Contacts of the helix formed by residues 265 - 277 (chain K) in PDB entry 5FWK
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 GLU 265 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114K ALA* 5.7 3.9 - - + +
118K LYS* 2.9 32.5 + - - -
258K GLN* 5.1 2.0 - - - +
263K GLU 3.1 10.1 + - - +
264K MET* 1.3 70.5 - - - +
266K GLU* 1.3 57.3 + - + +
267K SER* 4.1 12.4 + - - +
268K GLY* 2.7 28.8 + - - -
269K ALA 2.9 8.3 + - - -
294K TYR* 3.7 19.7 + - + +
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Residues in contact with GLU 266 (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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258K GLN* 3.9 32.0 + - - +
264K MET 3.4 2.2 + - - -
265K GLU* 1.3 74.3 - - + +
267K SER* 1.3 59.4 + - - +
269K ALA* 3.1 11.1 + - + +
270K GLN* 2.8 29.7 + - + +
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Residues in contact with SER 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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265K GLU* 3.0 10.8 + - - +
266K GLU* 1.3 79.4 - - - +
268K GLY* 1.3 57.1 + - - +
270K GLN* 3.3 7.6 + - - +
271K LEU* 3.0 30.1 + - - +
292K HIS* 4.2 13.7 + - - -
294K TYR* 3.7 28.0 - - - -
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Residues in contact with GLY 268 (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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121K MET* 5.5 2.6 - - - +
264K MET* 3.4 10.5 - - - +
265K GLU 2.7 11.9 + - - -
267K SER* 1.3 72.4 - - - +
269K ALA* 1.3 55.0 + - - +
271K LEU* 3.7 4.0 - - - +
272K LEU* 2.8 36.4 + - - +
294K TYR* 3.4 34.7 - - - -
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Residues in contact with ALA 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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257K VAL* 3.8 12.0 - - + +
258K GLN* 3.3 41.3 - - + +
264K MET* 3.5 15.5 - - + -
265K GLU 2.9 5.7 + - - +
266K GLU* 3.1 9.6 + - + +
268K GLY* 1.3 79.0 - - - +
270K GLN* 1.3 52.0 + - - +
273K LEU* 2.8 36.1 + - - +
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Residues in contact with GLN 270 (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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266K GLU* 2.8 14.1 + - + +
267K SER* 3.5 11.7 - - - +
268K GLY 3.2 0.2 - - - -
269K ALA* 1.3 75.4 - - - +
271K LEU* 1.3 61.4 + - + +
273K LEU* 3.4 15.0 + - - +
274K GLU* 2.9 69.4 + - - +
292K HIS* 6.3 1.8 - - - +
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Residues in contact with LEU 271 (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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121K MET* 5.1 6.5 - - + -
267K SER 3.0 14.1 + - - +
268K GLY* 3.3 6.3 + - - +
270K GLN* 1.3 77.1 - - + +
272K LEU* 1.3 57.6 + - - +
274K GLU* 3.4 9.3 + - - +
275K MET* 3.0 41.4 + - + +
284K ILE* 3.6 32.2 - - + +
289K ALA* 4.3 15.0 - - + +
292K HIS* 3.8 31.0 - - + +
294K TYR* 3.6 41.5 - - + -
295K LEU* 4.8 3.4 - - + -
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Residues in contact with LEU 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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121K MET* 6.1 1.5 - - + +
201K GLY* 3.1 46.7 - - - +
204K PHE* 5.1 2.5 - - + -
205K ALA* 3.9 16.6 - - + +
257K VAL* 3.7 16.4 - - + -
261K VAL* 4.5 1.3 - - + -
264K MET* 3.6 24.9 - - + -
268K GLY 2.8 21.7 + - - +
269K ALA 3.9 2.9 - - - +
271K LEU* 1.3 72.1 - - - +
273K LEU* 1.3 54.2 + - - +
275K MET* 2.9 11.9 + - + -
276K LEU* 2.7 52.8 + - + +
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Residues in contact with LEU 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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229K LEU 4.2 3.1 - - - +
230K ILE* 3.9 36.8 - - + +
254K PRO* 5.1 9.4 - - + -
256K PRO* 6.3 1.6 - - + -
257K VAL* 4.0 25.5 - - + +
269K ALA 2.8 23.0 + - - +
270K GLN* 3.8 17.5 - - - +
272K LEU* 1.3 73.6 - - - +
274K GLU* 1.3 51.4 + - + +
276K LEU* 4.3 2.7 - - - +
277K THR* 2.6 44.6 + - - +
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Residues in contact with GLU 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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270K GLN* 2.9 53.1 + - - +
271K LEU* 3.5 9.4 - - - +
273K LEU* 1.3 77.3 - - + +
275K MET* 1.3 60.5 + - - +
277K THR* 3.4 11.6 + - - +
282K LYS 4.5 8.7 - - - +
283K ARG* 3.1 27.8 - - - +
284K ILE* 3.4 41.5 - - + +
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Residues in contact with MET 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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121K MET* 4.7 9.2 - - + -
125K LEU* 5.0 2.9 - - + -
197K MET* 3.6 52.5 - - + +
198K TRP* 3.0 24.3 - - - +
200K VAL* 4.5 6.1 - - - -
201K GLY* 4.1 2.2 - - - -
204K PHE* 3.9 28.3 - - + -
271K LEU* 3.0 25.8 + - + +
272K LEU* 2.9 25.1 + - + +
274K GLU* 1.3 76.8 - - - +
276K LEU* 1.3 59.6 + - - +
283K ARG* 3.4 18.0 - - - +
284K ILE* 3.7 17.5 - - + +
289K ALA* 5.3 3.8 - - + -
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Residues in contact with LEU 276 (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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198K TRP* 2.9 32.2 + - + +
202K CYS* 3.4 42.4 - - - +
213K LEU* 3.7 19.7 - - + -
214K PHE* 4.3 1.8 - - + -
229K LEU* 3.7 19.3 - - + -
230K ILE* 3.3 28.0 - - + +
257K VAL* 4.7 3.6 - - + -
272K LEU* 2.7 45.1 + - + +
273K LEU* 3.8 2.5 - - - +
275K MET* 1.3 72.7 - - - +
277K THR* 1.3 67.8 + - - +
278K PHE 3.3 1.6 + - - -
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Residues in contact with THR 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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230K ILE* 4.2 9.4 - - - +
273K LEU* 2.6 33.1 + - - +
274K GLU* 3.5 17.0 + - - -
275K MET 3.4 0.6 - - - -
276K LEU* 1.3 73.2 - - - +
278K PHE* 1.3 59.9 + - + +
279K ASN* 3.8 7.4 - - + +
282K LYS* 3.7 38.9 + - + +
283K ARG* 2.6 35.0 + - - +
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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
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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