Contacts of the helix formed by residues 390 - 403 (chain B) in PDB entry 5D3O
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 390 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386B GLU 3.1 16.0 + - - -
387B ARG 3.7 4.5 + - - -
388B GLU 3.2 5.5 + - - -
389B SER* 1.3 75.1 - - - +
391B ASP* 1.3 57.9 + - - +
392B ARG 3.3 2.5 - - - -
393B ASN* 3.2 13.5 + - - +
394B PHE* 2.8 38.8 + - - -
420B PHE* 4.3 10.8 - - - -
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Residues in contact with ASP 391 (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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388B GLU 5.2 4.7 - - - +
389B SER* 3.0 9.0 + - - +
390B GLY* 1.3 75.5 - - - +
392B ARG* 1.3 65.6 + - - +
394B PHE* 3.1 10.6 + - - +
395B ALA* 2.9 24.1 + - - +
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Residues in contact with ARG 392 (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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327B PHE* 3.1 33.2 - - + -
340B ASN* 4.2 20.3 - - - +
389B SER 4.4 3.9 + - - +
390B GLY* 3.3 0.8 - - - -
391B ASP* 1.3 77.6 - - - +
393B ASN* 1.3 65.7 + - - +
395B ALA* 3.2 10.2 - - + +
396B ILE* 3.1 48.2 + - - +
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Residues in contact with ASN 393 (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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340B ASN* 3.2 32.9 + - - +
344B ILE* 4.1 5.2 - - + +
386B GLU* 5.4 3.2 + - - +
390B GLY* 3.2 14.0 + - - +
392B ARG* 1.3 80.7 - - - +
394B PHE* 1.3 64.9 + - - +
396B ILE* 3.3 10.7 + - - +
397B GLY 3.0 18.0 + - - -
416B LEU* 3.7 15.9 - - + +
419B TYR* 4.1 14.7 - - - -
420B PHE* 3.4 33.5 - - + -
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Residues in contact with PHE 394 (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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387B ARG* 4.4 16.4 - - + -
390B GLY 2.8 35.0 + - - +
391B ASP* 3.6 10.8 - - - +
393B ASN* 1.3 69.6 - - - +
395B ALA* 1.3 68.4 + - - +
397B GLY* 3.1 2.1 + - - -
398B TYR* 3.0 49.9 + + + -
413B VAL* 4.8 22.0 - - + -
416B LEU* 3.5 27.3 - - + +
420B PHE* 4.1 24.0 - + - -
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Residues in contact with ALA 395 (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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327B PHE* 5.3 5.4 - - + -
391B ASP 2.9 12.4 + - - +
392B ARG* 3.2 15.3 - - + +
394B PHE* 1.3 77.6 - - - +
396B ILE* 1.3 63.7 + - + +
398B TYR* 3.3 5.9 + - - +
399B TYR* 3.0 22.7 + - - +
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Residues in contact with ILE 396 (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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327B PHE* 3.6 29.8 - - + -
340B ASN* 4.1 11.0 - - + -
341B ALA* 3.8 23.1 - - + +
344B ILE* 4.0 6.1 - - + -
392B ARG* 3.1 44.9 + - - +
393B ASN* 3.3 20.8 + - - +
395B ALA* 1.3 76.3 - - - +
397B GLY* 1.3 58.2 + - - +
399B TYR* 3.3 8.0 + - - +
400B LEU* 2.9 55.1 + - + +
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Residues in contact with GLY 397 (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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393B ASN 3.0 14.5 + - - -
394B PHE 3.1 5.0 + - - -
396B ILE* 1.3 76.1 - - - +
398B TYR* 1.3 56.5 + - - +
400B LEU* 3.2 12.8 + - - +
401B LYS* 2.9 27.5 + - - +
406B PHE* 5.0 1.3 - - - -
412B MET* 3.7 27.0 - - - +
416B LEU* 4.3 9.1 - - - +
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Residues in contact with TYR 398 (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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394B PHE* 3.0 47.8 + + + -
395B ALA* 3.9 6.7 - - - +
397B GLY* 1.3 74.6 - - - +
399B TYR* 1.3 57.6 + - - +
401B LYS* 3.1 12.8 + - + +
402B GLU* 2.8 31.8 + - - +
412B MET* 3.8 23.1 - - + -
413B VAL* 4.5 12.1 - - + +
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Residues in contact with TYR 399 (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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326B LEU 4.6 7.2 + - - -
327B PHE* 4.1 32.5 - + + -
328B LEU* 3.9 29.4 - - + +
395B ALA 3.0 13.8 + - - +
396B ILE* 3.3 10.7 + - - +
398B TYR* 1.3 76.2 - - - +
400B LEU* 1.3 62.5 - - + +
402B GLU* 3.6 9.6 + - + +
403B LYS* 3.2 55.0 + - + +
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Residues in contact with LEU 400 (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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327B PHE* 6.3 0.7 - - + -
328B LEU* 4.3 10.3 - - + -
334B PRO* 4.0 18.4 - - + -
341B ALA* 3.8 13.2 - - + +
344B ILE* 3.8 26.0 - - + -
345B VAL* 4.2 4.0 - - + -
396B ILE* 2.9 45.5 + - + +
397B GLY* 3.4 4.5 - - - +
399B TYR* 1.3 76.3 - - + +
401B LYS* 1.3 66.1 + - - +
403B LYS 3.4 1.0 + - - -
404B LYS 3.2 3.5 + - - -
405B CYS* 3.0 53.3 + - + +
406B PHE* 3.7 18.7 - - + -
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Residues in contact with LYS 401 (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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397B GLY 2.9 13.3 + - - +
398B TYR* 3.1 20.2 + - + +
400B LEU* 1.3 75.8 - - - +
402B GLU* 1.3 64.7 + - - +
404B LYS* 2.9 25.4 + - - +
406B PHE* 3.8 10.9 - - + -
410B THR 4.8 6.7 + - - -
411B ASP* 5.6 1.6 + - - +
412B MET* 4.1 42.2 - - + +
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Residues in contact with GLU 402 (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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398B TYR 2.8 16.5 + - - +
399B TYR* 3.9 11.8 - - + +
401B LYS* 1.3 78.3 - - - +
403B LYS* 1.3 81.6 + - - +
404B LYS* 3.4 17.8 + - - +
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Residues in contact with LYS 403 (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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328B LEU* 3.5 32.5 - - + -
332B ASP* 4.0 21.6 + - - +
399B TYR* 3.2 47.8 + - + +
401B LYS 3.2 0.8 - - - -
402B GLU* 1.3 90.6 - - - +
404B LYS* 1.3 71.5 + - - +
405B CYS* 3.3 11.5 + - - -
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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