Contacts of the helix formed by residues 250 - 264 (chain Y) in PDB entry 5G04
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 250 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245Y PHE* 3.5 10.3 - - + +
246Y VAL 5.7 0.4 - - - -
248Y THR* 3.3 16.1 + - - +
249Y GLY* 1.3 76.8 - - - +
251Y ASN* 1.3 64.3 + - - +
252Y SER* 3.3 3.9 + - - +
253Y ARG* 4.3 16.0 - - + +
254Y ALA* 3.5 16.3 + - - +
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Residues in contact with ASN 251 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249Y GLY 3.2 14.3 + - - -
250Y ASP* 1.3 71.5 - - - +
252Y SER* 1.3 51.7 + - - +
254Y ALA* 3.4 4.8 + - - +
255Y ILE* 2.8 42.0 + - - +
280Y LEU* 2.9 33.9 - - + +
283Y ARG* 3.1 24.6 + - - +
284Y ALA* 3.7 32.3 - - + +
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Residues in contact with SER 252 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250Y ASP* 3.3 2.6 - - - -
251Y ASN* 1.3 75.8 - - - +
253Y ARG* 1.3 64.2 + - - +
255Y ILE* 3.2 20.6 - - - +
256Y SER* 3.3 13.3 + - - -
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Residues in contact with ARG 253 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245Y PHE* 3.7 45.5 - - + -
250Y ASP* 3.7 16.1 + - + +
251Y ASN 3.5 0.2 - - - -
252Y SER* 1.3 77.1 - - - +
254Y ALA* 1.3 60.0 + - - +
256Y SER* 2.9 24.4 + - - -
257Y THR* 3.2 14.1 - - - +
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Residues in contact with ALA 254 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242Y ALA 4.1 0.7 - - - +
245Y PHE* 3.6 13.4 - - - +
246Y VAL* 3.5 42.4 - - + +
250Y ASP 3.5 10.5 + - - +
251Y ASN 3.4 3.3 + - - +
252Y SER 3.4 0.4 - - - -
253Y ARG* 1.3 76.7 - - - +
255Y ILE* 1.3 65.0 + - - +
257Y THR* 3.3 5.9 - - - +
258Y ILE* 3.0 27.4 + - - +
280Y LEU* 4.1 10.8 - - + -
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Residues in contact with ILE 255 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251Y ASN* 2.8 33.0 + - + +
252Y SER* 3.2 22.4 - - - +
254Y ALA* 1.3 73.5 - - - +
256Y SER* 1.3 60.1 + - - +
258Y ILE* 3.3 2.8 + - - +
259Y CYS* 2.9 34.9 + - - -
277Y LEU* 3.7 7.6 - - + -
280Y LEU* 4.0 17.7 - - + +
281Y TYR* 3.3 50.3 - - + +
284Y ALA* 6.1 2.5 - - + -
286Y ASP* 5.5 4.3 - - - +
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Residues in contact with SER 256 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252Y SER 3.3 11.4 + - - -
253Y ARG* 2.9 29.1 + - - +
255Y ILE* 1.3 84.6 - - - +
257Y THR* 1.3 56.2 + - - +
259Y CYS* 3.4 9.3 + - - +
260Y SER* 3.1 23.0 + - - -
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Residues in contact with THR 257 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238Y VAL* 3.7 20.6 + - - +
241Y LYS* 5.1 2.4 - - - +
242Y ALA* 3.7 26.3 + - - +
245Y PHE* 4.1 13.5 - - + -
253Y ARG* 3.2 17.9 - - + +
254Y ALA* 3.3 13.0 - - - +
256Y SER* 1.3 78.2 + - - +
258Y ILE* 1.3 64.0 + - - +
260Y SER* 3.2 21.6 - - - -
261Y LEU* 3.3 11.1 + - - +
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Residues in contact with ILE 258 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242Y ALA* 3.7 23.1 - - + -
243Y TYR* 4.1 14.6 - - + +
246Y VAL* 4.7 8.7 - - + -
254Y ALA 3.0 21.2 + - - +
255Y ILE 3.5 4.3 - - - +
257Y THR* 1.3 75.3 - - - +
259Y CYS* 1.3 57.6 + - - +
261Y LEU* 3.0 23.1 + - + +
262Y GLU* 3.2 10.2 + - - +
273Y LEU* 3.8 35.4 - - + +
276Y SER* 4.7 5.8 - - - -
277Y LEU* 3.7 37.0 - - + -
280Y LEU* 4.1 13.2 - - + -
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Residues in contact with CYS 259 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255Y ILE* 2.9 26.7 + - - +
256Y SER* 3.5 11.7 - - - +
257Y THR 3.3 0.2 - - - -
258Y ILE* 1.3 73.7 - - - +
260Y SER* 1.3 62.8 + - - +
262Y GLU* 3.3 19.7 - - - +
263Y LYS* 3.1 29.0 + - - +
277Y LEU* 3.9 24.7 - - - -
281Y TYR* 4.5 3.6 - - - -
293Y LYS* 4.3 11.2 - - - -
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Residues in contact with SER 260 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238Y VAL* 4.7 8.2 - - - +
256Y SER 3.1 12.4 + - - -
257Y THR* 3.2 19.3 + - - -
259Y CYS* 1.3 76.2 - - - +
261Y LEU* 1.3 58.7 + - - +
263Y LYS* 3.2 19.7 + - - +
264Y LYS* 2.9 40.4 + - - +
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Residues in contact with LEU 261 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235Y TRP* 4.6 7.0 - - + +
238Y VAL* 3.8 30.5 - - + -
239Y TRP* 4.1 26.0 - - + +
242Y ALA* 4.4 12.1 - - + -
257Y THR 3.3 8.9 + - - +
258Y ILE* 3.0 11.0 + - + +
260Y SER* 1.3 74.6 - - - +
262Y GLU* 1.3 64.3 + - - +
264Y LYS* 3.2 21.5 + - + +
267Y LEU* 3.2 48.4 - - + +
273Y LEU* 3.7 33.0 - - + -
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Residues in contact with GLU 262 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F SER* 3.5 29.8 + - - +
67F THR* 5.2 4.6 - - + +
258Y ILE 3.2 7.5 + - - +
259Y CYS* 3.3 32.9 - - - +
261Y LEU* 1.3 74.3 - - - +
263Y LYS* 1.3 61.8 + - + +
267Y LEU 4.0 1.1 - - - -
268Y ARG* 3.3 50.5 + - - +
273Y LEU* 4.4 4.8 - - + +
274Y LEU* 3.8 19.3 - - + +
277Y LEU* 4.0 12.2 - - + +
293Y LYS* 4.1 15.6 - - - +
296Y GLN* 4.7 1.2 + - - -
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Residues in contact with LYS 263 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F THR* 3.7 36.3 + - + +
72F LYS* 6.2 1.3 - - - +
259Y CYS* 3.1 17.9 + - - +
260Y SER* 3.2 15.6 + - - +
262Y GLU* 1.3 73.6 - - - +
264Y LYS* 1.3 69.2 + - - +
265Y SER 3.4 0.9 + - - -
268Y ARG* 3.2 17.2 + - - +
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Residues in contact with LYS 264 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235Y TRP* 6.1 2.7 - - + -
238Y VAL* 5.6 7.9 - - - -
260Y SER* 2.9 38.4 + - - +
261Y LEU* 3.2 30.2 + - + +
263Y LYS* 1.3 82.3 - - - +
265Y SER* 1.3 58.9 + - - +
266Y LEU* 4.5 3.1 - - + +
267Y LEU* 3.9 15.3 - - + +
268Y ARG* 3.0 32.8 + - - +
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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