Contacts of the helix formed by residues 316 - 330 (chain B) in PDB entry 5TTE
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 LYS 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B HIS* 4.3 1.1 + - - -
315B VAL* 1.3 94.9 - - - +
317B CYS* 1.3 68.6 + - - +
318B LYS* 3.4 7.0 - - + +
319B TRP* 3.5 31.8 + - + +
320B LEU* 3.6 2.9 + - - +
547B TYR* 3.7 51.5 + - + +
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Residues in contact with CYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 4.3 9.4 - - - -
304B CYS* 3.5 8.3 - - - -
306B ASN* 4.0 19.7 - - - +
307B CYS* 4.0 8.3 - - + +
312B HIS* 3.0 15.1 - - + -
316B LYS* 1.3 76.3 - - - +
318B LYS* 1.3 66.1 + - - +
319B TRP 3.1 0.9 + - - -
320B LEU* 3.3 12.5 + - - +
321B LYS* 3.4 18.2 + - - +
606B ZN 2.3 36.3 - - - -
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LYS* 4.8 4.0 - - + -
317B CYS* 1.3 79.2 - - - +
319B TRP* 1.3 108.2 + - + +
321B LYS* 3.6 12.7 + - - +
322B LYS* 3.4 39.7 + - - +
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Residues in contact with TRP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 3.6 21.1 - - + -
316B LYS* 3.5 35.7 - - + +
317B CYS 3.2 1.2 - - - -
318B LYS* 1.3 106.4 - - + +
320B LEU* 1.3 64.8 + - - +
322B LYS* 3.1 29.8 + - + +
323B TRP* 3.0 17.0 + - - +
477B VAL* 4.7 0.7 - - - -
478B PHE* 5.8 3.6 - + - -
481B TYR* 3.4 63.5 - + + -
547B TYR* 5.5 1.7 - - - -
553B GLU* 3.0 35.6 + - + -
554B TYR* 4.8 18.8 - + + -
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Residues in contact with LEU 320 (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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309B GLU* 4.1 22.9 - - + -
310B ASN 4.7 0.4 - - - +
312B HIS* 3.3 30.7 - - + +
315B VAL* 4.3 5.6 - - + -
316B LYS 3.6 5.5 + - - +
317B CYS 3.3 8.8 + - - +
319B TRP* 1.3 78.4 - - - +
321B LYS* 1.3 63.0 + - + +
323B TRP* 3.0 21.9 + - + +
324B ILE* 3.1 33.3 + - + +
421B TYR* 4.6 6.5 - - - +
474B TYR* 3.9 37.7 - - + +
477B VAL* 4.3 14.0 - - + +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B CYS* 3.8 36.7 + - + +
309B GLU* 5.6 9.2 - - + +
317B CYS* 3.4 13.1 + - - +
318B LYS* 3.7 13.7 - - - +
319B TRP 3.2 0.6 - - - -
320B LEU* 1.3 78.5 - - - +
322B LYS* 1.3 62.5 + - + +
324B ILE* 3.5 6.8 + - - +
325B LYS* 3.0 35.0 + - - +
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LYS* 3.4 31.1 + - - +
319B TRP* 3.1 39.7 + - + +
321B LYS* 1.3 77.5 - - + +
323B TRP* 1.3 57.3 + - - +
325B LYS* 4.0 10.6 - - + +
326B LYS* 3.0 31.0 + - - +
481B TYR* 3.5 16.2 + - + +
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Residues in contact with TRP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TRP 3.0 10.1 + - - +
320B LEU* 3.0 16.8 + - + +
322B LYS* 1.3 73.7 - - - +
324B ILE* 1.3 71.7 + - + +
326B LYS* 3.0 6.2 + - - +
327B CYS* 2.9 39.6 + - + -
414B TYR* 3.2 32.3 - + - -
417B TYR* 4.5 2.7 + - - +
418B CYS* 3.4 41.5 - - + -
421B TYR* 3.8 35.4 - + + +
422B MET* 5.1 0.9 - - + -
476B TYR 5.1 0.6 + - - -
477B VAL* 3.4 46.1 - - + +
480B PHE* 4.6 14.1 - + - +
481B TYR* 3.6 17.9 + + - -
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Residues in contact with ILE 324 (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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309B GLU* 3.8 36.3 - - + +
320B LEU* 3.1 31.0 + - + +
321B LYS* 4.2 4.0 - - - +
323B TRP* 1.3 80.3 - - + +
325B LYS* 1.3 59.1 + - - +
327B CYS* 3.1 4.4 + - + +
328B ASP* 2.8 46.1 + - - +
421B TYR* 4.9 9.6 - - + +
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Residues in contact with LYS 325 (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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321B LYS* 3.0 25.7 + - - +
322B LYS* 4.0 8.4 - - + +
324B ILE* 1.3 77.9 - - - +
326B LYS* 1.3 61.8 + - - +
328B ASP* 4.8 3.8 - - - -
329B ASP* 2.9 50.5 + - - +
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Residues in contact with LYS 326 (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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322B LYS 3.0 19.7 + - - +
323B TRP* 3.0 5.8 + - - +
325B LYS* 1.3 78.4 - - - +
327B CYS* 1.3 64.0 + - - +
329B ASP* 3.7 8.1 + - - +
330B ASP* 3.8 14.0 + - - +
332B GLU* 4.1 3.6 - - + +
410B ALA 5.9 0.2 + - - -
411B LEU* 6.5 0.7 - - - -
414B TYR* 3.8 35.4 - - + +
480B PHE* 3.5 30.2 - - + -
481B TYR* 4.8 10.3 - - + +
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Residues in contact with CYS 327 (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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323B TRP* 2.9 38.0 + - + +
324B ILE* 3.1 7.4 + - + +
326B LYS* 1.3 77.8 - - - +
328B ASP* 1.3 65.3 + - - +
329B ASP 3.3 0.3 + - - -
330B ASP 3.9 0.9 + - - -
332B GLU* 3.2 49.1 + - - +
333B THR* 3.3 11.4 + - - -
336B TRP* 4.3 25.4 - - - -
414B TYR* 3.8 3.3 + - - +
418B CYS* 5.4 2.5 - - - -
422B MET* 5.3 4.3 - - - -
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ILE* 2.8 35.2 + - - +
325B LYS* 4.3 4.0 - - - +
327B CYS* 1.3 75.8 - - - +
329B ASP* 1.3 66.6 + - - +
330B ASP 3.6 0.2 + - - -
333B THR* 3.9 22.9 + - - +
336B TRP* 4.6 17.9 - - - -
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Residues in contact with ASP 329 (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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325B LYS* 2.9 43.2 + - - +
326B LYS* 4.1 5.3 - - - +
327B CYS 3.3 0.6 - - - -
328B ASP* 1.3 81.4 - - - +
330B ASP* 1.3 67.1 + - + +
333B THR* 5.2 1.7 - - - +
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Residues in contact with ASP 330 (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 LYS 3.8 6.1 + - - +
327B CYS 4.4 0.2 - - - -
328B ASP 3.5 1.0 - - - -
329B ASP* 1.3 85.5 - - + +
331B SER* 1.3 86.0 + - - +
332B GLU* 2.6 23.8 + - - +
333B THR* 4.8 1.6 - - - -
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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