Contacts of the helix formed by residues 245 - 256 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C PHE* 4.0 3.9 - - - -
233C LYS* 2.5 31.0 + - - -
237C GLN* 4.2 1.2 - - - +
243C ARG* 3.0 53.7 + - + +
244C PHE* 1.3 75.3 - - - +
246C GLU* 1.3 67.3 + - - +
247C ARG* 4.2 12.3 - - + +
248C ASN* 2.7 34.3 + - - +
249C VAL* 3.5 3.1 + - - +
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C PHE* 3.4 45.7 - - + -
245C GLU* 1.3 72.9 + - - +
247C ARG* 1.3 55.4 + - - +
249C VAL* 2.6 31.8 + - - +
250C GLY* 2.9 9.2 + - - -
282C LEU* 4.4 21.4 + - + +
360C LEU* 3.9 22.2 - - + +
362C GLN* 4.8 8.8 + - - +
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C GLU* 3.2 10.0 - - + +
246C GLU* 1.3 77.7 - - - +
248C ASN* 1.3 78.7 + - - +
250C GLY* 3.2 3.7 + - - +
251C GLN* 3.0 53.0 + - - +
355C ILE 5.0 2.0 + - - -
356C GLU* 5.8 1.0 + - - -
357C PRO* 3.4 30.5 - - + +
360C LEU* 5.2 2.9 - - - +
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Residues in contact with ASN 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 4.6 0.5 - - - +
209C MSE 3.6 29.1 - - - +
243C ARG* 4.0 2.4 + - - +
244C PHE* 3.5 25.9 - - + +
245C GLU* 2.7 46.4 + - - +
247C ARG* 1.3 80.3 + - - +
249C VAL* 1.3 64.5 + - - +
251C GLN* 2.9 31.3 + - - +
252C ILE* 2.9 18.7 + - - +
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Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C MSE 3.7 27.6 - - + -
229C PHE* 3.6 32.8 - - + -
244C PHE* 3.8 18.1 - - + -
246C GLU* 2.6 21.3 + - + +
248C ASN* 1.3 72.2 - - - +
250C GLY* 1.3 55.4 + - - +
251C GLN 3.2 0.3 + - - -
252C ILE* 3.2 11.2 + - + +
253C LYS* 2.8 28.9 + - - +
262C PHE* 3.7 24.7 - - + -
282C LEU* 4.8 4.9 - - + -
284C ILE* 5.2 0.7 - - + -
360C LEU* 4.8 8.1 - - + -
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Residues in contact with GLY 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU 2.9 10.8 + - - -
247C ARG* 3.2 5.8 + - - -
248C ASN 3.2 0.4 - - - -
249C VAL* 1.3 77.2 - - - +
251C GLN* 1.3 59.6 + - - +
253C LYS* 3.3 5.6 + - - -
254C THR 3.1 11.3 + - - -
357C PRO* 3.5 3.8 - - - -
358C ALA* 2.6 42.9 + - - +
360C LEU* 4.5 13.5 - - - +
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Residues in contact with GLN 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 3.6 24.1 - - + +
209C MSE 5.1 0.3 - - - +
247C ARG* 3.0 42.6 + - - +
248C ASN* 2.9 32.5 + - - +
250C GLY* 1.3 70.7 - - - +
252C ILE* 1.3 64.5 + - - +
253C LYS 2.9 3.8 - - - -
254C THR* 2.8 16.3 + - - -
255C VAL* 3.0 14.2 + - - +
355C ILE* 3.3 39.0 + - + +
357C PRO* 3.9 11.2 - - + -
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 4.5 9.4 - - + +
209C MSE 5.3 2.9 - - + -
210C PHE* 3.6 38.4 - - + +
213C MSE 3.9 18.2 - - + -
244C PHE* 5.2 4.3 - - + -
248C ASN 2.9 19.3 + - - +
249C VAL* 3.2 15.2 + - + +
251C GLN* 1.3 72.4 - - - +
253C LYS* 1.3 68.9 + - + +
256C TYR* 3.0 23.9 + - + +
259C SER* 5.2 0.7 - - - +
260C TYR* 3.7 28.9 - - + -
262C PHE* 5.0 0.4 - - + -
310C PHE* 3.6 25.9 - - + -
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Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C VAL 2.8 13.0 + - - +
250C GLY* 3.4 13.5 - - - +
251C GLN 2.8 1.0 + - - -
252C ILE* 1.3 79.3 - - - +
254C THR* 1.3 63.7 + - - +
256C TYR 2.9 4.3 + - - +
257C PRO* 2.8 58.3 + - + +
260C TYR* 4.2 6.6 + - - -
261C ARG* 5.7 0.6 - - - +
262C PHE* 3.7 37.1 - - + -
358C ALA* 3.6 18.4 - - + -
359C GLU 4.0 15.0 - - - +
360C LEU* 5.1 2.9 - - + -
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Residues in contact with THR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLY 3.1 1.1 + - - -
251C GLN 2.8 11.7 + - - -
253C LYS* 1.3 76.2 - - - +
255C VAL* 1.3 60.1 + - - +
256C TYR 3.4 0.2 + - - -
257C PRO* 3.6 11.2 - - - +
317C ARG* 3.8 21.5 + - - +
355C ILE* 4.3 8.7 - - + -
356C GLU* 2.5 31.1 + - + +
357C PRO 3.3 0.2 - - - -
358C ALA* 2.8 29.1 + - + +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 4.2 5.2 - - + -
251C GLN 3.0 12.5 + - - +
252C ILE 3.9 0.9 - - - +
254C THR* 1.3 76.8 - - - +
256C TYR* 1.3 56.8 + - - +
257C PRO* 3.6 3.7 - - - +
310C PHE* 3.3 49.1 - - + +
313C ASN* 3.1 26.6 + - + +
314C LEU* 3.6 35.0 - - + -
317C ARG* 4.4 9.8 + - - +
355C ILE* 4.0 22.9 - - + -
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Residues in contact with TYR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C PHE* 4.0 13.9 - + + -
252C ILE 3.0 12.7 + - - +
253C LYS* 2.9 8.5 + - - +
255C VAL* 1.3 80.5 - - + +
257C PRO* 1.3 67.6 - - - +
258C THR* 3.5 31.5 + - + -
259C SER* 2.9 40.0 - - - -
306C ARG* 3.8 34.4 + - + +
309C VAL* 3.5 39.3 - - + +
310C PHE* 3.9 20.2 - + + -
313C ASN* 4.7 4.0 - - - -
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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