Contacts of the helix formed by residues 447 - 458 (chain A) in PDB entry 2O8C
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 PHE 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A LEU* 5.3 1.8 - - + -
411A ILE* 3.6 44.9 - - + +
414A LEU* 5.1 1.6 - - + -
443A LEU* 3.2 29.7 + - + +
444A ARG 3.9 5.4 - - - +
445A SER 3.4 0.2 - - - -
446A ASP* 1.3 79.1 - - + +
448A SER* 1.3 56.3 + - - +
449A LYS 3.4 2.2 - - - -
450A PHE* 3.9 15.9 - + + -
451A GLN* 3.2 26.9 + - - +
588A TYR* 4.1 33.9 - + + -
591A PRO* 3.4 44.4 - - + -
592A MET* 4.3 13.9 - - - -
595A LEU* 3.8 23.1 - - + -
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Residues in contact with SER 448 (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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444A ARG* 3.6 20.2 + - - +
445A SER* 3.0 26.5 + - - -
446A ASP 3.3 1.4 - - - -
447A PHE* 1.3 78.0 - - - +
449A LYS* 1.3 72.5 + - - +
451A GLN* 3.7 4.1 + - - +
452A GLU* 3.3 23.4 + - - +
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Residues in contact with LYS 449 (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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446A ASP 4.8 1.9 + - - +
447A PHE 3.4 0.2 - - - -
448A SER* 1.3 87.6 + - - +
450A PHE* 1.3 64.0 + - - +
452A GLU* 3.8 5.1 + - - +
453A MET* 3.2 23.0 + - - +
588A TYR* 3.4 18.8 + - - +
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Residues in contact with PHE 450 (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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404A CYS* 4.1 14.6 - - + -
407A LEU* 3.8 23.1 - - + -
408A TYR* 4.6 5.2 - + + -
411A ILE* 3.7 32.5 - - + -
447A PHE* 3.7 15.4 + + + +
448A SER 3.3 0.2 - - - -
449A LYS* 1.3 78.3 - - - +
451A GLN* 1.3 66.0 + - - +
453A MET* 3.3 39.3 + - + +
454A ILE* 3.4 36.5 + - + +
581A ILE* 6.0 0.7 - - + -
585A SER* 3.7 28.0 - - - -
588A TYR* 3.8 33.3 + + + -
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Residues in contact with GLN 451 (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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408A TYR* 3.5 30.1 - - + +
411A ILE* 4.6 10.8 - - + -
412A ASN* 6.4 0.2 - - - -
444A ARG* 6.3 0.7 - - - +
447A PHE 3.2 16.9 + - - +
448A SER* 4.1 5.2 - - - +
449A LYS 3.4 0.2 - - - -
450A PHE* 1.3 78.7 - - - +
452A GLU* 1.3 61.8 + - - +
454A ILE 3.5 1.4 + - - -
455A GLU* 3.3 31.1 + - - +
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Residues in contact with GLU 452 (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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448A SER 3.3 16.0 + - - +
449A LYS* 4.2 5.8 - - - +
450A PHE 3.4 0.2 - - - -
451A GLN* 1.3 76.5 - - - +
453A MET* 1.3 63.2 + - - +
454A ILE 3.5 0.2 - - - -
455A GLU* 4.1 14.9 - - - +
456A THR* 3.3 26.5 + - - +
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Residues in contact with MET 453 (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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449A LYS 3.2 18.6 + - - +
450A PHE* 3.4 38.1 - - + +
451A GLN 3.2 0.8 - - - -
452A GLU* 1.3 76.7 - - - +
454A ILE* 1.3 60.5 + - + +
456A THR* 3.1 17.8 + - - -
457A THR* 2.7 35.4 + - + +
581A ILE* 4.1 32.1 - - + +
584A ILE* 3.8 38.6 - - + -
585A SER* 5.1 0.9 - - - -
588A TYR* 6.1 0.2 - - - -
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Residues in contact with ILE 454 (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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404A CYS* 3.7 24.7 - - + +
405A TYR* 5.0 6.5 - - + -
408A TYR* 3.8 28.3 - - + -
450A PHE* 3.4 44.6 + - + +
451A GLN 3.5 5.4 + - - +
452A GLU 3.5 0.2 - - - -
453A MET* 1.3 82.3 - - + +
455A GLU* 1.3 60.8 + - - +
456A THR 3.1 2.2 - - - -
457A THR* 3.0 6.9 + - - +
458A LEU* 2.9 59.3 + - + +
581A ILE* 5.9 3.4 - - + -
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Residues in contact with GLU 455 (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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408A TYR* 3.1 28.3 + - + +
451A GLN* 3.3 17.2 + - - +
452A GLU* 4.2 14.3 - - - +
453A MET 3.4 0.4 - - - -
454A ILE* 1.3 77.1 - - - +
456A THR* 1.3 61.7 + - + +
458A LEU 4.4 2.4 - - - +
471A LYS* 2.8 24.9 + - - -
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Residues in contact with THR 456 (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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452A GLU 3.3 15.2 + - - +
453A MET* 3.1 14.8 + - - -
455A GLU* 1.3 82.1 - - + +
457A THR* 1.3 62.8 + - - +
471A LYS* 3.4 19.4 - - - +
474A PHE* 3.3 30.6 - - - +
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Residues in contact with THR 457 (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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453A MET* 2.7 31.3 + - + +
454A ILE* 3.0 9.2 + - - +
456A THR* 1.3 83.0 - - - +
458A LEU* 1.3 68.8 + - - +
470A VAL* 3.4 12.7 - - + +
471A LYS* 2.6 34.4 + - - -
474A PHE* 3.8 33.9 - - + -
577A ILE* 5.7 0.7 - - + -
581A ILE* 4.4 21.6 - - + +
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Residues in contact with LEU 458 (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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401A LEU* 3.9 46.0 - - + +
404A CYS* 5.6 2.0 - - + -
405A TYR* 4.8 14.6 - - + +
454A ILE* 2.9 43.0 + - + +
455A GLU* 4.4 2.4 - - - +
457A THR* 1.3 91.8 - - - +
459A ASP* 1.3 60.1 + - - +
460A MET* 3.2 9.4 + - - +
463A VAL* 4.5 19.5 - - + -
468A PHE* 5.0 4.3 - - + -
469A LEU 3.9 13.7 - - - +
470A VAL* 5.4 2.2 - - + -
471A LYS* 3.5 12.4 - - - -
581A ILE* 4.9 7.2 - - + -
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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