Contacts of the helix formed by residues 440 - 451 (chain B) in PDB entry 5OF4
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 ALA 440 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B ILE* 5.8 0.7 - - + -
240B ASP* 4.4 17.7 - - + +
243B CYS* 4.2 13.7 - - + -
244B ILE* 5.6 1.8 - - - -
438B MET 3.0 7.3 + - - -
439B ASP* 1.3 72.2 - - - +
441B SER* 1.3 63.1 + - - +
442B LEU 3.3 0.2 - - - -
443B ALA 3.5 2.5 + - - -
444B ILE* 3.2 24.4 + - - +
469B LYS* 3.4 44.7 + - + +
470B ILE* 4.6 8.5 - - + -
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Residues in contact with SER 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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439B ASP* 3.3 23.1 + - - +
440B ALA* 1.3 74.9 - - - +
442B LEU* 1.3 64.5 + - - +
443B ALA 2.9 6.9 + - - -
444B ILE* 4.0 9.2 - - - -
445B LYS* 2.8 60.3 + - - +
469B LYS 4.4 3.0 + - - -
470B ILE 4.1 8.7 + - - -
471B LEU* 4.0 18.7 - - - +
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Residues in contact with LEU 442 (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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215B PRO* 5.8 0.2 - - - +
247B MET* 4.2 11.7 - - + +
410B TYR* 4.7 25.1 + - + +
413B GLY* 5.3 5.2 - - - +
414B PHE* 3.7 30.1 - - + -
437B CYS* 3.9 21.5 - - - -
439B ASP* 3.4 25.8 + - + +
440B ALA 3.3 1.0 - - - -
441B SER* 1.3 86.7 + - - +
443B ALA* 1.3 58.5 + - - +
445B LYS* 5.0 12.6 - - + +
446B PRO* 4.2 10.6 - - - +
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Residues in contact with ALA 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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213B LEU* 4.3 9.2 - - + +
215B PRO* 4.7 10.8 - - + -
243B CYS* 3.6 34.8 - - + +
246B SER* 4.9 0.9 - - - +
247B MET* 4.0 18.9 - - + +
439B ASP 4.5 0.2 + - - -
440B ALA 3.5 3.0 + - - -
441B SER 3.0 0.6 - - - -
442B LEU* 1.3 79.9 - - - +
444B ILE* 1.3 59.2 + - - +
446B PRO* 3.4 20.2 - - - +
447B VAL* 4.1 7.8 - - - +
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Residues in contact with ILE 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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209B TYR* 5.1 0.4 - - - +
213B LEU* 4.6 7.4 - - + -
233B PHE* 5.4 9.9 - - + -
239B ILE* 3.7 28.9 - - + -
243B CYS* 4.2 8.0 - - - -
440B ALA 3.2 19.0 + - - +
441B SER* 4.0 7.9 - - - -
443B ALA* 1.3 76.8 - - - +
445B LYS* 1.3 59.3 + - - +
446B PRO 3.1 2.5 - - - -
447B VAL* 2.8 32.3 + - + +
448B PHE* 2.9 36.1 + - + -
456B ILE* 6.2 1.3 - - + -
470B ILE* 3.6 30.7 - - + -
472B ASP* 4.0 6.7 - - - +
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Residues in contact with LYS 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 SER* 2.8 48.0 + - - +
442B LEU* 4.9 10.0 - - + +
444B ILE* 1.3 74.3 - - - +
446B PRO* 1.4 69.3 - - + +
448B PHE* 4.4 6.3 - - + +
449B GLU* 3.0 47.0 + - + +
471B LEU* 5.1 10.2 - - - +
472B ASP* 4.4 20.0 - - - +
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Residues in contact with PRO 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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310B LEU* 5.0 12.6 - - + -
311B PRO* 4.9 22.0 - - + -
442B LEU 4.2 7.6 - - - +
443B ALA* 3.4 27.8 - - - +
445B LYS* 1.4 90.9 - - + +
447B VAL* 1.3 62.1 + - + +
449B GLU* 4.1 3.7 - - + +
450B ARG* 2.9 52.8 + - + +
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Residues in contact with VAL 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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212B LEU* 4.7 10.1 - - + +
213B LEU* 3.7 32.1 - - + -
233B PHE* 3.6 30.7 - - + -
443B ALA 4.1 10.1 - - - +
444B ILE* 2.8 18.6 + - + +
446B PRO* 1.3 77.2 - - + +
448B PHE* 1.3 63.2 + - - +
450B ARG* 4.9 4.9 - - - +
451B PHE* 3.1 50.4 - - + +
454B VAL* 4.0 10.6 - - + +
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Residues in contact with PHE 448 (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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37B HIS* 3.3 48.5 - + + -
444B ILE* 2.9 53.3 + - + +
445B LYS* 4.1 4.9 - - - +
447B VAL* 1.3 77.8 - - + +
449B GLU* 1.3 67.7 + - + +
450B ARG 3.3 0.7 + - - -
451B PHE* 3.4 18.6 + - - +
454B VAL* 4.0 12.1 - - + -
467B TYR* 3.2 24.5 - + - -
470B ILE* 4.3 1.3 - - + -
472B ASP* 3.2 32.8 - - + +
473B PHE 4.6 2.5 - - - -
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Residues in contact with GLU 449 (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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224B GLU* 4.6 1.4 - - - +
226B ALA* 5.0 3.8 - - - +
311B PRO* 5.8 5.0 - - - +
445B LYS* 3.0 39.3 + - + +
446B PRO* 4.1 4.3 - - + +
448B PHE* 1.3 81.6 - - + +
450B ARG* 1.3 60.9 + - + +
451B PHE 4.5 1.6 - - - +
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Residues in contact with ARG 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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212B LEU* 4.2 27.7 + - - +
219B ASP 5.2 2.6 + - - -
220B LEU* 3.6 27.3 - - - +
221B VAL* 4.7 9.5 - - - +
222B SER 5.4 3.2 + - - +
224B GLU* 3.4 37.5 - - + +
226B ALA* 3.5 31.0 - - - +
229B ALA* 4.9 0.7 - - - +
310B LEU* 3.4 39.7 - - + +
446B PRO* 2.9 35.3 + - + +
447B VAL* 4.9 3.1 - - - +
448B PHE 3.2 0.2 - - - -
449B GLU* 1.3 78.6 - - + +
451B PHE* 1.3 90.1 + - + +
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Residues in contact with PHE 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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71B ILE* 5.5 6.1 - - + -
212B LEU* 4.4 15.7 - - + -
222B SER* 5.3 8.5 - - - -
224B GLU* 5.9 3.1 - - + -
226B ALA 5.1 4.4 - - - +
229B ALA* 3.5 29.2 - - + +
231B VAL* 3.5 31.6 - - + -
447B VAL* 3.1 39.7 + - + +
448B PHE* 3.4 14.3 + - - +
449B GLU 4.5 1.4 - - - +
450B ARG* 1.3 116.0 - - + +
452B GLN* 1.3 66.0 + - - +
453B SER* 4.0 6.1 - - - +
454B VAL* 3.7 13.0 - - + -
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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