Contacts of the helix formed by residues 298 - 313 (chain K) 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 298 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295K TYR* 3.3 28.0 + - + +
297K SER* 1.3 82.2 + - - +
299K PRO* 1.4 78.8 - - - +
300K VAL* 2.7 49.2 + - + +
301K SER* 3.3 17.0 + - - -
302K TRP* 3.7 8.8 - - - -
329K LEU* 4.3 0.2 - - - -
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Residues in contact with PRO 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297K SER 3.7 0.2 - - - -
298K ASN* 1.4 96.2 - - - +
300K VAL* 1.3 62.5 + - - +
302K TRP* 3.2 5.5 + - + +
303K PHE* 3.1 19.0 + - - +
326K ALA* 3.5 26.1 - - + +
329K LEU* 3.8 17.9 - - + -
330K GLU* 3.7 33.0 - - + +
333K TYR* 3.8 27.1 - - + -
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Residues in contact with VAL 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265K ALA* 5.3 10.1 - - + +
268K LEU* 3.7 31.9 - - + -
269K PRO* 5.3 6.7 - - + -
272K ILE* 4.8 2.0 - - + +
291K LEU* 4.2 4.0 - - + +
295K TYR* 5.8 3.1 - - + -
298K ASN* 2.7 32.6 + - + +
299K PRO* 1.3 71.8 - - - +
301K SER* 1.3 62.4 + - - +
303K PHE* 3.1 11.4 + - + +
304K ALA* 2.9 28.1 + - - +
333K TYR* 2.9 35.6 - - + +
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Residues in contact with SER 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291K LEU* 3.1 44.6 + - - +
292K VAL* 3.1 14.6 + - - +
295K TYR* 3.2 26.5 - - - -
298K ASN 3.3 6.1 + - - -
299K PRO 3.2 0.4 - - - -
300K VAL* 1.3 81.8 - - - +
302K TRP* 1.3 63.2 + - - +
304K ALA* 3.2 4.9 + - - +
305K VAL* 3.1 27.2 + - - +
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Residues in contact with TRP 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292K VAL* 3.5 28.3 - - + -
296K PRO* 3.0 24.7 + - + +
298K ASN 3.7 15.0 - - - -
299K PRO* 3.2 3.2 + - + +
301K SER* 1.3 74.4 - - - +
303K PHE* 1.3 61.1 + - - +
305K VAL* 3.2 11.7 + - + +
306K GLY* 2.9 26.7 + - - -
322K TYR* 3.6 50.0 - + - +
325K LYS* 3.4 43.8 - - + +
326K ALA* 3.6 22.9 - - + +
329K LEU* 4.4 9.9 - - + -
54M GLU 4.6 0.7 - - - -
55M MET* 4.0 16.7 - - + +
56M LYS 4.9 0.9 - - - -
57M TRP* 3.5 24.2 - + + -
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Residues in contact with PHE 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269K PRO* 4.6 13.5 - - + -
272K ILE* 3.6 33.2 - - + -
299K PRO 3.1 12.7 + - - +
300K VAL* 3.1 15.5 - - + +
302K TRP* 1.3 75.6 - - - +
304K ALA* 1.3 62.9 + - - +
306K GLY* 3.2 1.9 + - - -
307K CYS* 2.9 24.5 + - + +
323K LEU* 3.9 12.9 - - + +
326K ALA* 3.7 6.1 - - + +
333K TYR* 4.2 19.1 - + + -
335K PRO* 3.0 47.6 - - + -
336K ALA* 3.9 5.8 - - + -
339K ALA* 4.1 9.4 - - + -
1W MET* 5.7 2.9 - - + -
2W LEU* 3.8 27.6 - - + -
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Residues in contact with ALA 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K ILE* 3.6 26.5 - - + -
284K LEU* 4.9 2.0 - - + -
287K LEU* 5.5 0.9 - - + -
288K SER* 2.9 22.7 + - - +
291K LEU* 3.9 14.6 - - + -
300K VAL 2.9 9.8 + - - +
301K SER 3.2 8.9 + - - +
303K PHE* 1.3 73.4 - - - +
305K VAL* 1.3 63.3 + - - +
307K CYS* 3.1 15.8 - - - -
308K TYR* 3.0 19.6 + - - +
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Residues in contact with VAL 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288K SER* 3.4 10.5 - - - -
292K VAL* 3.7 15.3 - - + -
301K SER 3.1 17.8 + - - +
302K TRP* 3.2 13.2 + - + +
304K ALA* 1.3 76.9 - - - +
306K GLY* 1.3 61.0 + - - +
308K TYR* 3.3 4.5 + - - +
309K TYR* 3.1 25.4 + - + -
322K TYR* 3.6 30.7 - - + -
57M TRP* 3.4 51.1 - - + -
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Residues in contact with GLY 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K TRP 2.9 14.5 + - - -
303K PHE 3.7 2.5 - - - -
305K VAL* 1.3 76.7 - - - +
307K CYS* 1.3 62.7 + - - +
309K TYR 3.3 2.6 + - - -
310K LEU* 3.2 15.9 + - - +
319K ALA* 3.3 19.5 - - - +
322K TYR* 3.9 12.3 - - - -
323K LEU* 3.9 24.2 - - - -
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Residues in contact with CYS 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272K ILE* 3.0 37.5 - - + -
276K VAL* 4.3 7.5 - - + +
284K LEU* 3.7 14.4 - - - +
303K PHE* 2.9 18.0 + - + +
304K ALA* 3.1 21.3 - - - -
306K GLY* 1.3 78.1 - - - +
308K TYR* 1.3 61.9 + - - +
310K LEU* 3.0 21.9 + - + +
311K MET* 3.0 14.6 + - - +
323K LEU* 4.3 1.4 - - - +
339K ALA* 5.3 0.4 - - + -
2W LEU* 4.3 23.3 - - + -
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Residues in contact with TYR 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557F LYS* 4.0 8.7 + - - -
281K ALA* 3.7 16.6 - - + -
284K LEU* 3.4 19.7 - - + -
285K PHE* 3.3 54.6 - + + -
288K SER* 4.0 9.0 - - - +
304K ALA 3.0 10.7 + - - +
305K VAL* 3.5 8.3 - - - +
306K GLY 3.2 0.2 - - - -
307K CYS* 1.3 78.1 - - - +
309K TYR* 1.3 88.9 + + - +
310K LEU 3.2 0.7 + - - -
311K MET* 3.2 11.2 + - + +
312K VAL* 3.3 34.7 + - + +
315K LYS* 6.5 0.2 - - - -
57M TRP* 4.4 11.0 - + - -
59M ASP* 5.0 4.3 - - - -
61M ALA* 4.0 17.0 - - + +
64M TYR* 4.1 6.8 + - - -
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Residues in contact with TYR 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305K VAL* 3.1 22.7 + - + -
306K GLY 3.3 8.4 + - - +
308K TYR* 1.3 87.5 - + - +
310K LEU* 1.3 61.3 + - - +
312K VAL* 4.1 4.2 + - + -
313K GLY 3.7 10.7 + - - -
315K LYS* 3.5 67.8 - - + +
316K ASN* 3.8 1.7 + - - -
318K HIS* 3.7 18.6 - + + -
319K ALA* 3.8 8.5 - - + +
322K TYR* 3.4 34.1 + + - -
57M TRP* 3.2 31.0 + + - -
59M ASP* 2.8 35.4 + - - -
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Residues in contact with LEU 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K VAL* 6.2 3.4 - - + -
306K GLY 3.2 11.5 + - - +
307K CYS* 3.0 15.3 + - - +
309K TYR* 1.3 77.2 - - - +
311K MET* 1.3 64.5 + - - +
313K GLY* 3.3 12.6 + - - -
316K ASN* 3.3 24.5 + - - +
319K ALA* 3.6 14.1 - - + -
323K LEU* 4.3 1.3 - - + -
339K ALA* 4.0 18.4 - - + +
342K HIS* 4.4 10.5 - - + -
343K SER* 4.2 22.7 - - - +
346K VAL* 5.1 2.7 - - + -
2W LEU* 3.9 27.6 - - + -
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Residues in contact with MET 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275K LEU 3.3 24.7 - - - +
276K VAL* 3.5 28.2 - - + +
279K ASN* 3.4 35.2 - - - +
280K LYS 4.2 1.1 - - - +
281K ALA* 3.6 34.8 - - + -
284K LEU* 3.5 33.2 - - + -
307K CYS 3.0 8.1 + - - +
308K TYR* 3.2 8.5 + - + +
310K LEU* 1.3 78.8 - - - +
312K VAL* 1.3 63.3 + - - +
313K GLY* 3.5 0.5 + - - -
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Residues in contact with VAL 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281K ALA* 4.9 9.2 - - + -
308K TYR* 3.3 45.5 + - + +
309K TYR* 4.1 6.7 - - - +
311K MET* 1.3 78.6 - - - +
313K GLY* 1.3 70.8 + - - +
314K HIS* 4.1 6.6 + - - -
315K LYS* 4.1 15.3 - - + -
64M TYR* 3.4 31.6 - - + +
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Residues in contact with GLY 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309K TYR 3.7 3.7 + - - -
310K LEU 3.3 15.5 + - - -
311K MET 4.5 0.4 - - - -
312K VAL* 1.3 89.7 - - - +
314K HIS* 1.3 76.5 + - - +
315K LYS* 2.9 13.6 + - - +
316K ASN* 4.9 4.7 - - - -
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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
------------------------------------------------------------
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