Contacts of the helix formed by residues 492 - 503 (chain A) in PDB entry 2O2C
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 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LYS* 6.2 1.6 - - - -
489A ILE 5.5 0.2 + - - -
491A LYS* 1.3 74.6 - - - +
493A PRO* 1.4 74.9 - - - +
494A SER* 3.5 9.1 + - - -
495A GLU* 3.0 45.3 + - - +
496A VAL* 3.2 12.9 + - - +
519A THR* 4.5 1.1 - - - -
520A PHE 4.8 1.3 - - - -
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Residues in contact with PRO 493 (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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492A SER* 1.4 86.0 - - - +
494A SER* 1.3 61.3 + - - +
496A VAL* 3.5 2.1 + - + +
497A ARG* 3.3 22.0 + - - +
515A LEU* 3.6 31.3 - - + +
519A THR* 4.0 23.6 - - + +
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Residues in contact with SER 494 (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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492A SER* 3.2 8.8 + - - -
493A PRO* 1.3 76.1 - - - +
495A GLU* 1.3 59.6 + - - +
497A ARG* 3.4 9.5 + - - +
498A ARG* 3.1 43.6 + - - +
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Residues in contact with GLU 495 (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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72A LYS* 4.8 10.6 + - - -
489A ILE* 6.0 2.1 - - - +
490A GLY 4.5 4.3 - - - +
491A LYS* 3.7 23.5 - - + +
492A SER* 3.0 39.9 + - - +
494A SER* 1.3 73.8 - - - +
496A VAL* 1.3 60.6 + - - +
498A ARG* 3.4 32.4 + - - +
499A GLU* 3.1 29.3 + - - +
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Residues in contact with VAL 496 (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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491A LYS* 3.8 20.9 - - - +
492A SER 3.2 15.0 + - - +
493A PRO 3.7 1.6 - - - +
495A GLU* 1.3 73.8 - - - +
497A ARG* 1.3 61.8 + - - +
499A GLU* 3.4 6.9 + - + +
500A LEU* 3.1 37.4 + - + +
515A LEU* 3.3 25.6 - - + +
518A LYS* 3.7 44.6 - - + +
519A THR* 4.1 13.9 - - - +
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Residues in contact with ARG 497 (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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493A PRO 3.3 12.1 + - - +
494A SER* 3.6 11.6 - - - +
495A GLU 3.3 0.4 - - - -
496A VAL* 1.3 80.0 - - - +
498A ARG* 1.3 57.1 + - + +
500A LEU* 4.0 0.7 - - - +
501A GLU* 3.1 60.1 + - - +
508A ALA* 5.3 2.8 + - - +
511A ILE* 3.2 33.2 - - + +
512A ASN* 3.0 25.1 + - - +
515A LEU* 3.9 21.4 - - + +
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Residues in contact with ARG 498 (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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494A SER* 3.1 36.5 + - - +
495A GLU* 3.4 36.0 + - - +
496A VAL 3.3 0.2 - - - -
497A ARG* 1.3 77.7 - - + +
499A GLU* 1.3 57.6 + - - +
501A GLU* 3.9 7.1 - - - +
502A ALA* 3.1 32.1 + - - +
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Residues in contact with GLU 499 (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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491A LYS* 2.6 41.1 + - - +
495A GLU 3.1 15.1 + - - +
496A VAL* 3.8 5.2 - - + +
498A ARG* 1.3 77.8 - - - +
500A LEU* 1.3 63.5 + - + +
502A ALA* 3.6 4.5 + - - +
503A ALA* 3.3 22.7 + - - +
518A LYS* 5.8 2.1 + - - -
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Residues in contact with LEU 500 (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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496A VAL* 3.1 38.4 + - + +
497A ARG 4.1 3.1 - - - +
499A GLU* 1.3 77.8 - - + +
501A GLU* 1.3 61.5 + - - +
502A ALA 3.2 0.8 + - - -
503A ALA* 3.5 11.7 + - + +
504A GLY 3.5 0.7 + - - -
505A GLU* 3.0 37.0 + - + +
510A LYS* 6.6 0.4 - - + -
511A ILE* 4.2 40.8 - - + +
514A LEU* 5.0 11.4 - - + -
518A LYS* 4.4 25.4 - - + +
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Residues in contact with GLU 501 (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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497A ARG* 3.1 46.6 + - - +
498A ARG* 4.2 6.5 - - - +
500A LEU* 1.3 76.5 - - - +
502A ALA* 1.3 60.1 + - - +
504A GLY* 3.7 10.3 + - - -
505A GLU 4.0 12.2 + - - +
506A ARG* 5.6 10.4 - - - +
511A ILE* 3.6 21.9 - - + +
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Residues in contact with ALA 502 (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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498A ARG 3.1 19.6 + - - +
499A GLU* 3.9 6.1 - - - +
500A LEU 3.2 0.4 - - - -
501A GLU* 1.3 75.9 - - - +
503A ALA* 1.3 59.4 + - - +
504A GLY* 3.2 5.3 + - - -
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Residues in contact with ALA 503 (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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499A GLU 3.3 15.9 + - - +
500A LEU* 3.8 8.7 - - + +
501A GLU 3.4 0.4 - - - -
502A ALA* 1.3 77.2 - - - +
504A GLY* 1.3 57.6 + - - +
505A GLU* 3.9 0.9 - - + -
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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