Contacts of the helix formed by residues 270 - 285 (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 ASN 270 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267X LEU* 3.3 49.1 - - - +
268X ARG 3.8 3.0 + - - -
269X ASP* 1.3 78.0 - - - +
271X VAL* 1.3 66.2 + - - +
272X ASP* 4.2 4.3 - - + +
273X LEU* 3.4 33.8 - - + +
274X LEU* 2.8 33.4 + - - +
58Y SER* 6.0 0.7 - - - +
59Y LEU* 3.5 11.5 - - + +
62Y THR* 3.2 27.5 + - + -
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Residues in contact with VAL 271 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269X ASP 4.0 0.6 - - - -
270X ASN* 1.3 73.2 - - - +
272X ASP* 1.3 60.6 + - - +
274X LEU* 4.1 3.3 - - - +
275X GLY* 3.2 16.3 + - - -
297X ALA* 4.5 3.4 - - - +
300X LEU* 4.2 19.7 - - + +
301X ASP* 3.4 42.6 - - + +
304X LEU* 3.3 44.3 - - + +
54Y ARG* 6.4 0.2 - - - +
58Y SER* 5.1 7.4 - - - +
62Y THR* 4.2 11.9 - - + +
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Residues in contact with ASP 272 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239X TRP* 6.0 0.9 - - - -
243X TYR* 3.8 7.6 + - - -
270X ASN* 3.1 3.3 - - + +
271X VAL* 1.3 77.8 - - - +
273X LEU* 1.3 55.4 + - - +
275X GLY* 3.1 4.8 + - - -
276X SER* 2.7 42.8 + - - -
304X LEU* 6.2 0.2 - - - -
306X LYS* 4.2 30.0 + - - +
54Y ARG* 4.8 10.9 + - - -
55Y LEU* 4.0 30.0 - - - +
58Y SER* 4.4 17.8 + - - +
59Y LEU 6.1 0.7 - - - +
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Residues in contact with LEU 273 (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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239X TRP* 4.3 8.1 - - + +
243X TYR* 3.5 23.3 - - + +
258X ILE* 3.8 31.9 - - + +
261X LEU* 3.7 40.4 - - + -
262X GLU* 4.5 3.6 - - + +
267X LEU* 4.1 11.9 - - + +
268X ARG 5.6 0.7 - - - +
270X ASN* 3.2 36.3 + - + +
272X ASP* 1.3 77.7 - - - +
274X LEU* 1.3 58.0 + - - +
276X SER* 3.3 6.9 + - - -
277X LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 274 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262X GLU* 3.8 24.9 - - + +
268X ARG 5.0 3.4 - - - +
269X ASP* 4.3 4.7 - - - -
270X ASN 2.8 33.7 + - - +
273X LEU* 1.3 73.6 - - - +
275X GLY* 1.3 54.4 + - - +
277X LEU* 3.4 12.0 + - + +
278X ALA* 2.8 34.9 + - - +
293X LYS* 4.2 19.6 - - + +
296X GLN* 4.0 39.5 - - + +
297X ALA* 4.0 20.3 - - + +
300X LEU* 4.2 15.7 - - + -
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Residues in contact with GLY 275 (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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271X VAL 3.2 12.4 + - - -
272X ASP* 3.1 8.7 + - - -
274X LEU* 1.3 76.3 - - - +
276X SER* 1.3 55.3 + - - +
278X ALA* 3.2 9.0 + - - +
279X ASP* 3.1 32.9 + - - +
294X PHE* 5.8 0.7 - - - -
297X ALA* 4.4 7.0 - - - +
304X LEU* 5.8 2.5 - - - -
306X LYS* 5.6 9.0 - - - -
307X GLY* 5.3 14.0 - - - -
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Residues in contact with SER 276 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243X TYR* 2.6 41.1 + - - -
246X VAL* 5.8 3.7 - - - +
258X ILE* 4.8 7.2 - - - -
272X ASP* 2.7 27.5 + - - -
273X LEU* 3.4 8.0 - - - -
274X LEU 3.3 0.2 - - - -
275X GLY* 1.3 67.8 - - - +
277X LEU* 1.3 65.0 + - - +
279X ASP* 3.4 12.8 + - - +
280X LEU* 3.3 27.1 + - - +
283X ARG* 5.1 0.3 + - - -
306X LYS* 4.8 7.3 + - - +
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Residues in contact with LEU 277 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255X ILE* 3.7 24.0 - - + +
258X ILE* 3.7 28.8 - - + +
259X CYS* 3.9 14.1 - - - +
262X GLU* 4.0 15.9 - - + +
273X LEU 2.9 16.8 + - - +
274X LEU* 3.5 12.6 - - + +
276X SER* 1.3 76.4 - - - +
278X ALA* 1.3 60.0 + - - +
280X LEU* 3.2 9.1 + - + +
281X TYR* 3.2 50.4 + - + -
293X LYS* 3.7 31.2 - - + -
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Residues in contact with ALA 278 (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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274X LEU 2.8 20.0 + - - +
275X GLY* 3.2 8.9 + - - +
277X LEU* 1.3 73.8 - - - +
279X ASP* 1.3 63.5 + - - +
281X TYR* 3.7 8.0 + - - +
282X PHE* 3.2 22.2 + - - +
290X SER* 4.5 8.5 - - - +
293X LYS* 5.0 2.4 - - - +
294X PHE* 3.6 46.4 - - + +
297X ALA* 5.8 0.2 - - + -
310X VAL* 4.1 3.6 - - - +
314X LEU* 5.1 0.7 - - + +
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Residues in contact with ASP 279 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275X GLY 3.1 18.0 + - - +
276X SER* 3.4 13.0 - - - +
277X LEU 3.3 0.2 - - - -
278X ALA* 1.3 77.1 - - - +
280X LEU* 1.3 56.6 + - - +
282X PHE* 3.3 8.0 + - - +
283X ARG* 3.0 56.7 + - - +
294X PHE* 5.8 0.2 - - - -
306X LYS* 4.9 14.1 + - - +
307X GLY* 4.8 7.7 - - - +
310X VAL* 3.2 31.8 - - + +
406X ARG* 5.0 4.8 + - - +
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Residues in contact with LEU 280 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246X VAL* 3.8 35.9 - - + +
251X ASN* 2.9 22.8 - - - +
254X ALA* 4.1 14.6 - - + -
255X ILE* 4.0 37.0 - - + +
258X ILE* 4.1 17.9 - - + -
276X SER 3.4 15.5 - - - +
277X LEU* 3.2 13.8 + - + +
279X ASP* 1.3 72.7 - - - +
281X TYR* 1.3 56.0 + - - +
283X ARG* 3.4 14.5 + - - +
284X ALA* 2.8 33.5 + - - +
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Residues in contact with TYR 281 (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* 3.4 29.7 - - + +
259X CYS* 4.5 3.5 - - - -
277X LEU* 3.2 49.7 + - + +
278X ALA* 3.9 3.1 - - - +
280X LEU* 1.3 75.5 - - - +
282X PHE* 1.3 64.0 + - - +
284X ALA* 3.4 4.2 + - - -
285X GLY* 3.1 17.7 + - - -
286X ASP* 3.3 33.5 + - + -
289X ASN* 3.4 36.2 + - + -
290X SER* 3.1 26.7 + - - +
293X LYS* 2.7 36.4 + - + -
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Residues in contact with PHE 282 (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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278X ALA 3.2 12.4 + - - +
279X ASP 3.4 10.1 - - - +
281X TYR* 1.3 79.6 - - - +
283X ARG* 1.3 73.7 + - + +
285X GLY* 3.5 9.7 + - - -
287X ASN* 5.6 5.6 + - - +
290X SER* 3.3 6.6 + - - -
310X VAL* 3.6 31.9 - - + -
313X TYR* 3.1 40.4 - + + -
314X LEU* 3.5 28.3 - - + -
374X GLN* 3.7 33.0 - - - -
406X ARG* 5.5 3.1 - - + -
408X ASP* 3.8 20.0 - - + -
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Residues in contact with ARG 283 (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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246X VAL* 3.6 40.0 + - - +
247X HIS* 5.5 4.2 + - - -
249X GLY* 6.1 0.4 - - - -
251X ASN* 3.1 23.1 - - - +
276X SER 5.1 0.4 + - - -
279X ASP* 3.0 37.9 + - - +
280X LEU* 3.7 12.1 - - - +
282X PHE* 1.3 83.7 - - + +
284X ALA* 1.3 58.7 + - - +
285X GLY* 3.1 4.1 + - - -
405X CYS* 4.9 6.5 + - - +
406X ARG* 3.3 63.8 - - + +
407X LEU* 3.0 35.9 - - + +
408X ASP* 6.1 2.9 - - - +
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Residues in contact with ALA 284 (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* 3.2 25.3 + - + +
255X ILE* 6.1 3.6 - - + -
280X LEU 2.8 20.9 + - - +
281X TYR* 3.4 8.0 + - - +
283X ARG* 1.3 72.0 - - - +
285X GLY* 1.3 59.8 + - - +
286X ASP* 3.3 23.1 + - - +
407X LEU* 4.4 8.2 - - - +
442X GLN* 5.4 3.3 - - - +
443X THR* 5.4 0.9 - - - +
475X TYR* 4.9 8.7 + - - -
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Residues in contact with GLY 285 (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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281X TYR 3.1 3.6 + - - -
282X PHE 3.5 9.6 + - - -
283X ARG 3.1 5.5 - - - -
284X ALA* 1.3 78.4 - - - +
286X ASP* 1.3 58.8 + - - +
287X ASN* 3.0 20.7 + - - +
407X LEU* 5.8 0.2 - - - -
475X TYR* 4.7 18.0 + - - -
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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
------------------------------------------------------------
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