Contacts of the helix formed by residues 344 - 350 (chain D) in PDB entry 1F6A
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 344 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ARG 3.4 3.6 + - - -
343D PRO* 1.3 72.5 - - - +
345D PRO* 1.3 80.7 - - - +
346D PHE* 4.0 3.1 + - - +
347D ASP* 2.6 42.1 + - - +
348D LEU* 3.0 20.7 + - - +
475D SER* 3.7 9.2 - - - -
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Residues in contact with PRO 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D PRO 3.8 2.4 - - - +
344D SER* 1.3 81.0 - - - +
346D PHE* 1.3 54.0 + - - +
348D LEU* 2.8 29.4 + - + +
349D PHE* 2.8 24.1 + - + +
473D ASP* 3.5 24.5 - - + +
474D ILE* 3.4 11.9 - - - +
475D SER* 3.1 34.3 - - - +
527D VAL* 3.3 30.7 - - + +
528D HIS* 4.6 2.0 - - - +
529D GLU 5.6 0.2 - - - +
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Residues in contact with PHE 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D SER* 4.0 2.9 - - - +
345D PRO* 1.3 76.4 - - - +
347D ASP* 1.3 73.6 + - - +
348D LEU 2.6 15.9 + - - -
349D PHE 3.0 8.7 + - - -
350D ILE* 3.1 54.5 + - + -
351D ARG* 3.5 26.4 + - + -
475D SER* 3.3 21.3 + - - +
477D GLN* 3.5 25.4 - - - +
484D GLN* 3.9 28.3 - - - -
525D ARG* 4.9 0.2 - - - -
527D VAL* 3.8 8.7 - - + +
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Residues in contact with ASP 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D SER* 2.6 32.6 + - - +
346D PHE* 1.3 86.1 - - - +
348D LEU* 1.3 55.8 - - - +
351D ARG* 3.6 35.5 + - - -
352D LYS 3.8 0.2 + - - -
353D SER 3.1 38.9 + - - +
354D PRO* 3.2 7.5 - - + -
355D THR* 5.2 6.5 - - - +
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D PRO* 4.3 14.4 - - + +
344D SER 3.0 9.8 + - - +
345D PRO* 2.8 14.0 + - + +
346D PHE 2.6 6.1 + - - -
347D ASP* 1.3 77.3 - - - +
349D PHE* 1.3 80.5 + - + -
352D LYS* 3.9 6.9 - - - +
354D PRO* 3.1 27.4 - - + -
407D THR* 3.2 37.7 - - + +
410D TRP* 3.7 34.3 - - + +
411D ILE* 4.9 1.1 - - + -
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Residues in contact with PHE 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D PRO* 2.8 24.8 + - + +
348D LEU* 1.3 103.9 - - + +
350D ILE* 1.3 72.7 + - + +
352D LYS* 3.1 22.7 + - - +
407D THR* 5.2 1.1 - - + -
411D ILE* 4.1 24.2 - - + -
527D VAL* 3.9 21.3 - - + -
528D HIS 3.9 1.8 - - - -
529D GLU* 3.7 42.6 - - + -
534D SER 5.4 0.9 - - - +
535D GLN* 3.9 45.6 - - + +
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Residues in contact with ILE 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D PHE* 3.1 45.7 + - + +
349D PHE* 1.3 83.7 - - + +
351D ARG* 1.3 58.6 + - - +
352D LYS* 2.6 27.8 + - - +
484D GLN* 5.7 0.7 - - - +
525D ARG* 4.4 23.6 - - - +
527D VAL* 4.4 16.2 - - + -
534D SER 5.4 3.1 - - - +
535D GLN 6.4 0.2 - - - -
536D THR* 4.2 18.4 - - - +
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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