Contacts of the helix formed by residues 405 - 418 (chain B) in PDB entry 5FI6
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 ASP 405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403B GLY 3.7 2.8 + - - +
404B THR* 1.3 71.7 - - - +
406B MET* 1.3 59.6 + - - +
407B VAL* 3.8 9.7 + - - +
408B GLY* 3.2 24.0 + - - -
409B ILE* 2.8 28.8 + - + +
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Residues in contact with MET 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B GLY* 3.6 12.3 - - - +
392B TYR* 3.4 56.3 - - + +
395B LYS* 4.0 24.1 - - + +
400B PHE* 3.5 35.2 - - + -
404B THR* 3.5 10.3 + - - +
405B ASP* 1.3 73.4 + - - +
407B VAL* 1.3 72.0 + - + +
409B ILE* 3.1 9.2 + - + +
410B LEU* 2.9 44.8 + - + +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PHE* 4.6 17.6 - - + -
392B TYR* 4.2 20.9 - - + +
395B LYS* 6.3 0.9 - - - +
405B ASP* 3.3 8.8 + - - +
406B MET* 1.3 90.0 - - + +
408B GLY* 1.3 62.4 + - - +
410B LEU* 3.1 15.7 + - + +
411B ASP* 3.2 12.1 + - - +
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Residues in contact with GLY 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ASN* 3.1 18.3 + - - -
405B ASP* 3.0 24.5 + - - -
407B VAL* 1.3 77.8 - - - +
409B ILE* 1.3 63.8 + - - +
411B ASP* 3.1 7.4 + - - -
412B PHE* 3.0 21.1 + - - +
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Residues in contact with ILE 409 (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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338B ILE* 3.7 21.8 - - + +
341B THR* 3.8 9.4 - - + +
342B SER* 3.6 37.9 - - - +
350B ASN* 5.6 0.4 - - - +
353B LYS* 3.6 27.8 - - - +
400B PHE* 4.3 9.0 - - + -
404B THR* 3.4 27.4 - - + -
405B ASP 2.8 15.8 + - - +
406B MET* 3.1 10.3 + - - +
408B GLY* 1.3 72.8 - - - +
410B LEU* 1.3 58.1 + - - +
412B PHE* 3.7 7.6 - - + +
413B TYR* 3.0 26.3 + - - +
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Residues in contact with LEU 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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338B ILE* 3.7 36.8 - - + -
387B ASN* 3.7 20.4 - - + +
388B PHE* 3.4 46.2 - - + -
391B GLY* 4.3 2.5 - - - -
406B MET* 2.9 37.1 + - + +
407B VAL* 3.1 9.6 + - - +
409B ILE* 1.3 79.0 - - - +
411B ASP* 1.3 56.8 + - - +
413B TYR* 3.2 7.2 + - + +
414B PHE* 2.9 44.1 + - + -
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Residues in contact with ASP 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ASN* 4.0 8.7 + - - +
377B PHE* 3.1 30.5 - - - -
381B ARG* 2.6 41.2 + - - +
407B VAL 3.2 10.2 + - - +
408B GLY* 3.1 11.3 + - - +
410B LEU* 1.3 73.2 - - - +
412B PHE* 1.3 66.3 + - - +
414B PHE* 3.3 4.8 + - - -
415B GLN* 3.0 32.3 + - - +
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Residues in contact with PHE 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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341B THR* 3.6 28.7 - - + -
344B ILE* 4.6 8.5 - - + -
350B ASN* 3.5 22.6 - - - +
353B LYS* 3.4 53.4 - - + -
354B PHE* 3.8 25.4 - + + -
357B VAL* 4.0 10.8 - - + -
408B GLY 3.0 8.0 + - - +
409B ILE* 3.7 11.0 - - + +
411B ASP* 1.3 75.7 - - - +
413B TYR* 1.3 62.7 + - - +
415B GLN* 2.9 9.2 + - + +
416B LEU* 2.9 52.3 + - + +
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Residues in contact with TYR 413 (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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288B LYS* 3.1 23.5 + - - -
291B LYS* 3.3 28.9 - - - -
334B ASN* 3.2 15.1 + - - -
337B ALA* 3.8 13.7 - - + -
338B ILE* 3.6 34.1 - - + -
341B THR* 3.8 16.7 - - + +
380B GLU* 6.3 0.2 - - + -
387B ASN* 4.1 24.6 + - - -
409B ILE 3.0 15.7 + - - +
410B LEU* 3.2 12.3 + - + +
412B PHE* 1.3 76.4 - - - +
414B PHE* 1.3 80.1 + + - +
416B LEU* 3.3 5.2 + - - +
417B CYS* 3.1 41.7 + - - -
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Residues in contact with PHE 414 (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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377B PHE* 3.6 22.2 - - + +
380B GLU* 3.7 37.6 - - + +
381B ARG* 3.7 22.2 - - + -
384B GLY 4.3 2.9 - - - -
387B ASN* 3.3 44.6 - - + -
388B PHE* 3.6 34.1 - + - -
410B LEU* 2.9 34.2 + - + +
411B ASP* 3.3 5.1 + - - -
413B TYR* 1.3 82.6 - + - +
415B GLN* 1.3 60.0 + - - +
417B CYS* 3.6 7.1 + - - +
418B SER* 2.7 27.4 + - - -
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Residues in contact with GLN 415 (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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350B ASN* 4.1 21.0 - - - +
354B PHE* 3.7 38.5 - - + +
372B PHE* 3.9 13.9 - - + -
377B PHE* 3.5 35.1 - - + -
411B ASP* 3.0 27.7 + - - +
412B PHE* 2.9 13.4 + - - +
414B PHE* 1.3 72.6 - - - +
416B LEU* 1.3 57.4 + - - +
417B CYS 3.0 1.3 - - - -
418B SER* 2.7 27.0 + - - -
419B ILE* 3.4 10.4 + - - +
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 4.8 0.9 - - - +
287B VAL* 3.6 26.3 - - + +
291B LYS* 3.8 34.5 - - + +
341B THR* 3.9 17.3 - - + +
344B ILE* 5.2 1.1 - - + -
354B PHE* 4.3 4.9 - - + -
357B VAL* 3.7 30.3 - - + -
412B PHE* 2.9 56.7 + - + +
413B TYR 3.8 5.8 - - - +
415B GLN* 1.3 70.7 - - - +
417B CYS* 1.3 59.5 + - - +
418B SER 3.4 0.3 + - - -
419B ILE* 3.6 27.5 + - + +
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Residues in contact with CYS 417 (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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282B CYS* 3.8 3.1 - - - +
284B GLN* 2.9 66.9 + - - +
287B VAL* 4.4 5.4 - - - -
288B LYS* 5.1 4.0 - - - -
291B LYS* 5.1 0.2 - - - -
380B GLU* 5.1 7.9 - - + -
413B TYR* 3.1 52.7 + - - +
414B PHE* 3.8 9.6 - - - +
415B GLN 3.0 1.0 - - - -
416B LEU* 1.3 77.2 - - - +
418B SER* 1.3 60.1 + - - +
419B ILE 3.4 0.7 + - - -
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Residues in contact with SER 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B CYS* 3.1 15.2 - - - -
284B GLN* 5.6 0.5 + - - -
372B PHE* 3.8 11.9 - - - -
373B SER 3.0 31.6 + - - -
376B THR* 3.1 22.4 + - - -
377B PHE* 3.2 12.5 - - - -
380B GLU* 4.9 2.6 - - - +
414B PHE 2.7 16.6 + - - -
415B GLN 2.7 15.5 + - - -
417B CYS* 1.3 70.5 - - - +
419B ILE* 1.3 64.7 + - - -
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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