Contacts of the helix formed by residues 360 - 368 (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 SER 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358B PRO* 3.1 7.1 + - - -
359B TYR* 1.3 77.7 - - - +
361B THR* 1.3 62.2 + - - +
362B ASP* 2.9 27.2 + - - -
363B GLN* 3.0 21.3 + - - +
364B PHE* 2.7 26.8 + - - -
531B SER* 5.0 8.4 + - - -
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Residues in contact with THR 361 (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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360B SER* 1.3 73.2 + - - +
362B ASP* 1.3 60.7 + - - +
363B GLN 3.1 4.3 + - - -
364B PHE* 3.4 20.0 + - + -
365B ARG* 4.6 1.6 + - - +
443B HIS* 3.9 32.9 - - + +
444B GLU* 4.1 21.3 - - + +
447B THR* 3.0 42.9 - - - +
448B LEU* 5.7 4.7 - - + -
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Residues in contact with ASP 362 (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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360B SER* 2.9 23.5 + - - -
361B THR* 1.3 79.4 + - - +
363B GLN* 1.3 75.1 + - - +
365B ARG* 5.1 4.6 - - - +
366B LYS* 4.9 3.1 + - - +
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Residues in contact with GLN 363 (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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323B PRO* 6.0 1.8 - - - +
358B PRO* 4.2 30.6 - - + +
360B SER* 3.0 13.2 + - - +
362B ASP* 1.3 96.5 + - - +
364B PHE* 1.3 66.7 + - - +
365B ARG 3.2 2.2 - - - -
366B LYS* 2.9 32.4 + - - +
367B TYR* 2.8 47.3 + - + +
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Residues in contact with PHE 364 (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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354B CYS* 4.2 17.5 - - - -
357B SER* 5.9 0.2 - - - -
358B PRO 4.4 4.0 + - - -
359B TYR* 4.3 15.3 - + - -
360B SER* 2.7 46.7 - - - -
361B THR* 3.4 20.8 + - + +
363B GLN* 1.3 75.6 - - - +
365B ARG* 1.3 54.6 + - - +
367B TYR* 4.5 0.7 - - - +
368B SER* 2.7 40.3 + - - -
400B PRO* 3.8 24.6 - - + +
409B ILE* 4.2 5.4 - - + -
410B TYR 4.9 0.7 - - - -
411B ASN* 3.5 28.5 - - + -
447B THR* 4.4 0.2 - - + -
448B LEU* 3.6 40.4 - - + -
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Residues in contact with ARG 365 (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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361B THR 4.6 3.6 + - - +
362B ASP 5.4 4.5 - - - +
363B GLN 4.9 0.7 - - - -
364B PHE* 1.3 77.1 - - - +
366B LYS* 1.3 65.9 + - - +
368B SER* 2.8 24.1 + - - -
369B GLU 4.4 0.3 + - - -
402B LEU* 3.6 17.9 - - - +
407B ASP* 2.7 47.4 + - - -
408B LYS* 5.3 0.4 - - - +
409B ILE* 3.7 36.0 - - + +
447B THR* 5.1 3.2 + - + -
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Residues in contact with LYS 366 (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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362B ASP 4.9 2.0 - - - +
363B GLN* 2.9 31.9 + - - +
365B ARG* 1.3 81.6 - - - +
367B TYR* 1.3 70.8 + - + +
369B GLU* 3.2 21.9 - - - +
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Residues in contact with TYR 367 (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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322B SER 4.4 1.1 - - - -
323B PRO* 2.5 44.3 + - - +
325B LYS* 3.5 34.4 + - + -
356B ASN* 4.5 3.3 - - - +
357B SER* 3.3 35.4 - - - +
358B PRO* 3.5 19.4 - - + +
363B GLN* 2.8 49.8 + - + +
364B PHE 3.5 0.9 - - - +
366B LYS* 1.3 86.5 - - + +
368B SER* 1.3 53.4 + - - +
369B GLU* 2.7 25.1 + - - -
370B VAL* 5.3 0.2 - - - +
400B PRO* 4.0 11.8 - - + +
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Residues in contact with SER 368 (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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364B PHE 2.7 20.5 + - - -
365B ARG 2.8 18.2 + - - -
367B TYR* 1.3 69.4 - - - +
369B GLU* 1.3 50.3 + - - +
370B VAL 2.2 38.6 + - - +
400B PRO* 3.3 21.7 - - - +
401B GLU 4.0 5.4 - - - -
402B LEU* 3.5 33.9 + - - +
409B ILE* 3.8 14.7 - - - +
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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