Contacts of the helix formed by residues 247 - 262 (chain C) in PDB entry 2XZ0
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 ASP 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C LYS* 2.9 21.2 + - - -
39C ILE* 5.8 2.0 - - + -
186C TYR* 2.6 36.8 + - + +
243C LEU* 2.9 19.5 + - + +
246C ILE* 1.3 86.0 - - + +
248C PRO* 1.4 67.0 - - - +
249C ASP* 3.2 4.7 + - - +
250C GLY* 3.2 17.4 + - - -
251C THR* 3.2 11.8 + - - -
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Residues in contact with PRO 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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244C PHE* 3.3 27.8 - - + +
245C GLU 4.1 7.0 - - - +
246C ILE 3.8 6.1 - - - +
247C ASP* 1.4 89.8 - - - +
249C ASP* 1.3 61.7 + - + +
251C THR* 4.2 1.6 - - - -
252C VAL* 3.3 28.4 + - - +
313C LEU* 4.7 12.3 - - + -
314C THR 4.7 12.3 - - - +
315C GLY 5.3 4.0 - - - +
316C LEU* 4.2 11.7 - - + -
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Residues in contact with ASP 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ASP* 3.2 4.6 - - - +
248C PRO* 1.3 80.2 - - + +
250C GLY* 1.3 60.4 + - - +
252C VAL* 3.2 4.9 + - - +
253C LEU* 2.9 44.2 + - - +
315C GLY 4.9 6.5 - - - +
316C LEU* 4.0 11.6 - - + +
317C SER* 3.0 35.9 + - - -
319C GLU* 4.8 0.9 - - - +
320C GLY* 3.9 14.6 + - - -
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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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36C LYS* 5.2 1.3 - - - -
186C TYR* 3.5 17.9 - - - -
247C ASP* 3.2 23.7 + - - -
249C ASP* 1.3 78.4 - - - +
251C THR* 1.3 55.4 + - - +
253C LEU* 3.3 16.1 + - - +
254C ALA* 2.9 22.9 + - - +
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Residues in contact with THR 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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186C TYR* 3.8 13.6 - - + -
190C ILE* 4.0 5.7 - - + +
240C VAL* 4.1 13.2 - - + -
243C LEU* 2.7 37.6 + - + +
244C PHE* 3.6 44.9 - - + +
247C ASP 3.2 9.2 + - - -
248C PRO 4.2 0.2 - - - -
250C GLY* 1.3 72.1 - - - +
252C VAL* 1.3 55.5 + - - +
254C ALA* 3.1 4.3 + - - +
255C PHE* 2.8 33.7 + - - +
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C PHE* 3.5 21.5 - - + -
248C PRO 3.3 14.3 + - - +
249C ASP* 3.2 10.9 + - - +
251C THR* 1.3 77.2 - - - +
253C LEU* 1.3 56.1 + - - +
255C PHE* 3.9 6.7 - - - +
256C ALA* 2.9 28.6 + - - +
310C VAL* 4.6 8.7 - - + -
313C LEU* 4.1 13.0 - - + -
316C LEU* 4.4 9.9 - - + -
320C GLY* 3.4 29.2 - - - +
323C ALA* 3.5 13.8 - - + +
324C GLN* 3.7 11.2 - - + +
327C VAL* 5.1 0.6 - - + +
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Residues in contact with LEU 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 ASP* 2.9 34.7 + - - +
250C GLY* 3.4 15.5 - - - +
251C THR 3.2 0.2 - - - -
252C VAL* 1.3 73.6 - - - +
254C ALA* 1.3 60.2 + - - +
256C ALA* 4.0 1.2 - - - +
257C ASP* 3.1 29.1 + - - +
319C GLU* 4.3 27.8 - - + +
323C ALA* 4.3 16.4 - - + -
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Residues in contact with ALA 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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186C TYR* 3.6 30.5 - - + -
187C LEU* 3.4 25.1 - - + +
190C ILE* 3.9 12.8 - - + -
250C GLY 2.9 13.6 + - - +
251C THR* 3.1 8.3 + - - +
253C LEU* 1.3 75.0 - - - +
255C PHE* 1.3 58.4 - - - +
257C ASP* 3.3 1.1 + - - -
258C MET* 3.0 28.1 + - - +
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Residues in contact with PHE 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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190C ILE* 3.6 29.6 - - + +
194C PHE* 5.9 0.7 - + - -
244C PHE* 4.3 13.0 - + + -
251C THR 2.8 20.8 + - - +
252C VAL* 3.9 7.6 - - - +
254C ALA* 1.3 73.3 - - - +
256C ALA* 1.3 60.7 + - - +
258C MET 3.7 0.3 + - - -
259C MET* 3.3 48.7 + - + +
301C LEU* 4.1 17.3 - - + -
304C LEU* 4.1 17.3 - - + -
305C VAL* 4.3 9.2 - - + -
308C TRP* 3.5 39.5 - + - -
310C VAL* 4.3 7.4 - - + -
327C VAL* 3.5 29.6 - - + -
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Residues in contact with ALA 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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252C VAL 2.9 19.3 + - - +
253C LEU 4.0 2.7 - - - +
255C PHE* 1.3 74.6 - - - +
257C ASP* 1.3 63.8 + - - +
259C MET* 3.1 12.9 + - - +
260C ARG* 3.1 32.9 + - - +
323C ALA* 3.6 34.1 - - + +
326C TYR* 4.4 3.3 - - + -
327C VAL* 3.7 12.2 - - + +
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Residues in contact with ASP 257 (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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182C GLU* 4.2 3.5 - - - +
187C LEU* 3.4 20.3 - - + +
253C LEU 3.1 20.4 + - - +
254C ALA* 3.3 4.7 + - - +
256C ALA* 1.3 75.8 - - - +
258C MET* 1.3 61.3 + - - +
260C ARG* 3.5 10.1 + - - +
261C LYS* 3.0 62.9 + - - +
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Residues in contact with MET 258 (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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179C PRO 4.0 14.6 - - - +
180C ARG 3.9 12.8 - - - +
181C THR* 4.4 2.5 - - + -
187C LEU* 3.5 48.9 - - + +
190C ILE* 4.2 11.0 - - + -
191C TYR* 3.9 30.5 - - + -
254C ALA 3.0 19.0 + - - +
255C PHE 4.0 1.3 - - - +
256C ALA 3.3 0.2 - - - -
257C ASP* 1.3 75.0 - - - +
259C MET* 1.3 80.6 + - + +
261C LYS* 3.5 11.5 + - + +
262C LYS* 3.2 26.5 + - - +
263C ILE* 4.1 12.7 + - + +
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Residues in contact with MET 259 (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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190C ILE* 4.6 2.7 - - + -
194C PHE* 5.0 7.4 - - + -
255C PHE* 3.3 32.5 + - + +
256C ALA* 3.1 10.1 + - - +
258C MET* 1.3 95.2 - - + +
260C ARG* 1.3 60.2 + - - +
262C LYS* 3.4 15.7 + - - +
263C ILE* 3.7 22.0 - - + -
297C TYR* 4.6 13.1 + - - -
301C LEU* 3.4 38.8 - - + -
326C TYR* 3.8 14.1 + - + -
327C VAL* 4.5 7.6 - - + -
330C LEU* 3.8 20.6 - - + +
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Residues in contact with ARG 260 (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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336B ARG* 4.1 20.4 - - - +
256C ALA* 3.1 30.8 + - - +
257C ASP* 4.1 8.7 - - - +
258C MET 3.3 0.2 - - - -
259C MET* 1.3 73.4 - - - +
261C LYS* 1.3 62.3 + - + +
262C LYS* 3.1 12.3 + - - +
322C LYS* 4.5 12.7 - - - +
323C ALA* 5.0 4.8 - - - +
326C TYR* 3.7 31.0 - - + +
50D GLU* 3.3 37.7 + - - +
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Residues in contact with LYS 261 (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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180C ARG* 2.9 81.4 + - + +
182C GLU* 2.9 31.6 + - - -
187C LEU* 4.2 3.0 - - - +
257C ASP* 3.0 46.3 + - - +
258C MET* 4.0 10.5 - - + +
259C MET 3.4 0.2 - - - -
260C ARG* 1.3 77.4 - - + +
262C LYS* 1.3 77.2 + - - +
264C SER* 5.9 0.2 - - - -
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Residues in contact with LYS 262 (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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180C ARG* 4.7 2.4 + - - -
258C MET* 3.2 15.0 + - - +
259C MET 3.4 11.8 + - - +
260C ARG 3.1 8.2 - - - +
261C LYS* 1.3 95.4 - - - +
263C ILE* 1.3 61.7 + - - +
264C SER* 3.1 10.2 + - - -
297C TYR* 4.0 13.5 - - + +
50D GLU 5.4 7.4 + - - -
51D GLU* 4.6 14.3 + - - +
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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
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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