Contacts of the helix formed by residues 406 - 412 (chain B) 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 GLY 406 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B ASN* 5.5 2.4 + - - -
405B VAL* 1.3 76.0 - - - +
407B THR* 1.3 65.9 + - - -
408B ARG* 2.9 19.8 + - - -
409B ASP* 3.2 30.6 + - - +
410B TRP 3.3 9.9 + - - -
416B TYR* 4.2 3.6 + - - -
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Residues in contact with THR 407 (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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348B LEU* 3.2 43.6 - - + +
349B PHE* 5.1 1.1 - - + -
352B LYS* 3.5 23.6 + - + +
354B PRO* 3.7 12.3 - - + +
405B VAL 3.0 7.0 + - - -
406B GLY* 1.3 69.8 - - - +
408B ARG* 1.3 82.5 + - - +
410B TRP* 3.9 3.5 + - - +
411B ILE* 3.0 37.2 + - + +
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Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LYS 5.3 0.8 + - - -
406B GLY* 2.9 15.5 + - - -
407B THR* 1.3 106.5 + - - +
409B ASP* 1.3 75.2 + - - +
410B TRP 2.8 2.1 + - - -
411B ILE* 2.9 21.7 + - - +
412B GLU* 3.1 24.5 + - - +
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Residues in contact with ASP 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ARG* 3.6 24.8 + - - +
380B LYS* 5.1 7.8 + - - +
406B GLY* 3.5 23.7 + - - +
408B ARG* 1.3 84.9 + - - +
410B TRP* 1.3 61.5 + - - +
412B GLU* 3.2 16.2 + - - +
414B GLU* 3.2 26.9 + - + +
416B TYR* 3.7 14.4 - - - +
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Residues in contact with TRP 410 (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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342B ARG* 4.0 16.2 - - + -
343B PRO* 3.3 41.5 - - + -
348B LEU* 3.7 29.9 - - + +
356B ILE* 4.2 9.4 - - + -
405B VAL* 4.2 13.2 - - + -
406B GLY 3.3 11.6 + - - +
407B THR* 4.0 5.4 - - - +
408B ARG 2.8 4.6 + - - -
409B ASP* 1.3 72.7 - - - +
411B ILE* 1.3 76.2 + - + +
413B GLY* 2.9 17.3 + - - -
414B GLU* 3.7 9.2 + - - +
416B TYR* 3.8 27.3 + + + -
433B THR* 4.2 10.1 - - + -
434B THR* 3.8 24.5 - - - -
435B LYS* 3.8 34.7 - - + +
529B GLU* 6.3 0.2 - - - -
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Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.9 1.3 - - + -
349B PHE* 4.2 26.5 - - + -
407B THR* 3.0 28.3 - - + +
408B ARG* 2.9 8.2 + - - +
410B TRP* 1.3 84.5 - - + +
412B GLU* 1.3 59.6 + - + +
413B GLY 3.0 0.9 + - - -
435B LYS* 2.8 45.1 - - - +
529B GLU* 4.4 13.7 - - + +
535B GLN* 5.1 7.2 - - - +
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Residues in contact with GLU 412 (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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408B ARG* 3.1 21.3 + - - +
409B ASP* 3.6 10.9 - - - +
410B TRP 3.0 1.8 - - - -
411B ILE* 1.3 77.9 - - + +
413B GLY* 1.3 59.1 + - - +
414B GLU 3.3 3.6 + - - -
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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