Contacts of the helix formed by residues 406 - 419 (chain B) in PDB entry 3UO9
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 406 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B GLY 3.8 3.6 + - - +
405B THR* 1.3 71.1 - - - +
407B MET* 1.3 65.3 + - - +
408B VAL* 3.6 12.3 + - - +
409B GLY* 3.6 18.2 + - - -
410B ILE* 3.1 24.6 + - - +
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Residues in contact with MET 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B GLY* 3.6 28.9 - - - +
393B TYR* 3.6 52.3 - - + -
396B LYS* 4.0 22.4 - - + +
401B PHE* 3.7 26.5 - - + -
405B THR* 3.6 10.3 + - + +
406B ASP* 1.3 73.8 + - - +
408B VAL* 1.3 74.5 + - + +
410B ILE* 3.1 7.7 + - - +
411B LEU* 3.1 37.8 + - + +
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PHE* 4.7 16.9 - - + -
393B TYR* 4.1 15.0 - - + +
396B LYS* 6.2 1.3 - - - +
406B ASP* 3.4 7.4 + - - +
407B MET* 1.3 97.8 - - + +
409B GLY* 1.3 61.4 + - - +
411B LEU* 3.5 7.5 + - - +
412B ASP* 3.3 27.4 + - - +
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Residues in contact with GLY 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ASN* 3.2 23.0 + - - +
406B ASP* 3.3 23.9 + - - -
407B MET 3.3 0.2 - - - -
408B VAL* 1.3 76.3 - - - +
410B ILE* 1.3 64.5 + - - +
412B ASP* 3.3 9.0 + - - +
413B PHE 3.1 17.8 + - - -
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Residues in contact with ILE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 3.6 37.0 - - + +
342B THR* 3.9 8.2 - - + +
343B SER* 3.4 29.6 - - - +
351B ASN* 5.9 1.1 - - - +
354B LYS* 5.1 12.6 - - - +
401B PHE* 4.3 4.0 - - + -
405B THR* 3.1 38.8 - - + +
406B ASP 3.1 13.7 + - - +
407B MET* 3.1 9.3 + - - +
409B GLY* 1.3 74.6 - - - +
411B LEU* 1.3 59.2 + - - +
413B PHE* 3.3 8.3 + - + +
414B TYR* 2.8 28.5 + - + +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 4.1 32.5 - - + -
388B ASN* 3.7 24.7 - - + +
389B PHE* 3.5 48.2 - - + +
392B GLY* 4.6 3.1 - - - -
407B MET* 3.1 32.3 + - + +
408B VAL* 3.7 7.4 - - - +
409B GLY 3.3 0.2 - - - -
410B ILE* 1.3 73.9 - - - +
412B ASP* 1.3 58.6 + - - +
414B TYR* 3.3 5.9 + - + +
415B PHE* 2.9 48.1 + - + -
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Residues in contact with ASP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ASN* 3.7 12.1 + - - +
378B PHE* 3.4 10.3 - - + -
382B ARG* 3.1 43.0 + - - -
389B PHE* 5.9 1.4 - - - -
408B VAL* 3.3 18.3 + - - +
409B GLY* 3.3 13.3 + - - +
411B LEU* 1.3 77.3 - - - +
413B PHE* 1.3 56.0 + - - +
415B PHE* 3.4 5.9 + - - -
416B GLN* 3.0 34.6 + - - +
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Residues in contact with PHE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B THR* 3.4 34.3 - - + -
345B ILE* 4.6 10.8 - - + -
351B ASN* 3.8 14.0 - - - +
354B LYS* 3.5 42.8 - - + -
355B PHE* 3.7 27.4 - + + -
358B VAL* 3.9 11.2 - - + -
409B GLY 3.1 11.0 + - - +
410B ILE* 3.6 11.2 - - + +
412B ASP* 1.3 79.0 - - - +
414B TYR* 1.3 57.5 + - - +
416B GLN* 3.3 17.6 + - - +
417B LEU* 3.0 56.9 + - + +
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Residues in contact with TYR 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LYS* 3.2 21.2 + - - -
292B LYS* 3.4 26.2 - - - -
335B ASN* 3.6 16.7 - - - -
338B ALA* 3.8 16.2 - - + -
339B ILE* 3.7 29.2 - - + -
342B THR* 3.9 16.5 - - + +
388B ASN* 4.0 24.5 - - - -
410B ILE* 2.8 20.7 + - + +
411B LEU* 3.4 8.7 - - + +
413B PHE* 1.3 73.2 - - - +
415B PHE* 1.3 73.8 + + - +
417B LEU* 3.4 5.2 + - - +
418B CYS* 3.0 49.9 + - - -
600B GLU 3.8 8.7 - - - -
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Residues in contact with PHE 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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378B PHE* 3.6 18.2 - - + +
381B GLU* 3.9 35.7 - - + +
382B ARG* 3.7 29.8 - - + -
385B GLY* 4.4 2.7 - - - -
388B ASN* 3.8 34.8 - - + -
389B PHE* 4.0 26.2 - + - -
411B LEU* 2.9 36.6 + - + +
412B ASP* 3.7 7.6 - - - +
414B TYR* 1.3 86.0 - + - +
416B GLN* 1.3 63.7 + - - +
418B CYS* 3.4 6.9 + - - +
419B SER* 2.9 28.2 + - - -
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Residues in contact with GLN 416 (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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351B ASN* 4.2 16.4 + - - +
355B PHE* 3.8 32.7 - - + +
373B PHE* 3.7 18.0 - - + -
378B PHE* 3.6 31.8 - - + -
412B ASP* 3.0 16.4 + - - +
413B PHE* 3.3 34.0 + - - +
415B PHE* 1.3 75.0 - - - +
417B LEU* 1.3 63.2 + - - +
419B SER* 3.1 12.6 + - - -
420B ILE* 3.3 14.4 + - - +
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU* 4.9 0.5 - - - +
288B VAL* 3.8 28.1 - - + +
292B LYS* 4.2 17.9 - - + +
342B THR* 4.0 22.4 - - + +
345B ILE* 5.5 2.0 - - + -
355B PHE* 4.0 5.6 - - + -
358B VAL* 3.5 33.0 - - + -
413B PHE* 3.0 52.5 + - + +
414B TYR* 3.7 4.7 - - - +
416B GLN* 1.3 74.4 - - - +
418B CYS* 1.3 62.5 + - - +
420B ILE* 3.3 33.6 + - + +
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Residues in contact with CYS 418 (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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283B CYS* 3.9 4.0 - - - +
285B GLN* 3.1 59.2 + - - +
288B VAL* 4.3 6.0 - - - +
289B LYS* 5.1 3.4 - - - -
381B GLU* 4.7 4.3 - - - +
414B TYR* 3.0 49.5 + - - -
415B PHE* 3.4 11.4 - - - +
417B LEU* 1.3 76.3 - - - +
419B SER* 1.3 59.0 + - - +
420B ILE 3.3 1.5 + - - -
600B GLU* 3.7 20.9 - - - +
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Residues in contact with SER 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B CYS* 3.5 14.0 - - - -
373B PHE* 3.9 8.7 - - - -
374B SER 3.1 40.7 + - - -
377B THR* 3.5 11.7 + - - +
378B PHE* 3.2 21.3 + - - -
381B GLU* 4.1 2.9 - - - +
415B PHE 2.9 17.7 + - - -
416B GLN 3.1 7.7 + - - -
418B CYS* 1.3 74.4 - - - +
420B ILE* 1.3 63.3 + - - +
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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