Contacts of the helix formed by residues 449 - 456 (chain B) in PDB entry 4OIV
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 HIS 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326B GLY 5.7 3.1 - - - -
329B VAL* 3.9 33.9 - - + -
330B GLU* 2.7 35.1 + - + +
333B PHE* 5.0 1.5 - + - -
444B LEU 3.6 17.5 - - - -
445B ARG 3.6 10.8 - - - -
447B PHE* 2.7 29.4 + - + +
448B ASN* 1.3 72.5 + - - +
450B HIS* 1.3 64.5 + - + +
451B HIS 3.4 2.2 - - - -
452B ALA* 3.5 5.6 + - - +
453B GLU* 3.0 40.2 + - + +
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Residues in contact with HIS 450 (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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365B TYR* 5.2 2.7 - - - +
448B ASN* 2.8 27.9 + - - +
449B HIS* 1.3 84.4 - - + +
451B HIS* 1.3 61.1 + - - +
453B GLU* 3.4 9.9 + - + +
454B MET* 3.0 22.0 + - - +
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Residues in contact with HIS 451 (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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285A GLU* 2.6 43.0 + - - -
361B ILE* 3.9 23.2 - - + +
365B TYR* 3.4 57.4 + + + +
448B ASN 5.7 0.2 - - - +
449B HIS 3.4 0.2 - - - -
450B HIS* 1.3 74.9 - - - +
452B ALA* 1.3 67.4 + - - +
454B MET* 3.1 14.3 + - + +
455B LEU* 3.0 44.5 + - + +
501B XX9 4.1 16.1 + + - +
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Residues in contact with ALA 452 (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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329B VAL* 3.5 32.8 - - + -
333B PHE* 3.8 10.1 - - + -
448B ASN 5.5 0.4 + - - -
449B HIS 3.5 4.3 + - - +
450B HIS 3.4 0.2 - - - -
451B HIS* 1.3 80.5 - - - +
453B GLU* 1.3 55.5 + - - +
455B LEU* 3.2 3.3 + - - +
456B MET* 2.9 33.5 + - - +
501B XX9 3.6 36.1 - - + +
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Residues in contact with GLU 453 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325B LYS* 4.2 18.7 - - - +
326B GLY 5.8 0.7 - - - +
328B ALA* 6.0 0.7 - - - +
329B VAL* 3.4 24.5 - - + +
449B HIS* 3.0 32.0 + - + +
450B HIS* 3.8 11.2 - - + +
452B ALA* 1.3 73.1 - - - +
454B MET* 1.3 66.3 + - - +
456B MET* 3.5 21.6 + - - +
457B SER* 4.7 1.9 + - - -
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Residues in contact with MET 454 (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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283A SER* 4.3 11.7 - - - +
285A GLU* 4.2 21.1 - - + +
286A GLU* 3.7 41.3 - - - +
289A LEU* 4.5 0.2 - - - -
450B HIS 3.0 14.0 + - - +
451B HIS* 3.1 21.3 + - - +
453B GLU* 1.3 79.0 - - - +
455B LEU* 1.3 88.9 + - + +
456B MET 3.5 0.3 + - - -
457B SER* 4.3 4.5 + - - -
458B TRP* 3.3 18.8 + - - -
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Residues in contact with LEU 455 (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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285A GLU* 4.1 2.2 - - - +
289A LEU* 3.4 32.3 - - + -
288B PHE* 4.3 13.7 - - + -
292B THR* 4.9 6.3 - - + -
361B ILE* 5.6 0.2 - - + -
451B HIS* 3.0 49.4 + - + +
452B ALA 3.2 3.3 + - - +
454B MET* 1.3 89.2 - - + +
456B MET* 1.3 64.2 + - - +
457B SER 3.1 2.9 - - - -
458B TRP* 3.0 19.9 + - + +
501B XX9 3.4 50.6 + - + +
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Residues in contact with MET 456 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A LEU* 4.5 10.0 - - + +
299B VAL* 4.0 24.1 - - - +
302B LEU* 6.0 0.4 - - - -
328B ALA* 3.6 18.8 - - + +
329B VAL* 3.4 45.3 - - + +
332B MET* 3.8 12.6 - - + -
452B ALA 2.9 19.7 + - - +
453B GLU* 3.5 20.4 + - - +
454B MET 3.3 2.4 - - - -
455B LEU* 1.3 77.0 - - - +
457B SER* 1.3 52.9 + - - +
458B TRP 3.5 0.2 - - - -
459B ARG* 2.7 31.3 + - - -
501B XX9 3.9 15.2 - - + -
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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