Contacts of the helix formed by residues 239 - 259 (chain H) in PDB entry 5ZRV
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 LEU 239 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237H SER* 3.3 0.8 - - - +
238H ARG* 1.3 76.5 - - - +
240H GLU* 1.3 62.2 + - - +
242H ASP* 3.4 9.4 + - - -
243H GLU* 3.4 10.7 + - - -
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Residues in contact with GLU 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H VAL* 6.1 0.7 - - - -
237H SER* 3.5 11.6 + - - +
238H ARG 3.4 0.2 - - - -
239H LEU* 1.3 75.7 - - - +
241H GLN* 1.3 60.1 + - - +
242H ASP 3.4 0.5 + - - -
243H GLU* 4.0 6.0 + - - +
244H TYR 4.4 4.5 + - - -
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Residues in contact with GLN 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H VAL* 6.0 0.6 - - - +
237H SER 3.0 16.3 + - - -
238H ARG* 3.5 3.8 + - - +
239H LEU 3.2 0.8 - - - -
240H GLU* 1.3 76.2 - - - +
242H ASP* 1.3 57.3 + - - +
244H TYR* 4.4 2.8 + - - -
245H ALA* 4.1 8.1 + - - -
383H SER* 4.8 6.3 - - - -
384H GLY* 4.5 23.9 + - - -
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Residues in contact with ASP 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H ARG 3.6 7.2 + - - -
239H LEU 3.4 5.6 + - - -
240H GLU 3.2 0.2 - - - -
241H GLN* 1.3 79.7 - - - +
243H GLU* 1.3 59.8 + - - +
244H TYR 3.1 0.9 - - - -
245H ALA* 3.5 6.2 - - - +
246H LEU* 2.9 24.8 + - - -
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Residues in contact with GLU 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H LEU 3.4 12.4 + - - -
240H GLU* 4.0 3.4 + - - +
241H GLN 3.8 0.4 - - - -
242H ASP* 1.3 76.5 - - - +
244H TYR* 1.3 55.1 + - - +
246H LEU* 3.2 3.3 + - - +
247H ARG* 3.0 23.7 + - - -
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Residues in contact with TYR 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H GLU 4.4 5.3 + - - -
241H GLN 4.4 2.6 + - - -
242H ASP* 3.1 2.8 - - - +
243H GLU* 1.3 73.5 - - - +
245H ALA* 1.3 59.9 + - - +
247H ARG* 3.3 2.3 + - - +
248H SER* 2.9 26.5 + - - -
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Residues in contact with ALA 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H GLN 4.1 4.1 + - - -
242H ASP* 3.2 15.1 + - - +
244H TYR* 1.3 76.7 - - - +
246H LEU* 1.3 61.2 + - - +
248H SER* 3.6 7.7 + - - +
249H HIS* 3.6 8.8 + - - -
307H ASN* 5.6 10.3 - - - +
383H SER* 6.2 2.6 - - - +
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Residues in contact with LEU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H ASP 2.9 13.6 + - - -
243H GLU 3.2 4.4 + - - -
245H ALA* 1.3 74.6 - - - +
247H ARG* 1.3 57.8 + - - +
249H HIS* 3.5 1.4 + - - -
250H SER* 2.9 27.4 + - - -
284H SER 5.7 5.4 - - - -
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Residues in contact with ARG 247 (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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243H GLU 3.0 14.0 + - - -
244H TYR* 3.3 4.4 + - - +
246H LEU* 1.3 75.1 - - - +
248H SER* 1.3 55.9 + - - +
249H HIS 3.0 0.7 + - - -
250H SER* 5.0 1.1 - - - +
251H LEU* 3.0 31.1 + - - +
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Residues in contact with SER 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H TYR 2.9 15.6 + - - -
245H ALA* 3.6 4.2 + - - +
246H LEU 3.4 0.4 - - - -
247H ARG* 1.3 73.6 - - - +
249H HIS* 1.3 55.1 + - - +
252H ALA* 4.8 5.2 + - - -
421H GLY* 5.0 11.6 - - - -
422H GLY 6.0 0.4 - - - +
423H SER 5.1 5.8 - - - +
424H LEU 3.9 4.9 - - - +
425H SER* 3.4 28.6 + - - -
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Residues in contact with HIS 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H ALA 3.6 6.5 + - - -
246H LEU 3.5 4.1 + - - -
247H ARG 3.1 0.4 - - - -
248H SER* 1.3 78.4 - - - +
250H SER* 1.3 59.4 + - - +
251H LEU 3.2 2.0 - - - -
252H ALA* 3.0 17.4 + - - +
253H LYS* 3.0 15.1 + - - -
281H ILE* 6.3 1.6 - - - +
282H ARG 4.9 14.1 - - - +
283H PRO* 5.4 8.6 - - - +
424H LEU 5.6 0.4 - - - -
425H SER* 5.4 1.6 - - - +
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Residues in contact with SER 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H LEU 2.9 17.8 + - - -
247H ARG* 3.8 1.3 - - - +
249H HIS* 1.3 76.5 - - - +
251H LEU* 1.3 60.3 + - - +
253H LYS* 4.1 0.5 + - - -
254H LYS* 3.8 11.6 + - - -
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Residues in contact with LEU 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H ARG* 3.0 14.1 + - - +
250H SER* 1.3 75.9 - - - +
252H ALA* 1.3 59.0 + - - +
254H LYS* 3.3 2.9 + - - +
255H ALA* 2.9 25.3 + - - -
419H ASN 4.4 18.1 - - - +
420H TRP* 5.8 0.3 - - - -
421H GLY* 5.0 2.4 + - - +
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Residues in contact with ALA 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H ARG 4.6 0.8 + - - -
248H SER 4.8 4.9 + - - -
249H HIS* 3.0 12.8 + - - +
251H LEU* 1.3 74.5 - - - +
253H LYS* 1.3 60.2 + - - +
255H ALA* 3.1 2.7 + - - +
256H GLN* 3.0 24.8 + - - -
281H ILE* 6.6 0.4 - - - -
421H GLY* 4.9 13.2 - - - +
425H SER* 5.8 4.5 - - - +
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Residues in contact with LYS 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H HIS 3.0 13.0 + - - -
250H SER 4.1 1.1 + - - -
252H ALA* 1.3 76.7 - - - +
254H LYS* 1.3 57.0 + - - +
256H GLN* 3.4 1.8 + - - +
257H ASP* 2.9 24.8 + - - -
281H ILE* 6.4 0.6 - - - +
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Residues in contact with LYS 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H SER 3.8 9.7 + - - -
251H LEU* 3.3 6.1 + - - +
252H ALA 3.3 0.4 - - - -
253H LYS* 1.3 76.5 - - - +
255H ALA* 1.3 57.5 + - - +
257H ASP* 3.6 2.2 - - - +
258H GLU* 2.9 26.3 + - - -
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Residues in contact with ALA 255 (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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251H LEU 2.9 15.5 + - - -
252H ALA* 3.1 5.1 + - - +
254H LYS* 1.3 76.9 - - - +
256H GLN* 1.3 59.6 + - - +
258H GLU* 4.3 0.3 - - - -
259H GLY* 3.2 18.2 + - - -
260H LEU 4.1 5.0 + - - -
261H LEU* 4.4 7.5 + - - -
420H TRP* 6.3 2.9 - - - +
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Residues in contact with GLN 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252H ALA 3.0 13.6 + - - -
253H LYS* 3.7 2.7 - - - +
255H ALA* 1.3 74.2 - - - +
257H ASP* 1.3 64.9 + - - +
259H GLY* 3.4 13.0 + - - +
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Residues in contact with ASP 257 (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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253H LYS 2.9 16.1 + - - -
254H LYS* 3.1 5.7 + - - +
256H GLN* 1.3 76.3 - - - +
258H GLU* 1.3 63.5 + - - +
259H GLY* 4.3 0.3 - - - -
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Residues in contact with GLU 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H LYS 2.9 15.0 + - - -
255H ALA* 4.3 0.7 - - - +
257H ASP* 1.3 74.1 - - - +
259H GLY* 1.3 62.4 - - - +
260H LEU 3.3 3.7 + - - -
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Residues in contact with GLY 259 (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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255H ALA 3.2 11.2 + - - -
256H GLN* 3.7 13.5 - - - -
257H ASP 3.2 2.5 - - - -
258H GLU* 1.3 78.4 - - - +
260H LEU* 1.3 59.5 + - - +
261H LEU 3.4 5.6 - - - +
262H SER* 5.1 2.3 + - - -
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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
------------------------------------------------------------
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