Contacts of the helix formed by residues 286 - 301 (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 286 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255X ILE* 5.4 4.7 - - - +
281X TYR* 3.3 28.7 + - + +
284X ALA* 3.9 19.7 - - - +
285X GLY* 1.3 77.6 - - - +
287X ASN* 1.3 56.1 + - - +
288X LYS 3.5 2.0 - - - -
289X ASN* 3.4 7.0 + - + -
290X SER* 2.9 31.1 + - - -
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Residues in contact with ASN 287 (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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282X PHE* 5.6 5.8 + - - +
285X GLY* 3.0 14.4 + - - +
286X ASP* 1.3 73.8 - - - +
288X LYS* 1.3 63.1 + - + +
290X SER* 3.4 20.0 - - - -
291X VAL* 3.4 12.0 - - - +
313X TYR* 5.9 2.8 - - - -
314X LEU* 3.7 31.6 - - - +
317X ARG* 4.1 21.6 - - - +
318X GLU* 4.9 4.7 + - - +
476X ILE* 5.8 8.1 - - + -
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Residues in contact with LYS 288 (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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286X ASP 3.5 0.4 - - - -
287X ASN* 1.3 77.8 - - + +
289X ASN* 1.3 65.7 + - - +
290X SER 3.5 0.3 + - - -
291X VAL* 3.5 9.0 + - - +
292X LEU* 3.5 19.1 + - - +
476X ILE* 6.5 0.4 - - - -
505X ASN 5.2 2.8 + - - -
506X GLN 4.1 18.6 + - - -
507X SER* 4.2 18.4 + - - +
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Residues in contact with ASN 289 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281X TYR* 3.4 28.1 + - + -
286X ASP* 3.4 8.5 + - + +
288X LYS* 1.3 79.7 - - - +
290X SER* 1.3 66.3 + - - +
292X LEU* 3.7 13.1 - - - +
293X LYS* 3.4 39.8 + - - +
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Residues in contact with SER 290 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278X ALA* 4.5 7.2 - - - +
281X TYR* 3.1 37.5 + - - +
282X PHE* 3.3 5.2 + - - -
286X ASP 2.9 18.7 + - - -
287X ASN* 3.4 11.3 + - - -
289X ASN* 1.3 76.2 - - - +
291X VAL* 1.3 53.3 + - - +
293X LYS* 3.2 5.0 + - - +
294X PHE* 2.8 36.4 + - - +
314X LEU* 3.9 21.9 - - - +
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Residues in contact with VAL 291 (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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287X ASN* 3.4 20.9 - - - +
288X LYS* 3.5 8.2 + - - +
289X ASN 3.5 0.2 - - - -
290X SER* 1.3 78.5 - - - +
292X LEU* 1.3 53.8 + - - +
294X PHE* 3.2 5.7 + - - +
295X GLU* 2.5 53.8 + - - +
311X TYR* 4.0 18.4 - - + +
314X LEU* 4.3 27.8 - - + +
315X LEU* 4.7 3.6 - - + -
318X GLU* 5.5 6.7 - - + -
320X ARG* 4.1 20.4 - - - +
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Residues in contact with LEU 292 (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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288X LYS 3.5 10.2 + - - +
289X ASN* 3.7 17.5 - - - +
291X VAL* 1.3 77.7 - - - +
293X LYS* 1.3 77.5 + - + +
295X GLU* 3.5 12.8 + - - +
296X GLN* 3.2 27.0 + - - +
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Residues in contact with LYS 293 (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* 4.4 5.4 - - - -
262X GLU* 4.1 23.1 - - - +
274X LEU* 4.2 17.2 - - + +
277X LEU* 3.7 30.5 - - + -
278X ALA* 5.0 4.9 - - - -
281X TYR* 2.7 40.4 + - + -
289X ASN* 3.4 22.8 + - - +
290X SER 3.2 4.4 + - - +
292X LEU* 1.3 88.2 - - + +
294X PHE* 1.3 60.4 + - - +
296X GLN* 3.4 14.6 - - - +
297X ALA* 3.2 23.4 + - - +
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Residues in contact with PHE 294 (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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275X GLY* 5.8 0.9 - - - -
278X ALA* 3.6 25.5 - - + +
279X ASP* 5.8 0.2 - - - -
290X SER 2.8 20.9 + - - +
291X VAL* 3.6 5.2 - - - +
293X LYS* 1.3 69.5 - - - +
295X GLU* 1.3 66.4 + - - +
296X GLN 3.1 1.3 - - - -
297X ALA* 2.9 19.8 + - + +
298X GLN* 3.0 19.7 + - + -
304X LEU* 5.1 5.2 - - + -
307X GLY* 3.2 45.3 - - - -
308X MET* 3.6 16.8 - - - -
310X VAL* 5.0 4.9 - - + -
311X TYR* 3.2 60.1 - + + -
314X LEU* 5.1 2.5 - - + -
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Residues in contact with GLU 295 (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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291X VAL* 2.5 36.7 + - - +
292X LEU* 3.6 12.8 - - + +
294X PHE* 1.3 74.3 - - - +
296X GLN* 1.3 56.5 + - - +
298X GLN* 3.5 8.7 + - - +
299X MET* 2.9 46.0 + - + +
311X TYR* 4.1 15.6 + - - +
320X ARG* 4.1 16.5 + - - -
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Residues in contact with GLN 296 (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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262X GLU* 4.9 6.9 + - - +
269X ASP* 4.2 20.4 + - - -
274X LEU* 4.0 32.6 - - + +
292X LEU* 3.2 17.0 + - - +
293X LYS* 3.4 17.4 - - - +
295X GLU* 1.3 76.6 - - - +
297X ALA* 1.3 61.1 + - - +
299X MET* 3.1 10.0 + - - +
300X LEU* 2.9 36.4 + - + +
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Residues in contact with ALA 297 (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* 4.5 3.9 - - - +
274X LEU* 4.0 23.8 - - + -
275X GLY* 4.4 10.8 - - - +
293X LYS 3.2 13.0 + - - +
294X PHE* 2.9 21.3 + - + +
296X GLN* 1.3 72.5 - - - +
298X GLN* 1.3 63.0 + - - +
300X LEU* 3.3 16.0 + - - +
301X ASP* 3.3 9.9 + - - +
304X LEU* 3.4 25.1 - - + +
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Residues in contact with GLN 298 (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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294X PHE* 3.0 21.2 + - + +
295X GLU* 4.0 6.7 + - - +
297X ALA* 1.3 74.5 - - - +
299X MET* 1.3 62.3 + - - +
301X ASP 2.8 26.9 - - - +
302X PRO* 4.1 9.1 - - + +
304X LEU* 4.0 4.2 - - - +
308X MET* 3.5 34.2 - - + +
311X TYR* 3.9 27.2 + - - -
327X LEU* 4.0 5.5 - - - +
330X ARG* 3.9 29.2 + - - +
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Residues in contact with MET 299 (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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295X GLU* 2.9 39.1 + - + +
296X GLN* 3.1 10.3 + - - +
298X GLN* 1.3 75.1 - - - +
300X LEU* 1.3 67.5 + - + +
301X ASP 5.0 0.5 - - - -
302X PRO* 5.4 1.2 - - - +
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Residues in contact with LEU 300 (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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269X ASP* 3.8 42.4 - - + +
271X VAL* 4.2 22.2 - - + +
274X LEU* 4.2 11.9 - - + -
296X GLN* 2.9 36.1 + - + +
297X ALA* 3.4 11.0 - - - +
299X MET* 1.3 79.3 - - + +
301X ASP* 1.3 68.2 + - - +
302X PRO* 4.0 5.4 - - - +
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Residues in contact with ASP 301 (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* 3.4 42.8 - - + +
297X ALA 3.3 2.7 + - - +
298X GLN* 2.8 26.7 - - - +
300X LEU* 1.3 84.7 - - - +
302X PRO* 1.3 68.5 - - + +
303X TYR* 3.3 11.2 + - + +
304X LEU* 4.1 11.6 - - + +
95Y ASN* 6.0 0.2 + - - -
99Y LYS* 4.8 14.1 + - - -
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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