Contacts of the helix formed by residues 474 - 484 (chain B) in PDB entry 1F89
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 PHE 474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A VAL* 6.3 0.2 - - + -
275A PRO 4.4 9.0 - - - -
277A THR 4.1 7.6 - - - -
278A LYS* 3.3 50.9 - - + -
282A PHE* 5.0 2.5 - + + -
430B HIS* 3.5 55.9 - + + +
470B TYR* 3.5 43.5 - + - -
471B ASP 3.3 11.6 + - - +
472B MET 3.2 1.4 - - - -
473B ARG* 1.3 88.6 - - + +
475B PRO* 1.3 64.2 - - - +
476B GLU* 3.0 14.5 + - - +
477B LEU* 3.3 14.2 + - + +
478B ALA 4.3 0.7 + - - -
491B TYR* 5.1 0.9 + - - -
511B ARG* 4.2 3.3 + - - -
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Residues in contact with PRO 475 (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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175A PRO* 5.8 3.6 - - + -
179A MET* 4.4 11.9 - - + -
183A ARG* 5.1 1.8 - - - +
214A ASP* 3.5 26.9 - - + +
278A LYS* 5.3 6.5 - - - +
473B ARG 3.7 3.4 - - - +
474B PHE* 1.3 80.7 - - - +
476B GLU* 1.3 76.8 + - - +
477B LEU 3.3 0.4 - - - -
478B ALA* 3.1 4.3 + - + +
479B MET* 2.9 43.9 + - + +
511B ARG* 3.4 32.9 - - - +
514B ASP* 5.8 2.5 - - - +
515B ASN* 6.1 0.4 - - - +
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Residues in contact with GLU 476 (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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179A MET* 4.3 1.9 - - - +
183A ARG* 2.8 37.9 + - - -
278A LYS* 4.7 3.6 - - - +
280A ARG* 5.6 2.4 + - - -
282A PHE* 3.0 48.7 - - + -
474B PHE* 3.0 6.0 + - - +
475B PRO* 1.3 90.8 - - - +
477B LEU* 1.3 65.4 + - - +
478B ALA 3.1 0.3 + - - -
479B MET* 3.6 16.1 - - + +
480B LEU* 2.8 30.8 + - + +
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Residues in contact with LEU 477 (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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282A PHE* 3.8 22.4 - - + -
426B HIS* 5.0 7.9 - - + +
429B VAL* 4.8 11.0 - - + -
430B HIS* 3.4 25.1 - - + +
454B SER* 4.4 14.7 + - - +
466B VAL 5.9 0.2 - - - +
467B GLY* 5.1 3.8 - - - -
471B ASP* 3.4 50.9 - - + +
474B PHE 3.3 8.5 + - - +
476B GLU* 1.3 78.1 - - - +
478B ALA* 1.3 61.2 + - - +
480B LEU* 3.6 6.7 - - + +
481B SER* 3.3 26.5 + - - -
489B MET* 4.0 12.8 - - + +
491B TYR* 4.8 0.9 - - + +
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Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B PHE 4.3 0.8 + - - -
475B PRO 3.1 8.9 + - - +
477B LEU* 1.3 76.6 - - - +
479B MET* 1.3 66.9 + - - +
480B LEU 3.1 0.2 + - - -
481B SER* 3.4 1.9 + - - -
482B ALA* 2.8 27.4 + - - +
489B MET* 3.9 20.1 - - + +
491B TYR* 3.8 8.9 + - - +
511B ARG* 3.6 30.3 - - + +
515B ASN* 3.5 15.7 - - - +
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Residues in contact with MET 479 (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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175A PRO* 4.6 8.3 - - + -
176A GLU* 4.2 3.1 - - - +
179A MET* 3.7 29.2 - - + +
475B PRO* 2.9 55.6 + - + +
476B GLU* 3.4 15.5 - - + +
478B ALA* 1.3 75.7 - - - +
480B LEU* 1.3 59.4 + - + +
483B ARG* 2.9 72.2 + - - +
514B ASP* 6.3 0.9 - - + -
515B ASN* 3.0 21.5 - - - +
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Residues in contact with LEU 480 (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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282A PHE* 4.1 36.3 - - + +
454B SER* 3.7 26.5 - - - +
476B GLU* 2.8 22.5 + - + +
477B LEU* 3.6 7.2 - - + +
479B MET* 1.3 79.7 - - + +
481B SER* 1.3 65.0 + - - +
483B ARG* 3.4 2.5 + - - +
484B LYS* 3.2 45.8 + - - +
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Residues in contact with SER 481 (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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454B SER* 4.2 6.4 + - - -
455B THR 3.5 12.0 + - - -
456B THR* 2.8 31.6 + - - +
465B GLY* 3.7 22.5 - - - -
477B LEU 3.3 14.8 + - - -
480B LEU* 1.3 76.5 - - - +
482B ALA* 1.3 58.8 + - - +
484B LYS* 3.4 10.5 + - - +
485B GLY 3.6 0.5 + - - -
486B ALA* 2.9 26.7 + - - +
489B MET* 3.9 9.7 - - - -
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Residues in contact with ALA 482 (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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478B ALA 2.8 19.2 + - - +
479B MET 3.8 0.2 - - - +
481B SER* 1.3 79.3 - - - +
483B ARG* 1.3 59.4 + - + +
485B GLY* 3.2 15.6 + - - -
486B ALA* 3.5 19.2 + - - +
489B MET* 5.4 2.4 - - + +
515B ASN* 3.6 34.1 - - + +
517B VAL* 3.9 13.9 - - + -
571B ARG* 4.6 9.4 + - - -
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Residues in contact with ARG 483 (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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175A PRO* 5.1 3.0 - - - +
176A GLU* 3.0 32.9 + - - -
479B MET* 2.9 49.1 + - - +
480B LEU* 4.1 2.9 - - - +
482B ALA* 1.3 74.1 - - + +
484B LYS* 1.3 60.3 + - - +
485B GLY* 3.0 6.4 + - - -
514B ASP 5.7 0.8 + - - -
515B ASN* 5.1 3.8 - - - +
576B LEU* 6.2 3.6 - - + -
578B LYS* 3.3 41.6 - - - +
580B ARG* 4.6 22.9 - - - +
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Residues in contact with LYS 484 (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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454B SER* 5.2 6.2 + - - -
456B THR* 4.1 28.3 + - + +
463B LYS* 3.7 21.6 + - + -
480B LEU* 3.2 44.6 + - - +
481B SER* 3.6 10.3 - - - +
482B ALA 3.2 1.2 - - - -
483B ARG* 1.3 76.7 - - - +
485B GLY* 1.3 57.4 + - - +
486B ALA 3.8 0.2 - - - -
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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