Contacts of the helix formed by residues 547 - 552 (chain A) in PDB entry 2JED
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 ALA 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A TYR 3.6 3.0 + - - -
546A ILE* 1.3 78.0 - - - +
548A PRO* 1.4 72.8 - - + +
549A GLU* 3.6 24.9 - - + +
550A ILE* 3.0 17.8 + - + +
551A LEU* 3.2 11.1 + - - +
560A VAL* 3.7 26.4 - - + +
563A TRP* 3.6 18.2 - - + -
564A SER* 5.1 0.6 + - - -
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Residues in contact with PRO 548 (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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546A ILE 3.8 0.4 - - - -
547A ALA* 1.4 82.0 - - - +
549A GLU* 1.3 67.2 + - - +
551A LEU* 3.1 12.9 + - + +
552A LEU* 2.9 39.0 + - + +
563A TRP* 3.4 47.6 - - + +
591A ILE* 4.1 13.9 - - + +
592A ARG* 4.6 9.1 - - + +
616A ARG* 4.1 26.2 - - + +
621A ARG* 4.2 2.9 - - - +
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Residues in contact with GLU 549 (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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547A ALA* 3.6 10.0 - - - +
548A PRO* 1.3 77.1 - - - +
550A ILE* 1.3 63.6 + - - +
552A LEU* 3.6 6.9 + - - +
553A GLY 3.5 2.4 + - - -
554A GLN* 3.0 45.8 + - + +
555A LYS 5.4 0.4 - - - +
556A TYR* 4.1 12.6 - - + -
559A SER* 2.6 25.3 + - - +
560A VAL* 3.5 18.8 - - + +
616A ARG 4.3 3.1 + - - +
618A PRO* 4.2 19.1 - - + -
621A ARG* 2.7 38.1 + - - -
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Residues in contact with ILE 550 (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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503A ARG* 5.4 4.3 - - + +
538A GLU 4.0 15.3 - - - +
539A PHE* 3.9 24.2 - - + -
540A CYS 3.9 14.6 - - - +
546A ILE* 3.5 29.4 - - + -
547A ALA* 3.0 12.2 + - + +
549A GLU* 1.3 76.6 - - - +
551A LEU* 1.3 56.6 + - - +
553A GLY* 3.0 20.3 + - - -
554A GLN 5.0 0.7 - - - -
556A TYR* 3.8 27.1 - - + +
560A VAL* 3.6 39.0 - - + -
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Residues in contact with LEU 551 (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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539A PHE* 3.7 31.7 - - + -
546A ILE* 3.8 21.5 - - + -
547A ALA 3.2 9.3 + - - +
548A PRO* 3.1 8.8 + - + +
550A ILE* 1.3 74.6 - - - +
552A LEU* 1.3 59.0 + - - +
553A GLY 3.3 1.1 + - - -
588A PHE* 3.6 50.5 - - + +
591A ILE* 3.7 27.4 - - + -
592A ARG* 4.1 17.4 + - + +
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Residues in contact with LEU 552 (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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548A PRO* 2.9 28.0 + - + +
549A GLU* 3.6 3.1 + - - +
550A ILE 3.2 0.4 - - - -
551A LEU* 1.3 77.4 - - - +
553A GLY* 1.3 62.2 + - - +
554A GLN* 3.2 32.3 + - + +
592A ARG* 4.0 26.7 - - + +
616A ARG 6.1 0.4 - - - +
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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