Contacts of the helix formed by residues 314 - 329 (chain H) in PDB entry 5O9Z
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 314 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H ILE* 6.3 2.5 - - - -
313H GLU* 1.3 74.4 - - - +
315H LYS* 1.3 52.9 + - - +
316H VAL 3.5 0.2 - - - -
317H GLY* 4.5 1.6 - - - -
318H TYR* 2.7 43.6 + - - +
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Residues in contact with LYS 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H GLU* 3.0 9.6 - - + +
314H GLY* 1.3 78.8 - - - +
316H VAL* 1.3 57.3 + - - +
318H TYR* 3.8 2.0 - - - +
319H GLU* 2.9 29.6 + - - +
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Residues in contact with VAL 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H ASN* 5.4 2.0 - - + -
302H ALA* 6.3 0.9 - - - -
305H VAL* 5.3 7.6 - - + -
312H THR* 3.7 28.9 - - - -
313H GLU 3.3 3.0 + - - +
315H LYS* 1.3 78.0 - - - +
317H GLY* 1.3 60.0 + - - +
319H GLU* 3.2 6.4 + - - +
320H LEU* 2.9 30.3 + - - +
62O PRO* 5.4 11.9 - - + -
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Residues in contact with GLY 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H ASN* 4.8 16.1 - - - +
221H ILE* 4.6 24.5 - - - +
222H ILE* 5.3 2.6 - - - +
302H ALA* 6.1 1.1 - - - -
313H GLU 3.3 10.4 + - - -
314H GLY* 4.7 1.6 - - - -
316H VAL* 1.3 78.4 - - - +
318H TYR* 1.3 57.2 + - - +
320H LEU* 4.1 4.1 - - - +
321H LYS* 2.9 30.8 + - - +
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Residues in contact with TYR 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314H GLY* 2.7 24.6 + - - +
315H LYS* 4.1 2.2 - - - +
317H GLY* 1.3 75.1 - - - +
319H GLU* 1.3 58.4 + - - +
321H LYS* 3.9 6.5 - - - +
322H ASP* 2.9 31.2 + - - +
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Residues in contact with GLU 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H LYS 2.9 20.9 + - - +
316H VAL* 3.4 8.5 - - - +
318H TYR* 1.3 76.5 - - - +
320H LEU* 1.3 60.8 + - - +
322H ASP* 3.4 4.0 + - - +
323H GLU* 2.9 29.9 + - - +
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Residues in contact with LEU 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H ILE* 5.3 9.0 - - + -
298H LYS* 4.8 17.7 - - + +
301H LEU* 6.4 1.1 - - + -
302H ALA* 4.7 19.3 - - + +
316H VAL 2.9 15.4 + - - +
317H GLY* 4.2 3.6 - - - +
319H GLU* 1.3 76.9 - - - +
321H LYS* 1.3 58.7 + - - +
323H GLU* 4.0 6.1 - - - +
324H ILE* 2.9 30.8 + - - +
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Residues in contact with LYS 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H ILE 4.6 11.2 - - - +
222H ILE* 5.6 5.1 - - - +
317H GLY 2.9 19.8 + - - +
318H TYR* 3.9 8.1 - - - +
319H GLU 3.2 0.2 - - - -
320H LEU* 1.3 78.0 - - - +
322H ASP* 1.3 57.7 + - - +
324H ILE* 3.8 4.5 - - - +
325H GLU* 2.9 28.1 + - - +
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Residues in contact with ASP 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318H TYR 2.9 20.1 + - - +
319H GLU* 3.8 4.9 - - - +
320H LEU 3.3 0.2 - - - -
321H LYS* 1.3 76.2 - - - +
323H GLU* 1.3 59.1 + - - +
325H GLU* 3.3 6.9 + - - +
326H ARG* 2.9 29.8 + - - +
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Residues in contact with GLU 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298H LYS* 6.1 3.4 - - + -
319H GLU 2.9 18.6 + - - +
320H LEU* 4.0 6.5 - - - +
322H ASP* 1.3 77.1 - - - +
324H ILE* 1.3 58.0 + - - +
326H ARG* 3.5 5.5 + - - +
327H LYS* 2.9 28.2 + - - +
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Residues in contact with ILE 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279H ILE* 6.4 2.0 - - + -
295H VAL* 4.9 17.9 - - + +
298H LYS* 5.2 9.6 - - + +
320H LEU 2.9 19.2 + - - +
321H LYS* 4.0 5.4 - - - +
323H GLU* 1.3 74.4 - - - +
325H GLU* 1.3 60.5 + - - +
327H LYS* 3.8 6.0 - - - +
328H PHE* 2.9 31.5 + - - +
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Residues in contact with GLU 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H LYS 2.9 20.2 + - - +
322H ASP* 3.3 8.0 + - - +
324H ILE* 1.3 78.1 - - - +
326H ARG* 1.3 56.3 + - - +
328H PHE* 4.3 2.5 - - - +
329H ASP* 2.9 31.9 + - - +
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Residues in contact with ARG 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322H ASP 2.9 17.2 + - - +
323H GLU* 3.9 6.1 - - - +
325H GLU* 1.3 75.4 - - - +
327H LYS* 1.3 60.6 + - - +
329H ASP* 3.4 6.3 - - - -
330H LYS* 2.9 27.9 + - - +
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Residues in contact with LYS 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291H ALA* 5.6 3.3 - - + +
294H LEU* 4.9 18.2 - - + -
295H VAL 6.1 0.2 - - - +
323H GLU 2.9 18.8 + - - +
324H ILE* 3.8 7.6 - - - +
326H ARG* 1.3 77.5 - - - +
328H PHE* 1.3 61.1 + - - +
330H LYS* 3.2 21.2 - - - +
331H TRP 4.8 0.3 + - - -
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Residues in contact with PHE 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H ILE 5.9 2.7 - - - +
283H LEU* 5.7 7.9 - - + -
287H LEU* 5.9 4.0 - - - +
291H ALA* 4.6 20.8 - - + +
324H ILE 2.9 17.4 + - - +
325H GLU* 4.3 3.6 - - - +
327H LYS* 1.3 77.1 - - - +
329H ASP* 1.3 58.9 + - - +
330H LYS 3.2 1.4 + - - -
331H TRP 4.2 11.4 + - - +
332H GLN* 5.6 0.5 - - - +
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Residues in contact with ASP 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325H GLU 2.9 22.0 + - - +
326H ARG* 3.4 7.2 - - - +
327H LYS 3.2 0.4 - - - -
328H PHE* 1.3 74.7 - - - +
330H LYS* 1.3 65.1 + - - +
331H TRP 3.4 3.5 + - - -
332H GLN* 4.2 16.5 + - + +
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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