Contacts of the helix formed by residues 444 - 451 (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 PHE 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU* 3.8 14.4 - - + -
433A PHE* 3.9 25.8 - + + -
434A GLY* 4.2 4.9 - - - -
435A GLU* 3.9 43.7 - - + -
440A GLY* 3.0 16.6 + - - -
443A ALA* 1.3 88.8 - - + +
445A TYR* 1.3 84.3 + + - +
446A GLN* 3.1 8.1 - - - +
447A LEU* 3.1 21.4 + - + +
448A ILE* 3.5 19.0 + - + +
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Residues in contact with TYR 445 (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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392A LEU* 3.2 31.7 - - + +
394A TYR* 3.0 37.9 + - - -
435A GLU 5.3 0.3 + - - -
437A GLY* 4.9 3.9 - - - -
440A GLY* 3.0 29.1 + - - +
441A GLN* 3.6 30.6 + - + +
443A ALA 3.9 0.4 - - - -
444A PHE* 1.3 97.8 - + - +
446A GLN* 1.3 65.2 + - - +
447A LEU 3.1 0.2 - - - -
448A ILE* 3.1 13.3 + - + +
449A HIS* 2.9 39.1 + + + -
459A PHE* 3.8 8.9 - + - -
483A GLN* 3.3 27.6 - - + +
487A LEU* 6.3 0.9 - - + -
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Residues in contact with GLN 446 (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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441A GLN 5.0 2.8 + - - +
443A ALA 5.5 2.9 - - - +
444A PHE* 4.7 3.4 - - - -
445A TYR* 1.3 78.2 - - - +
447A LEU* 1.3 53.4 + - + +
449A HIS* 4.0 3.8 - - - +
450A GLN* 2.8 64.9 + - - +
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Residues in contact with LEU 447 (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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433A PHE* 6.0 1.1 - - + -
444A PHE* 3.1 13.9 + - + +
446A GLN* 1.3 81.4 - - + +
448A ILE* 1.3 62.6 + - + +
451A GLY* 2.8 37.4 + - - +
453A ASN* 3.9 25.9 - - + +
455A ILE* 3.5 26.9 - - + -
524A ARG* 4.7 0.2 + - - -
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Residues in contact with ILE 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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390A ALA* 4.7 0.7 - - + -
392A LEU* 4.5 3.6 - - + -
433A PHE* 4.6 10.1 - - + -
444A PHE* 3.8 37.5 - - + +
445A TYR* 3.1 23.2 + - + +
447A LEU* 1.3 77.1 - - + +
449A HIS* 1.3 58.9 + - + +
453A ASN 4.8 1.4 - - - +
455A ILE* 4.1 32.4 + - + +
457A CYS* 3.9 30.3 - - - -
487A LEU* 3.7 22.2 - - + -
524A ARG* 3.2 31.1 + - + +
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Residues in contact with HIS 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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445A TYR* 2.9 36.8 + + + +
446A GLN* 4.0 4.0 - - - +
448A ILE* 1.3 79.8 - - + +
450A GLN* 1.3 61.7 + - + +
483A GLN* 2.8 28.7 + - - -
486A ALA* 3.7 27.6 + - + -
487A LEU* 3.6 31.8 - - + +
520A PHE* 3.9 35.7 - + + +
521A ILE* 4.9 6.9 + - - +
522A GLY 5.5 0.9 + - - -
524A ARG* 2.9 22.3 + - - +
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Residues in contact with GLN 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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446A GLN* 2.8 44.5 + - - +
447A LEU* 4.7 0.4 - - - -
449A HIS* 1.3 78.4 - - + +
451A GLY* 1.3 62.0 + - - +
452A THR* 5.6 0.3 - - - +
516A PRO 4.8 1.0 + - - -
517A HIS* 2.9 28.6 + - - +
519A THR 3.0 26.3 + - - +
520A PHE* 4.1 28.5 - - + -
524A ARG* 3.7 1.8 - - - +
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Residues in contact with GLY 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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447A LEU* 2.8 37.9 + - - -
450A GLN* 1.3 76.7 - - - +
452A THR* 1.3 62.0 + - - -
453A ASN 3.3 7.5 + - - -
521A ILE* 5.5 0.7 - - - +
524A ARG* 3.0 21.6 + - - +
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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