Contacts of the helix formed by residues 266 - 279 (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 SER 266 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208K LYS* 5.9 2.5 - - - -
232K ASP* 4.3 9.4 + - - -
235K VAL* 3.6 16.1 - - - +
239K GLU* 5.6 1.0 - - - +
264K HIS* 2.8 26.7 + - - -
265K ALA* 1.3 78.1 - - - +
267K CYS* 1.3 61.2 + - - +
269K PRO* 3.3 19.2 - - - +
270K VAL* 3.5 9.2 - - - +
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Residues in contact with CYS 267 (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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235K VAL* 3.4 35.0 - - + -
254K THR* 4.1 6.9 + - - +
257K VAL* 3.3 26.7 - - + -
258K MET* 3.4 30.7 - - - -
264K HIS* 3.2 20.6 - - + -
265K ALA 3.2 0.6 - - - -
266K SER* 1.3 80.2 + - - +
268K LEU* 1.3 57.4 + - - +
269K PRO 3.5 0.2 - - - -
270K VAL* 3.4 4.2 + - - +
271K HIS* 2.8 29.7 + - - +
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Residues in contact with LEU 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258K MET* 3.7 34.1 - - + -
263K PHE* 4.3 19.5 - - + +
264K HIS 3.2 19.3 + - - +
265K ALA* 4.0 8.3 - - - +
266K SER 3.3 0.4 - - - -
267K CYS* 1.3 74.3 - - - +
269K PRO* 1.4 68.9 - - + +
271K HIS* 4.2 2.9 - - - -
272K ILE* 2.7 45.6 + - + +
287K LEU* 4.8 7.2 - - + -
291K LEU* 3.8 24.5 - - + -
295K TYR* 6.2 0.7 - - + -
300K VAL* 3.7 28.9 - - + -
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Residues in contact with PRO 269 (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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173K HIS* 6.2 1.8 - - - +
265K ALA 3.4 11.4 - - - +
266K SER* 3.3 19.3 - - - +
268K LEU* 1.4 91.0 - - + +
270K VAL* 1.3 58.8 + - + +
272K ILE* 4.0 5.3 - - + +
273K GLY* 3.0 24.3 + - - -
300K VAL* 5.3 4.7 - - + -
303K PHE* 4.6 14.0 - - + -
333K TYR* 5.0 13.5 - - - +
335K PRO* 5.3 9.9 - - + -
1W MET* 4.3 25.4 - - + +
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Residues in contact with VAL 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235K VAL* 3.9 14.6 - - + -
238K ALA* 4.1 18.2 - - + +
239K GLU* 4.0 37.7 - - + +
242K TYR* 4.7 2.0 - - + -
250K CYS* 4.2 8.3 - - - -
254K THR* 4.3 4.9 - - - +
266K SER 3.5 21.5 - - - +
267K CYS* 3.5 5.6 - - - +
268K LEU 3.1 0.2 - - - -
269K PRO* 1.3 72.8 - - + +
271K HIS* 1.3 56.5 - - - +
273K GLY* 3.3 1.7 + - - -
274K THR* 2.8 37.9 + - - +
1W MET* 3.6 20.9 - - + -
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Residues in contact with HIS 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K TYR* 4.7 4.0 - + - -
254K THR* 3.2 31.2 + - + +
255K SER* 4.5 6.7 + - - -
258K MET* 3.2 39.8 - - + +
267K CYS 2.8 20.8 + - - +
268K LEU* 3.7 5.8 - - - +
270K VAL* 1.3 73.6 - - - +
272K ILE* 1.3 59.4 + - - +
274K THR* 3.0 8.1 + - - -
275K LEU* 3.0 57.4 + - + +
283K GLU* 5.6 2.7 - - + -
287K LEU* 3.4 24.0 - - + +
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Residues in contact with ILE 272 (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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268K LEU* 2.7 38.3 + - + +
269K PRO 4.0 2.7 - - - +
271K HIS* 1.3 73.5 - - - +
273K GLY* 1.3 64.0 + - - +
275K LEU* 3.2 6.7 + - - +
276K VAL* 3.0 29.1 + - + +
284K LEU* 4.2 18.3 - - + +
287K LEU* 4.6 10.8 - - + -
291K LEU* 4.9 4.5 - - + -
300K VAL* 4.8 4.0 - - + +
303K PHE* 3.6 29.8 - - + -
304K ALA* 3.6 24.0 - - + -
307K CYS* 3.0 34.5 - - - -
2W LEU* 4.4 0.7 - - + -
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Residues in contact with GLY 273 (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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242K TYR* 3.7 9.6 - - - -
269K PRO 3.0 15.9 + - - -
270K VAL* 3.7 1.1 - - - -
272K ILE* 1.3 76.5 - - - +
274K THR* 1.3 61.4 + - - +
276K VAL* 3.2 10.7 + - - +
277K GLU* 3.2 21.2 + - - +
1W MET 3.4 24.5 - - - -
2W LEU* 4.3 9.6 - - - +
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Residues in contact with THR 274 (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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242K TYR* 3.3 21.5 - - + -
247K PHE* 4.4 13.4 - - + +
250K CYS* 2.8 40.2 - - + -
251K TYR* 4.7 7.5 - - - -
254K THR* 3.7 12.2 - - - +
270K VAL 2.8 20.0 + - - +
271K HIS* 3.0 15.8 + - - -
273K GLY* 1.3 72.8 - - - +
275K LEU* 1.3 61.0 + - - +
277K GLU* 3.4 4.7 + - - +
278K LEU* 3.1 28.5 + - - +
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Residues in contact with LEU 275 (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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251K TYR* 3.3 35.9 - - + -
271K HIS* 3.0 44.8 + - + +
272K ILE 3.2 4.2 + - - +
274K THR* 1.3 72.8 - - - +
276K VAL* 1.3 61.1 + - - +
278K LEU* 4.5 2.7 - - - +
279K ASN 2.9 23.4 + - - -
280K LYS* 3.1 24.7 + - + +
283K GLU* 3.8 13.0 - - + +
284K LEU* 3.6 48.5 - - + +
287K LEU* 4.5 2.0 - - + -
311K MET* 3.3 4.8 - - + +
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Residues in contact with VAL 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K ILE 3.0 21.2 + - - +
273K GLY 3.2 7.4 + - - +
275K LEU* 1.3 75.1 - - - +
277K GLU* 1.3 75.8 + - - +
279K ASN* 3.2 15.2 + - - +
284K LEU* 4.6 1.1 - - + -
307K CYS* 4.3 20.0 - - + +
310K LEU* 6.2 2.9 - - + -
311K MET* 3.5 31.0 - - + +
443K LYS* 5.4 0.5 - - - -
2W LEU* 3.8 27.8 - - + -
3W ARG 4.5 9.6 - - - +
5W LYS* 5.8 1.2 + - - -
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Residues in contact with GLU 277 (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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242K TYR* 3.5 9.6 + - + -
247K PHE* 3.7 34.3 - - + -
273K GLY 3.2 19.0 + - - +
274K THR 3.8 5.4 - - - +
275K LEU 3.3 0.2 - - - -
276K VAL* 1.3 86.3 - - - +
278K LEU* 1.3 59.7 + - - +
279K ASN* 3.2 3.5 + - - +
440K THR* 5.2 4.6 - - - +
443K LYS* 3.0 51.4 + - - +
2W LEU* 4.4 0.5 - - - -
3W ARG* 3.2 46.6 + - - +
5W LYS* 5.8 1.4 + - - -
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Residues in contact with LEU 278 (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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247K PHE* 3.8 31.2 - - + +
248K LYS* 4.2 16.2 - - + +
251K TYR* 3.5 42.8 - - + -
274K THR 3.1 18.8 + - - +
277K GLU* 1.3 73.1 - - - +
279K ASN* 1.3 70.5 + - - +
280K LYS* 3.3 31.2 + - + +
440K THR* 4.3 19.7 - - + -
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Residues in contact with ASN 279 (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 2.9 7.5 + - - -
276K VAL 3.2 7.6 + - - +
277K GLU 3.2 5.1 - - - +
278K LEU* 1.3 81.3 - - - +
280K LYS* 1.3 57.2 + - - +
281K ALA* 3.0 11.1 + - - +
311K MET* 3.4 32.4 - - - +
442K ASP* 5.5 3.4 + - - +
5W LYS* 4.4 20.5 + - - +
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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