Contacts of the helix formed by residues 239 - 259 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D SER* 3.3 0.8 - - - +
238D ARG* 1.3 75.6 - - - +
240D GLU* 1.3 63.2 + - - +
242D ASP* 3.4 9.8 + - - +
243D GLU* 3.4 10.9 + - - -
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Residues in contact with GLU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D VAL* 6.3 0.4 - - - -
237D SER* 3.5 11.8 + - - +
239D LEU* 1.3 75.7 - - - +
241D GLN* 1.3 59.9 + - - +
242D ASP 3.4 0.7 + - - -
243D GLU* 4.0 6.1 + - - +
244D TYR 4.4 4.7 + - - -
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Residues in contact with GLN 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D VAL* 6.3 0.4 - - - +
237D SER 3.0 17.1 + - - -
238D ARG* 3.5 4.2 + - - +
239D LEU 3.2 0.8 - - - -
240D GLU* 1.3 76.9 - - - +
242D ASP* 1.3 57.4 + - - +
243D GLU 3.8 0.2 - - - -
244D TYR* 4.4 2.6 + - - -
245D ALA* 4.1 8.0 + - - -
383D SER* 4.8 6.1 - - - -
384D GLY* 4.5 24.1 + - - -
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Residues in contact with ASP 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ARG 3.6 7.1 + - - -
239D LEU 3.4 5.6 + - - -
240D GLU 3.2 0.4 - - - -
241D GLN* 1.3 79.2 - - - +
243D GLU* 1.3 60.8 + - - +
244D TYR 3.1 0.9 - - - -
245D ALA* 3.2 7.0 + - - +
246D LEU* 2.9 24.4 + - - -
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Residues in contact with GLU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D LEU 3.4 11.7 + - - -
240D GLU* 4.0 3.9 + - - +
241D GLN 3.8 0.2 - - - -
242D ASP* 1.3 75.0 - - - +
244D TYR* 1.3 55.3 + - - +
246D LEU* 3.2 3.8 + - - +
247D ARG* 3.0 23.2 + - - -
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Residues in contact with TYR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D GLU 4.4 4.8 + - - -
241D GLN 4.4 3.0 + - - -
242D ASP* 3.1 2.8 - - - +
243D GLU* 1.3 72.8 - - - +
245D ALA* 1.3 60.0 + - - +
247D ARG* 3.3 2.3 + - - +
248D SER* 2.9 26.7 + - - -
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Residues in contact with ALA 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D GLN 4.1 3.9 + - - -
242D ASP* 3.2 15.3 + - - +
244D TYR* 1.3 76.5 - - - +
246D LEU* 1.3 61.9 + - - +
248D SER* 3.6 8.5 + - - +
249D HIS* 3.6 8.3 + - - -
307D ASN* 5.6 10.1 - - - +
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Residues in contact with LEU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D ASP 2.9 13.8 + - - -
243D GLU* 3.2 4.9 + - - +
245D ALA* 1.3 73.6 - - - +
247D ARG* 1.3 59.3 + - - +
249D HIS* 3.5 1.4 + - - -
250D SER* 2.9 27.0 + - - -
284D SER 5.7 5.2 - - - -
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Residues in contact with ARG 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D GLU 3.0 14.0 + - - -
244D TYR* 3.3 4.4 + - - +
246D LEU* 1.3 75.2 - - - +
248D SER* 1.3 55.3 + - - +
249D HIS 3.0 0.8 + - - -
250D SER* 4.4 0.9 - - - +
251D LEU* 3.0 31.0 + - - +
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Residues in contact with SER 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D TYR 2.9 15.7 + - - -
245D ALA* 3.6 4.8 + - - +
246D LEU 3.4 0.6 - - - -
247D ARG* 1.3 74.0 - - - +
249D HIS* 1.3 55.5 + - - +
252D ALA* 4.8 5.4 + - - -
421D GLY* 5.0 11.7 - - - -
422D GLY 6.0 0.4 - - - +
423D SER 5.4 5.4 - - - -
424D LEU 3.9 4.9 - - - +
425D SER* 3.4 28.4 + - - -
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Residues in contact with HIS 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ALA 3.6 6.5 + - - -
246D LEU 3.5 3.6 + - - -
247D ARG 3.1 0.4 - - - -
248D SER* 1.3 78.9 - - - +
250D SER* 1.3 59.1 + - - +
251D LEU 3.2 2.0 - - - -
252D ALA* 3.0 16.7 + - - +
253D LYS* 3.0 14.9 + - - -
281D ILE* 6.3 1.3 - - - +
282D ARG 4.9 14.3 - - - +
283D PRO* 5.4 9.2 - - - +
424D LEU 5.6 0.4 - - - -
425D SER* 5.4 1.6 - - - +
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Residues in contact with SER 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D LEU 2.9 17.5 + - - -
247D ARG* 3.8 0.9 - - - +
249D HIS* 1.3 74.7 - - - +
251D LEU* 1.3 61.4 + - - +
253D LYS* 4.1 0.9 + - - +
254D LYS* 3.8 12.1 + - - -
283D PRO* 5.7 2.4 - - - +
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D ARG* 3.0 14.7 + - - +
250D SER* 1.3 75.3 - - - +
252D ALA* 1.3 60.1 + - - +
254D LYS* 3.3 2.8 + - - +
255D ALA* 2.9 25.1 + - - -
419D ASN 4.4 18.3 - - - +
420D TRP* 5.8 0.5 - - - -
421D GLY* 5.0 2.8 + - - +
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Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ARG 4.6 0.6 + - - -
248D SER 4.8 4.6 + - - -
249D HIS* 3.0 12.6 + - - +
251D LEU* 1.3 75.2 - - - +
253D LYS* 1.3 59.6 + - - +
255D ALA* 3.1 3.0 + - - +
256D GLN* 3.0 24.9 + - - -
421D GLY* 4.9 13.4 - - - +
425D SER* 5.8 5.2 - - - +
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Residues in contact with LYS 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D HIS 3.0 13.0 + - - -
250D SER 4.7 0.9 - - - -
252D ALA* 1.3 76.7 - - - +
254D LYS* 1.3 56.8 + - - +
256D GLN* 3.4 1.6 + - - +
257D ASP* 2.9 24.9 + - - -
281D ILE* 6.6 0.2 - - - +
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Residues in contact with LYS 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D SER 3.8 9.7 + - - -
251D LEU* 3.3 5.7 + - - +
252D ALA 3.3 0.4 - - - -
253D LYS* 1.3 76.2 - - - +
255D ALA* 1.3 57.0 + - - +
257D ASP* 3.6 2.0 - - - +
258D GLU* 2.9 26.3 + - - -
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Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D LEU 2.9 15.2 + - - -
252D ALA* 3.1 5.1 + - - +
254D LYS* 1.3 76.9 - - - +
256D GLN* 1.3 59.3 + - - +
258D GLU* 3.8 0.5 + - - -
259D GLY* 3.2 18.0 + - - -
260D LEU 4.1 4.9 + - - -
261D LEU* 4.4 6.6 + - - -
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Residues in contact with GLN 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D ALA 3.0 14.1 + - - -
253D LYS* 3.7 2.5 - - - +
255D ALA* 1.3 74.4 - - - +
257D ASP* 1.3 64.8 + - - +
259D GLY* 3.4 13.2 + - - +
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Residues in contact with ASP 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D LYS 2.9 15.9 + - - -
254D LYS* 3.1 5.7 + - - +
256D GLN* 1.3 76.3 - - - +
258D GLU* 1.3 64.0 + - - +
259D GLY* 4.3 0.3 - - - -
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Residues in contact with GLU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D LYS 2.9 14.5 + - - -
255D ALA* 4.3 0.7 - - - +
257D ASP* 1.3 74.3 - - - +
259D GLY* 1.3 64.2 + - - +
260D LEU 3.3 3.2 + - - -
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Residues in contact with GLY 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ALA 3.2 11.0 + - - -
256D GLN* 3.7 13.5 - - - -
257D ASP 3.2 2.7 - - - -
258D GLU* 1.3 79.8 - - - +
260D LEU* 1.3 59.8 + - - +
261D LEU 3.4 6.3 - - - +
262D SER* 5.1 1.9 + - - -
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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