3.7 24.9 - - + +
530B ILE 3.6 18.2 - - - +
532B SER* 4.1 11.4 - - - +
534B VAL* 3.8 18.4 - - + -
539B GLN 3.3 13.8 + - - +
540B ILE* 3.1 15.4 + - - +
542B GLU* 1.3 77.7 - - - +
544B PHE* 1.3 55.9 + - + +
545B ASP* 3.0 9.7 + - - +
548B SER* 2.9 31.5 + - - +
998B ARG* 4.4 1.3 - - - -
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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