Contacts of the helix formed by residues 545 - 554 (chain A) in PDB entry 2OZO
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 GLY 545 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A LYS* 1.3 100.6 - - - +
546A PRO* 1.3 75.5 - - - +
547A GLU* 3.0 5.2 + - - +
548A VAL* 3.2 10.4 + - - +
549A MET* 4.2 0.7 + - - +
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Residues in contact with PRO 546 (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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545A GLY* 1.3 80.6 - - - +
547A GLU* 1.3 68.2 + - + +
548A VAL 2.9 0.2 - - - -
549A MET* 2.7 28.0 + - + +
550A ALA* 2.8 14.4 + - + +
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Residues in contact with GLU 547 (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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542A LYS 4.9 2.7 - - - +
543A MET* 3.1 31.0 - - + +
544A LYS* 2.9 28.1 + - - +
545A GLY 3.0 2.4 + - - +
546A PRO* 1.3 77.5 - - + +
548A VAL* 1.3 56.1 + - - +
550A ALA* 3.7 7.1 - - - +
551A PHE* 3.0 26.7 + - - +
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Residues in contact with VAL 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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504A LYS* 4.4 16.6 - - + +
540A TYR* 4.0 42.8 - - + +
543A MET* 4.0 21.5 - - + -
544A LYS 3.3 20.9 - - - +
545A GLY 3.8 3.4 - - - +
546A PRO 2.7 4.2 + - - -
547A GLU* 1.3 70.8 - - - +
549A MET* 1.3 67.9 + - - +
550A ALA 3.0 1.8 - - - -
551A PHE* 2.8 9.1 + - - +
552A ILE* 2.7 31.8 + - + +
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Residues in contact with MET 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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508A PRO* 3.9 34.8 - - + -
511A ILE* 3.7 37.0 - - + -
512A ASN* 4.1 16.8 - - - +
545A GLY 4.2 1.0 + - - -
546A PRO* 2.7 23.8 + - + +
548A VAL* 1.3 76.5 - - - +
550A ALA* 1.3 64.6 + - - +
552A ILE* 3.2 13.2 + - + +
553A GLU* 3.2 19.8 + - + +
578A TYR* 4.9 3.6 - - + +
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Residues in contact with ALA 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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546A PRO* 2.8 10.7 + - + +
547A GLU* 3.7 12.3 - - - +
549A MET* 1.3 74.1 - - - +
551A PHE* 1.3 68.2 + - - +
552A ILE 2.8 1.7 + - - -
553A GLU* 3.0 17.4 + - - +
554A GLN* 3.3 23.6 + - - +
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Residues in contact with PHE 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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540A TYR* 3.8 33.7 - + - -
543A MET* 4.1 18.4 - - + -
547A GLU 3.0 13.8 + - - +
548A VAL* 2.8 16.5 + - - +
550A ALA* 1.3 76.0 - - - +
552A ILE* 1.3 64.0 + - + +
554A GLN* 3.6 13.2 + - - +
556A LYS* 3.1 75.0 + - + +
557A ARG 3.3 28.0 - - - -
558A MET* 4.7 2.0 - - + -
559A GLU* 5.8 2.2 - - - -
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Residues in contact with ILE 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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508A PRO* 3.8 12.8 - - + -
523A TRP* 4.1 14.1 - - + -
540A TYR* 3.9 21.8 - - + +
548A VAL* 2.7 29.6 + - + +
549A MET* 3.4 14.4 - - + +
550A ALA 2.8 0.8 + - - -
551A PHE* 1.3 78.4 - - + +
553A GLU* 1.3 56.2 + - - +
555A GLY* 2.7 27.0 + - - -
556A LYS 3.5 15.5 - - - +
557A ARG* 3.1 38.5 + - - +
578A TYR* 3.7 26.3 - - + -
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Residues in contact with GLU 553 (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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549A MET* 3.2 9.4 + - + +
550A ALA* 3.0 9.9 + - - +
552A ILE* 1.3 81.4 - - - +
554A GLN* 1.3 58.2 + - + +
555A GLY* 2.9 6.4 + - - -
578A TYR* 4.7 15.5 - - + +
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Residues in contact with GLN 554 (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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550A ALA* 3.3 25.8 + - - +
551A PHE* 3.8 12.4 + - - +
552A ILE 2.9 1.8 + - - -
553A GLU* 1.3 75.5 - - + +
555A GLY* 1.3 61.4 + - - +
556A LYS* 3.2 26.5 + - + +
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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