Contacts of the helix formed by residues 453 - 461 (chain A) in PDB entry 3ODX
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 PRO 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A LEU* 6.0 0.7 - - + -
451A PHE 4.6 1.3 - - - +
452A PHE* 1.4 89.2 - - + +
454A LEU* 1.3 65.2 + - - +
455A GLU* 3.2 15.5 - - - +
456A GLU* 3.1 48.6 + - + +
457A LEU 3.3 3.8 + - - -
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Residues in contact with LEU 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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443A PHE* 5.5 5.6 - - + -
447A ALA* 5.0 8.5 - - + -
452A PHE 3.6 2.3 + - - -
453A PRO* 1.3 66.1 - - - +
455A GLU* 1.3 74.8 + - - +
456A GLU 3.0 1.8 - - - -
457A LEU* 2.8 36.6 + - + +
458A GLN* 2.8 40.7 + - + +
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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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453A PRO* 3.2 14.6 - - - +
454A LEU* 1.3 88.1 + - - +
456A GLU* 1.3 63.3 + - + +
458A GLN* 3.2 26.8 + - - +
459A ASN* 3.3 14.2 + - - +
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Residues in contact with GLU 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 PHE* 3.4 25.9 - - + -
453A PRO* 3.1 35.1 + - + +
454A LEU 3.0 0.4 - - - -
455A GLU* 1.3 79.6 - - + +
457A LEU* 1.3 67.9 + - - +
458A GLN 3.0 1.3 - - - -
459A ASN* 2.9 22.6 + - - +
460A ILE* 3.0 17.7 + - + +
521A PHE* 5.0 1.6 - - + -
525A GLN* 5.0 6.8 + - - -
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Residues in contact with LEU 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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443A PHE* 3.8 21.5 - - + +
446A MET* 4.1 22.9 - - + +
447A ALA* 3.5 40.2 - - + +
452A PHE* 4.3 21.9 - - + +
453A PRO 3.3 4.0 + - - +
454A LEU* 2.8 27.9 + - + +
456A GLU* 1.3 75.6 - - - +
458A GLN* 1.3 57.6 + - - +
460A ILE* 2.9 11.5 + - + +
461A PHE* 2.8 54.3 + - + +
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Residues in contact with GLN 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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443A PHE* 5.3 9.8 - - + -
454A LEU* 2.8 42.3 + - + +
455A GLU* 3.3 20.4 - - - +
457A LEU* 1.3 78.2 - - - +
459A ASN* 1.3 58.3 + - - +
461A PHE 4.3 7.0 - - - +
462A PRO* 2.9 36.0 - - - +
514A ARG* 5.0 3.6 + - - +
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Residues in contact with ASN 459 (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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455A GLU* 3.3 13.1 + - - +
456A GLU* 2.9 15.1 + - - +
458A GLN* 1.3 78.9 - - - +
460A ILE* 1.3 64.0 + - - +
462A PRO* 3.4 5.3 - - - +
514A ARG* 5.7 2.8 + - - -
518A ARG* 2.9 61.1 + - - +
521A PHE* 3.9 19.9 - - + -
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Residues in contact with ILE 460 (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 PHE* 3.6 46.2 - - + -
456A GLU* 3.2 15.3 - - + +
457A LEU* 2.9 8.6 + - + +
459A ASN* 1.3 80.7 - - - +
461A PHE* 1.3 77.2 + - + +
462A PRO* 3.2 7.4 - - - +
515A PHE* 4.9 2.3 - - - -
521A PHE* 4.3 11.9 - - + -
522A ALA* 3.4 44.6 - - + +
525A GLN* 3.7 13.0 - - + +
526A LEU* 3.9 18.6 - - + -
558A ILE* 5.3 0.5 - - - +
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Residues in contact with PHE 461 (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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438A LEU* 4.1 30.3 - - + -
442A PHE* 4.9 1.6 - - + -
443A PHE* 3.3 47.9 - + + -
446A MET* 4.2 17.5 - - + -
457A LEU* 2.8 27.7 + - + -
458A GLN* 3.4 9.6 - - - +
460A ILE* 1.3 94.2 - - + +
462A PRO* 1.3 64.5 - - - +
463A SER 3.2 3.5 + - - -
464A LEU* 3.4 20.3 + - + +
515A PHE* 4.2 11.0 - + - -
526A LEU* 4.8 4.5 - - + -
554A LEU* 4.5 11.7 - - + -
558A ILE* 3.9 26.2 - - + -
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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