Contacts of the helix formed by residues 438 - 449 (chain A) in PDB entry 5OC9
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 ILE 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A ALA* 2.9 25.7 + - + +
437A LEU* 1.3 80.5 - - + +
439A THR* 1.4 70.9 + - - +
440A SER 3.4 0.9 - - - -
441A GLN* 3.2 5.9 + - - +
442A ILE* 3.1 41.8 + - + +
515A TYR* 3.6 20.9 - - - +
521A PHE* 3.9 32.5 - - + -
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Residues in contact with THR 439 (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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434A ALA 4.9 0.2 + - - -
435A THR* 3.3 24.1 + - + +
438A ILE* 1.4 78.7 - - - +
440A SER* 1.3 62.1 + - - +
442A ILE* 3.4 11.1 + - - +
443A LEU* 3.1 42.0 + - + +
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Residues in contact with SER 440 (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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435A THR* 2.8 25.6 + - - +
436A LEU* 3.4 25.1 - - - +
439A THR* 1.3 72.3 - - - +
441A GLN* 1.4 56.5 + - - +
443A LEU* 3.6 9.2 + - - +
444A ASN* 2.9 29.2 + - - +
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Residues in contact with GLN 441 (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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436A LEU 3.4 16.3 + - - +
437A LEU* 2.8 35.5 + - - +
438A ILE 3.2 8.8 + - - +
440A SER* 1.4 73.6 - - - +
442A ILE* 1.4 64.7 + - + +
444A ASN* 3.5 7.7 + - + +
445A GLN* 3.2 28.6 + - - +
500A GLU* 5.2 3.1 - - - +
504A GLN* 2.9 32.6 + - - +
507A TYR* 6.2 2.0 - - + -
521A PHE 3.8 8.7 + - - -
525A ASN* 3.1 35.6 + - + +
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Residues in contact with ILE 442 (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 ILE* 3.1 42.1 + - + +
439A THR* 3.8 9.2 - - - +
441A GLN* 1.4 74.4 - - + +
443A LEU* 1.4 63.7 + - + +
445A GLN* 3.3 16.3 + - - +
446A ILE* 3.3 29.0 + - + +
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Residues in contact with LEU 443 (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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439A THR* 3.1 40.1 + - + +
440A SER* 3.9 7.4 - - - +
442A ILE* 1.4 73.2 - - + +
444A ASN* 1.4 64.1 + - - +
446A ILE* 3.3 18.5 + - + +
447A MET* 3.1 32.4 + - + +
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Residues in contact with ASN 444 (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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440A SER* 2.9 20.3 + - - +
441A GLN* 3.6 10.0 - - - +
442A ILE 3.3 0.2 - - - -
443A LEU* 1.4 75.3 - - - +
445A GLN* 1.4 51.7 + - - +
447A MET* 3.3 6.7 + - - +
448A GLU* 2.8 43.4 + - - +
500A GLU* 3.1 22.7 + - - +
701A CA 2.3 31.9 - - - -
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Residues in contact with GLN 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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441A GLN 3.2 15.1 + - - +
442A ILE* 3.3 9.8 + - - +
444A ASN* 1.4 72.5 - - - +
446A ILE* 1.3 64.1 + - - +
448A GLU* 3.2 6.5 - - - +
449A SER* 3.2 21.5 + - - -
450A PHE* 3.3 29.8 + - + -
525A ASN* 4.0 7.7 + - - +
528A THR* 3.3 33.6 + - - +
529A GLU* 3.1 12.8 + - - +
532A SER* 2.7 37.7 + - - -
701A CA 2.8 19.4 - - - -
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Residues in contact with ILE 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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442A ILE* 3.3 34.3 + - + +
443A LEU* 3.3 21.2 + - + +
444A ASN 3.3 0.4 - - - -
445A GLN* 1.3 77.7 - - - +
447A MET* 1.3 67.7 + - - +
450A PHE* 3.6 19.4 + - + -
451A LEU* 2.8 47.1 + - + +
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Residues in contact with MET 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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443A LEU* 3.1 22.6 + - + +
444A ASN* 3.8 6.3 - - - +
446A ILE* 1.3 82.9 - - - +
448A GLU* 1.4 61.0 + - - +
451A LEU* 4.1 24.7 - - + +
452A PRO* 3.3 17.5 - - - +
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASN* 2.8 25.0 + - - +
445A GLN* 3.2 9.4 - - - +
447A MET* 1.4 73.4 - - - +
449A SER* 1.3 61.2 + - - +
452A PRO* 3.7 10.8 - - - +
496A ASP* 5.6 0.7 - - - +
497A ASP* 3.4 0.7 - - - +
500A GLU* 3.0 12.8 - - - +
529A GLU* 3.0 4.0 - - - +
532A SER* 4.7 0.9 - - - -
533A ASP* 2.9 9.2 - - - +
536A LYS* 2.8 37.2 + - + +
540A VAL* 5.4 0.9 - - - +
541A PHE* 5.3 6.2 - - - -
701A CA 2.6 28.1 - - - -
702A CA 2.2 25.8 - - - -
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Residues in contact with SER 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 GLN 3.2 6.7 + - - -
447A MET 3.7 0.2 - - - -
448A GLU* 1.3 79.4 - - - +
450A PHE* 1.3 67.2 + - - +
452A PRO* 3.5 7.2 - - - -
453A TYR* 2.8 35.3 + - - +
532A SER* 3.4 46.7 + - - -
535A LEU* 4.0 7.7 - - - +
536A LYS* 3.7 15.7 - - - -
540A VAL* 4.0 2.2 - - - +
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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