Contacts of the helix formed by residues 250 - 264 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245X PHE* 3.5 10.8 - - + +
246X VAL 5.7 0.7 - - - -
248X THR* 3.3 15.7 + - - +
249X GLY* 1.3 76.8 - - - +
251X ASN* 1.3 65.7 + - - +
252X SER* 3.3 3.7 + - - +
253X ARG* 4.3 16.1 - - + +
254X ALA* 3.5 16.0 + - - +
436X THR 4.8 2.1 - - - +
437X LEU* 3.2 29.1 - - - +
439X ALA 6.0 0.7 - - - -
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Residues in contact with ASN 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249X GLY 3.3 14.5 + - - -
250X ASP* 1.3 71.4 - - - +
252X SER* 1.3 50.0 + - - +
254X ALA* 3.4 4.7 + - - +
255X ILE* 2.8 42.5 + - + +
280X LEU* 2.9 32.2 - - - +
283X ARG* 3.1 21.0 - - - +
284X ALA* 3.7 29.4 - - + +
405X CYS 5.2 1.4 + - - -
407X LEU* 3.8 23.8 - - - +
437X LEU* 5.6 0.4 - - - +
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Residues in contact with SER 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250X ASP* 3.3 3.9 - - - -
251X ASN* 1.3 76.2 - - - +
253X ARG* 1.3 64.5 + - - +
255X ILE* 3.2 21.0 - - - +
256X SER* 3.2 12.5 + - - -
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Residues in contact with ARG 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245X PHE* 3.7 46.0 - - + -
250X ASP* 3.7 16.3 + - + +
251X ASN 3.5 0.2 - - - -
252X SER* 1.3 77.7 - - - +
254X ALA* 1.3 60.9 + - - +
256X SER* 2.9 25.9 + - - -
257X THR* 3.2 14.8 - - + +
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Residues in contact with ALA 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242X ALA 4.3 0.7 - - - -
245X PHE* 3.6 13.1 - - - +
246X VAL* 3.5 42.6 - - + +
250X ASP 3.5 10.1 + - - +
251X ASN 3.4 3.5 + - - +
252X SER 3.4 0.2 - - - -
253X ARG* 1.3 76.9 - - - +
255X ILE* 1.3 65.7 + - - +
257X THR* 3.3 6.5 - - - +
258X ILE* 3.0 27.4 + - - +
280X LEU* 4.1 11.4 - - + -
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Residues in contact with ILE 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251X ASN* 2.8 32.0 + - + +
252X SER* 3.2 22.2 - - - +
254X ALA* 1.3 72.7 - - - +
256X SER* 1.3 60.3 + - - +
258X ILE* 3.3 3.1 + - - +
259X CYS* 2.9 34.3 + - - -
277X LEU* 3.7 7.1 - - + +
280X LEU* 4.0 17.2 - - + +
281X TYR* 3.4 49.8 - - + +
286X ASP* 5.4 4.3 - - - +
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Residues in contact with SER 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252X SER 3.2 11.6 + - - -
253X ARG* 2.9 30.3 + - - -
255X ILE* 1.3 84.5 - - - +
257X THR* 1.3 56.2 + - - +
259X CYS* 3.4 9.4 + - - +
260X SER* 3.1 23.4 + - - -
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Residues in contact with THR 257 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238X VAL* 3.7 21.7 + - - +
241X LYS* 5.3 2.8 - - + +
242X ALA* 3.8 26.6 + - - +
245X PHE* 4.1 13.9 - - + -
253X ARG* 3.2 18.8 - - + +
254X ALA* 3.3 12.6 - - - +
256X SER* 1.3 79.3 + - - +
258X ILE* 1.3 65.2 + - - +
260X SER* 3.2 21.9 - - - -
261X LEU* 3.3 10.9 + - - +
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Residues in contact with ILE 258 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242X ALA* 3.7 22.9 - - + -
243X TYR* 4.1 14.8 - - + +
246X VAL* 4.7 8.7 - - + -
254X ALA 3.0 21.5 + - - +
255X ILE 3.5 3.8 - - - +
257X THR* 1.3 73.7 - - - +
259X CYS* 1.3 58.6 + - - +
261X LEU* 3.0 23.7 + - + +
262X GLU* 3.2 10.4 + - - +
273X LEU* 3.8 35.5 - - + +
276X SER* 4.8 5.2 - - - -
277X LEU* 3.7 37.5 - - + -
280X LEU* 4.1 12.6 - - + -
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Residues in contact with CYS 259 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255X ILE* 2.9 27.0 + - - +
256X SER* 3.5 11.7 - - - +
257X THR 3.3 0.2 - - - -
258X ILE* 1.3 73.6 - - - +
260X SER* 1.3 61.6 + - - +
262X GLU* 3.3 21.2 - - - +
263X LYS* 3.1 33.8 + - - +
277X LEU* 3.9 24.5 - - - -
281X TYR* 4.5 3.6 - - - -
293X LYS* 4.4 10.1 - - - -
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Residues in contact with SER 260 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238X VAL* 4.8 7.9 - - - +
256X SER 3.1 12.2 + - - -
257X THR* 3.2 19.7 + - - -
259X CYS* 1.3 76.8 - - - +
261X LEU* 1.3 58.0 + - - +
263X LYS* 3.2 24.9 + - - +
264X LYS* 3.4 27.6 + - - -
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Residues in contact with LEU 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235X TRP* 4.7 6.3 - - + +
238X VAL* 3.8 31.2 - - + -
239X TRP* 4.1 24.7 - - + +
242X ALA* 4.4 13.2 - - + -
257X THR 3.3 9.2 + - - +
258X ILE* 3.0 10.8 + - + +
260X SER* 1.3 73.8 - - - +
262X GLU* 1.3 63.9 + - - +
264X LYS* 3.3 21.2 + - + +
267X LEU* 3.2 49.6 - - + +
273X LEU* 3.7 32.5 - - + -
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Residues in contact with GLU 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258X ILE 3.2 8.6 + - - +
259X CYS* 3.3 32.4 - - - +
261X LEU* 1.3 74.5 - - - +
263X LYS* 1.3 66.3 + - + +
267X LEU 4.0 1.5 + - - -
268X ARG* 3.3 53.3 + - + +
269X ASP* 5.6 0.4 - - - +
273X LEU* 4.5 4.3 - - + +
274X LEU* 3.8 21.6 - - + +
277X LEU* 4.0 12.4 - - + +
293X LYS* 4.1 14.2 - - - +
296X GLN* 4.9 7.4 + - - +
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Residues in contact with LYS 263 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259X CYS* 3.1 21.7 + - - +
260X SER* 3.2 15.9 + - - +
262X GLU* 1.3 78.7 + - - +
264X LYS* 1.3 68.7 + - - +
265X SER 3.4 0.5 + - - -
268X ARG* 3.2 18.8 + - - +
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Residues in contact with LYS 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235X TRP* 6.1 2.7 - - + -
238X VAL* 5.8 7.0 - - - -
260X SER* 3.6 28.5 + - - +
261X LEU* 3.3 30.2 + - + +
263X LYS* 1.3 79.6 - - - +
265X SER* 1.3 59.5 - - - +
266X LEU* 4.4 4.5 - - + +
267X LEU* 4.0 15.0 - - + +
268X ARG* 3.0 32.3 + - - +
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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