Contacts of the helix formed by residues 252 - 270 (chain A) in PDB entry 1MZC
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A THR* 4.9 9.5 + - - +
249A GLY 4.5 4.0 + - - +
250A TYR 3.3 3.0 - - - +
251A ASN* 1.3 76.3 - - - +
253A ARG* 1.3 62.5 + - - +
254A ALA* 2.8 24.0 + - - +
255A VAL* 3.0 39.0 + - + +
256A LEU 3.0 11.1 + - - -
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A TYR 5.2 0.2 - - - -
251A ASN 2.9 16.1 + - - +
252A ASP* 1.3 72.4 + - - +
254A ALA* 1.3 56.8 - - - +
256A LEU* 3.8 20.0 - - + +
257A GLU* 2.9 29.8 + - - +
287A ARG* 6.3 0.6 - - - +
292A TYR* 5.5 7.7 + - - -
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ASP* 2.8 14.8 + - - +
253A ARG* 1.3 78.6 - - - +
255A VAL* 1.3 60.0 - - + +
257A GLU* 3.5 5.6 + - - +
258A ARG* 3.0 27.0 + - - +
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ILE* 4.0 9.2 - - + -
248A THR* 3.7 27.1 - - + +
249A GLY 3.6 18.2 - - - +
250A TYR* 4.9 2.2 - - + -
252A ASP* 3.0 35.5 + - + +
254A ALA* 1.3 74.9 - - + +
256A LEU* 1.3 65.8 + - - +
258A ARG* 3.2 35.3 + - - +
259A GLU* 3.0 24.3 + - + +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A TYR* 3.8 39.0 + - + +
252A ASP 3.0 7.6 + - - +
253A ARG* 3.8 20.9 - - + +
255A VAL* 1.3 78.5 - - - +
257A GLU* 1.3 58.0 + - - +
259A GLU* 3.1 5.6 + - - +
260A VAL* 2.8 40.0 + - + +
283A ILE* 3.8 29.6 - - + +
284A LEU* 4.1 7.2 - - + -
292A TYR* 3.8 36.1 - - + +
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ARG 2.9 18.1 + - - +
254A ALA* 3.8 7.2 - - - +
256A LEU* 1.3 75.9 - - - +
258A ARG* 1.3 63.1 + - - +
260A VAL* 4.5 10.4 - - - +
261A GLN* 2.9 62.2 + - + +
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 4.1 20.7 - - - +
240A ARG* 4.8 2.9 - - - +
244A ILE* 3.6 21.6 - - - +
248A THR* 5.2 4.8 + - - +
254A ALA 3.0 14.7 + - - +
255A VAL* 3.4 33.4 - - - +
256A LEU 3.2 0.2 - - - -
257A GLU* 1.3 76.6 - - - +
259A GLU* 1.3 86.4 + - - +
261A GLN* 3.7 5.8 - - - +
262A TYR* 2.9 32.2 + - + +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ARG* 2.7 32.1 + - - -
244A ILE* 3.2 22.0 - - + -
250A TYR* 4.0 10.5 - - + -
255A VAL* 3.0 17.9 + - + +
256A LEU* 3.5 8.1 - - - +
258A ARG* 1.3 106.2 + - - +
260A VAL* 1.3 59.5 + - - +
262A TYR* 3.4 2.5 + - - +
263A THR* 2.8 35.7 + - - -
279A TYR* 2.6 26.3 + - + +
283A ILE* 4.0 17.0 - - + -
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 2.8 29.0 + - + +
257A GLU* 3.9 13.5 - - - +
259A GLU* 1.3 73.1 - - - +
261A GLN* 1.3 58.2 + - + +
263A THR* 3.8 1.2 - - - -
264A LEU* 2.9 46.7 + - + +
280A LEU* 4.1 16.6 - - + -
283A ILE* 3.9 19.3 - - + -
284A LEU* 4.0 22.9 - - + -
292A TYR* 6.2 0.7 - - + -
295A LEU* 5.1 7.2 - - + -
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Residues in contact with GLN 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLU* 2.9 45.7 + - + +
258A ARG* 3.7 6.3 - - - +
260A VAL* 1.3 75.2 - - - +
262A TYR* 1.3 65.5 + - - +
264A LEU* 3.3 15.3 + - - +
265A GLU* 3.0 24.5 + - - +
298A GLN* 5.3 8.1 + - - +
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Residues in contact with TYR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ASP* 3.8 14.3 + - - +
227A LEU* 3.1 29.4 - - + +
237A TRP* 3.8 23.1 - + - -
240A ARG* 3.8 41.5 - - - +
258A ARG* 2.9 21.4 + - + +
259A GLU* 3.6 7.2 - - - +
260A VAL 3.4 0.2 - - - -
261A GLN* 1.3 77.2 - - - +
263A THR* 1.3 72.2 + - - +
265A GLU* 3.3 7.0 + - + +
266A MET* 3.1 46.3 + - + +
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Residues in contact with THR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A TRP* 4.0 4.6 - - + -
259A GLU 2.8 18.2 + - - -
260A VAL 3.8 3.8 - - - -
262A TYR* 1.3 78.5 - - - +
264A LEU* 1.3 59.6 + - - +
266A MET* 3.1 7.2 + - - +
267A ILE* 2.9 29.9 + - + +
276A ALA* 3.1 35.7 - - + +
279A TYR* 3.1 26.6 - - + -
280A LEU* 3.8 25.6 - - + +
283A ILE* 4.8 0.5 - - - +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A VAL* 2.9 39.3 + - + +
261A GLN* 3.3 15.5 + - - +
263A THR* 1.3 76.3 - - - +
265A GLU* 1.3 61.8 + - - +
267A ILE* 3.2 11.6 + - + +
268A LYS* 3.0 39.7 + - - +
280A LEU* 4.1 23.8 - - + -
295A LEU* 4.4 14.8 - - + -
298A GLN* 3.7 27.4 - - + +
299A LEU* 4.4 12.3 - - + -
302A LEU* 5.4 7.9 - - + -
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A GLN 3.0 13.4 + - - +
262A TYR* 3.5 10.3 - - - +
264A LEU* 1.3 77.3 - - - +
266A MET* 1.3 79.2 + - + +
268A LYS* 3.3 19.0 + - - +
269A LEU* 3.1 36.8 + - + +
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LEU* 5.8 2.0 - - - +
231A VAL* 3.9 25.5 - - + +
237A TRP* 4.0 18.8 - - + -
262A TYR* 3.1 47.9 + - + +
263A THR 3.1 6.7 + - - +
265A GLU* 1.3 90.3 - - + +
267A ILE* 1.3 58.4 + - - +
269A LEU* 3.2 31.3 + - + +
270A VAL* 2.9 31.4 + - - +
273A ASN* 5.7 0.7 + - - -
276A ALA* 4.4 5.8 - - + +
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A THR* 2.9 27.8 + - + +
264A LEU* 3.5 15.5 - - + +
266A MET* 1.3 75.4 - - - +
268A LYS* 1.3 61.9 + - + +
270A VAL 4.2 5.8 - - - -
271A PRO* 2.9 37.3 - - + +
273A ASN 5.5 0.2 - - - +
276A ALA* 3.8 16.2 - - + -
277A TRP* 3.5 65.3 - - + +
280A LEU* 4.0 19.3 - - + -
302A LEU* 5.5 8.5 - - + -
306A HIS* 4.4 4.0 - - + -
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Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A LEU* 3.0 31.1 + - - +
265A GLU* 3.3 20.2 + - - +
267A ILE* 1.3 78.0 - - + +
269A LEU* 1.3 63.9 + - + +
271A PRO* 3.7 3.6 - - - +
298A GLN* 5.8 4.8 - - - +
302A LEU* 4.8 28.7 - - + -
306A HIS* 3.2 37.1 + - + +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 3.1 32.8 + - + +
266A MET* 3.4 40.4 - - + +
267A ILE 3.2 0.2 - - - -
268A LYS* 1.3 81.1 - - + +
270A VAL* 1.3 70.0 + - + +
271A PRO* 3.5 5.0 - - - +
538B ASP* 4.4 2.8 - - - +
540B VAL* 3.9 14.9 - - + +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A VAL* 3.9 24.0 - - + -
232A ARG* 3.6 25.1 - - - +
266A MET 2.9 12.4 + - - +
267A ILE* 3.2 8.1 - - - +
269A LEU* 1.3 90.1 - - + +
271A PRO* 1.3 65.1 - - - +
272A HIS 3.2 0.2 - - - -
273A ASN* 3.1 38.4 + - + +
277A TRP* 5.3 0.2 + - - -
538B ASP* 3.2 17.3 - - + +
540B VAL* 4.0 21.3 - - + -
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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