Contacts of the helix formed by residues 438 - 449 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B ALA* 2.9 26.1 + - + +
437B LEU* 1.3 80.4 - - - +
439B THR* 1.4 69.3 + - - +
440B SER 3.4 0.7 - - - -
441B GLN* 3.2 5.4 + - - +
442B ILE* 3.1 42.5 + - + +
515B TYR* 3.6 20.9 - - - +
521B PHE* 3.9 33.7 - - + -
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Residues in contact with THR 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B ALA 4.9 0.2 + - - -
435B THR* 3.3 23.8 + - + +
438B ILE* 1.4 78.9 - - - +
440B SER* 1.3 62.7 + - - +
442B ILE* 3.4 11.0 + - - +
443B LEU* 3.1 45.2 + - + +
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B THR* 2.8 25.7 + - - +
436B LEU* 3.4 24.5 - - - +
439B THR* 1.3 71.8 - - - +
441B GLN* 1.4 57.2 + - - +
443B LEU* 3.6 8.5 + - - +
444B ASN* 2.9 29.3 + - - +
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Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B LEU 3.4 16.5 + - - +
437B LEU* 2.8 34.9 + - - +
438B ILE 3.2 8.6 + - - +
440B SER* 1.4 73.4 - - - +
442B ILE* 1.4 64.0 + - + +
444B ASN* 3.6 8.3 - - + +
445B GLN* 3.2 28.9 + - - +
500B GLU* 5.2 3.6 - - - +
504B GLN* 2.9 33.4 + - - +
507B TYR* 6.2 2.2 - - + -
521B PHE 3.8 8.9 + - - -
522B ALA* 4.6 0.2 - - - +
525B ASN* 3.1 35.8 + - + +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ILE* 3.1 41.0 + - + +
439B THR* 3.4 9.4 + - - +
441B GLN* 1.4 74.2 - - + +
443B LEU* 1.4 63.8 + - + +
445B GLN* 3.3 15.8 + - - +
446B ILE* 3.3 28.2 + - + +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B THR* 3.1 41.5 + - + +
440B SER* 3.9 7.0 - - - +
442B ILE* 1.4 73.7 - - + +
444B ASN* 1.4 64.3 + - - +
446B ILE* 3.3 18.0 + - + +
447B MET* 3.1 33.7 + - + +
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Residues in contact with ASN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B SER* 2.9 20.1 + - - +
441B GLN* 3.6 10.3 - - - +
443B LEU* 1.4 75.7 - - - +
445B GLN* 1.4 49.7 + - - +
447B MET* 3.3 6.3 + - - +
448B GLU* 2.8 42.3 + - - +
500B GLU* 3.1 24.2 + - - +
701B CA 2.5 31.2 - - - -
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Residues in contact with GLN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B GLN 3.2 14.4 + - - +
442B ILE* 3.3 10.7 + - - +
444B ASN* 1.4 71.7 - - - +
446B ILE* 1.4 62.4 + - - +
448B GLU* 3.1 4.5 - - - +
449B SER* 3.2 21.3 + - - -
450B PHE* 3.3 30.5 + - + -
525B ASN* 3.9 8.2 + - - +
528B THR* 3.3 26.3 + - - +
529B GLU* 3.0 16.9 + - - +
532B SER* 2.7 38.2 + - - -
701B CA 2.5 26.2 - - - -
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Residues in contact with ILE 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B ILE* 3.4 33.7 - - + +
443B LEU* 3.6 19.5 - - + +
444B ASN 3.3 0.6 - - - -
445B GLN* 1.4 76.9 - - - +
447B MET* 1.3 67.0 + - - +
450B PHE* 3.6 18.9 + - + -
451B LEU* 2.8 46.0 + - + +
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Residues in contact with MET 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B LEU* 3.1 22.4 + - + +
444B ASN* 3.8 6.1 - - - +
446B ILE* 1.3 83.9 - - - +
448B GLU* 1.4 58.9 + - - +
451B LEU* 4.1 24.9 - - + +
452B PRO* 3.3 17.2 - - - +
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Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ASN* 2.8 28.1 + - - +
445B GLN* 3.1 9.8 - - - +
447B MET* 1.4 72.6 - - - +
449B SER* 1.4 59.2 + - - +
452B PRO* 3.6 10.5 - - - +
496B ASP* 5.3 1.6 - - - +
497B ASP* 3.4 1.7 - - - +
500B GLU* 2.9 15.7 - - - +
529B GLU* 3.0 5.5 - - - +
532B SER* 3.5 4.3 + - - -
533B ASP* 3.3 12.7 - - - +
536B LYS* 2.9 38.9 + - + +
540B VAL* 5.5 0.7 - - - +
541B PHE* 5.4 3.3 - - - -
701B CA 2.7 20.4 - - - -
702B CA 2.5 22.1 - - - -
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Residues in contact with SER 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLN 3.2 5.2 + - - -
447B MET 3.7 0.4 - - - -
448B GLU* 1.4 80.2 - - - +
450B PHE* 1.3 64.3 + - - +
452B PRO* 3.5 6.7 - - - +
453B TYR* 2.8 38.3 + - - +
532B SER* 2.9 48.3 + - - -
535B LEU* 4.5 5.2 - - - -
536B LYS* 3.9 16.4 - - - -
540B VAL* 4.1 3.3 - - - +
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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