Contacts of the helix formed by residues 245 - 256 (chain F) in PDB entry 2ZXX
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 GLU 245 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229F PHE* 3.9 5.0 - - - -
233F LYS* 3.4 25.1 + - - -
243F ARG* 2.8 50.6 + - - +
244F PHE* 1.3 77.7 - - - +
246F GLU* 1.3 68.0 + - - +
247F ARG* 3.3 17.3 - - + +
248F ASN* 2.8 30.9 + - - +
249F VAL* 3.5 5.9 + - - +
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Residues in contact with GLU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F PHE* 3.6 30.8 - - + -
245F GLU* 1.3 74.1 + - - +
247F ARG* 1.3 56.1 + - - +
248F ASN 2.6 1.9 + - - -
249F VAL* 2.6 30.7 + - + +
250F GLY 2.9 8.6 + - - -
282F LEU* 5.1 14.2 - - + +
360F LEU* 3.7 27.5 - - + +
361F PRO 5.5 0.5 - - - +
362F GLN* 3.5 25.1 + - - +
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Residues in contact with ARG 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F GLU* 4.2 12.1 - - + +
246F GLU* 1.3 75.6 - - - +
248F ASN* 1.3 65.3 + - - +
250F GLY* 3.2 4.0 + - - +
251F GLN* 2.9 33.2 + - - +
356F GLU* 5.0 5.1 + - - -
357F PRO* 3.2 45.6 - - + +
360F LEU* 5.8 0.7 - - - -
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Residues in contact with ASN 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F LEU* 4.8 1.2 - - - +
209F MSE 3.3 36.0 - - - +
243F ARG* 4.8 1.0 - - - +
244F PHE* 3.3 23.4 - - + +
245F GLU* 2.8 39.8 + - - +
246F GLU 2.6 4.9 + - - -
247F ARG* 1.3 75.6 - - - +
249F VAL* 1.3 65.8 + - - +
251F GLN* 3.0 32.1 + - - +
252F ILE* 3.0 15.1 + - - +
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Residues in contact with VAL 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F MSE 3.6 35.2 - - + -
229F PHE* 3.7 28.3 - - + -
244F PHE* 3.7 18.3 - - + -
245F GLU 4.2 0.4 - - - +
246F GLU* 2.6 12.7 + - - +
248F ASN* 1.3 72.2 - - - +
250F GLY* 1.3 65.0 + - - +
252F ILE* 2.8 21.0 + - + +
253F LYS* 3.1 11.8 + - - +
262F PHE* 3.8 28.7 - - + -
282F LEU* 4.7 5.4 - - + -
360F LEU* 4.6 9.0 - - + -
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Residues in contact with GLY 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F GLU 2.9 10.6 + - - -
247F ARG* 3.3 8.3 - - - -
249F VAL* 1.3 77.5 - - - +
251F GLN* 1.3 61.7 + - - +
253F LYS* 3.3 3.8 + - - +
254F THR* 2.9 10.7 + - - -
357F PRO* 3.5 9.0 - - - -
358F ALA 2.9 32.9 + - - -
360F LEU* 4.0 15.0 - - - +
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Residues in contact with GLN 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F LEU* 4.0 25.5 - - + +
209F MSE 5.2 0.2 - - - +
247F ARG* 2.9 25.3 + - - +
248F ASN* 3.0 30.8 + - - +
250F GLY* 1.3 72.9 - - - +
252F ILE* 1.3 65.0 + - - +
254F THR* 3.0 12.4 + - - -
255F VAL* 2.9 23.1 + - - +
354F ASP* 5.7 1.8 + - - -
355F ILE* 3.2 46.5 + - + +
357F PRO* 3.9 9.9 - - + -
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Residues in contact with ILE 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F LEU* 4.8 7.6 - - + +
209F MSE 4.2 7.6 - - + -
210F PHE* 3.5 53.4 - - + +
213F MSE 3.7 25.4 - - + -
244F PHE* 4.6 5.4 - - + -
248F ASN 3.0 14.4 + - - +
249F VAL* 2.8 15.3 + - + +
251F GLN* 1.3 72.1 - - - +
253F LYS* 1.3 56.3 + - - +
255F VAL* 3.2 1.8 + - - +
256F TYR* 2.7 27.6 + - + +
259F SER* 4.5 3.4 - - - +
260F TYR* 4.2 16.2 - - + -
262F PHE* 6.2 0.2 - - + -
310F PHE* 4.0 24.2 - - + -
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Residues in contact with LYS 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F VAL 3.1 10.0 + - - +
250F GLY* 3.6 9.4 - - - +
251F GLN 3.1 0.2 - - - -
252F ILE* 1.3 73.5 - - - +
254F THR* 1.3 69.9 + - - +
256F TYR 2.8 13.6 + - - -
257F PRO* 3.0 40.8 - - + +
259F SER* 5.4 1.1 - - - -
260F TYR* 6.3 0.2 - - - -
261F ARG* 4.8 16.7 - - - +
262F PHE* 4.0 28.4 - - + -
358F ALA* 3.6 17.4 - - + +
359F GLU* 2.6 29.5 + - - +
360F LEU* 4.2 7.4 - - + +
361F PRO* 5.1 3.2 - - - +
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Residues in contact with THR 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F GLY 2.9 3.1 + - - -
251F GLN 3.1 8.1 - - - -
253F LYS* 1.3 79.1 - - - +
255F VAL* 1.3 63.4 + - - +
257F PRO* 4.0 9.9 - - - +
317F ARG* 4.0 23.1 + - - +
355F ILE* 4.1 10.3 - - + -
356F GLU* 2.5 35.4 + - + +
358F ALA* 2.7 23.8 + - + +
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Residues in contact with VAL 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F LEU* 4.6 4.5 - - + -
251F GLN 2.9 14.8 + - - +
252F ILE 3.7 1.6 - - - +
254F THR* 1.3 78.3 - - - +
256F TYR* 1.3 56.7 + - + +
257F PRO* 4.0 3.4 - - - +
310F PHE* 3.3 49.8 - - + +
313F ASN* 3.1 28.5 - - + +
314F LEU* 3.7 32.3 - - + -
317F ARG* 3.7 13.0 + - - +
355F ILE* 4.1 21.3 - - + -
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Residues in contact with TYR 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F PHE* 3.9 20.0 - + - -
252F ILE* 2.7 17.1 + - + +
253F LYS* 2.8 3.6 + - - -
255F VAL* 1.3 78.3 - - - +
257F PRO* 1.3 59.9 - - - +
258F THR* 3.9 25.4 - - + -
259F SER* 2.7 52.9 + - - +
306F ARG* 3.7 39.8 + - + +
309F VAL* 3.7 28.6 - - + +
310F PHE* 4.0 21.8 - + + -
313F ASN* 4.3 9.4 - - - +
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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