Contacts of the helix formed by residues 260 - 274 (chain K) in PDB entry 4ZZ7
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 260 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482J PRO* 6.0 0.4 - - + -
483J SER* 3.4 26.1 + - - +
258K ASP 3.9 0.8 + - - -
259K ALA* 1.3 70.6 - - - +
261K MET* 1.3 65.8 + - - +
262K ASP* 3.3 20.1 + - - +
263K ASN* 3.7 27.3 + - + +
264K ALA* 3.2 21.3 + - - +
415K PHE* 5.5 0.5 - - - +
417K ARG* 5.0 4.2 - - - +
437K ASN* 5.9 0.4 + - - -
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Residues in contact with MET 261 (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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255K VAL* 3.5 34.3 - - + -
256K MET 4.8 4.0 - - - +
257K PRO 5.7 1.6 - - - +
259K ALA 3.3 9.9 + - - +
260K ASP* 1.3 74.2 + - - +
262K ASP* 1.3 60.3 + - - +
264K ALA* 3.2 3.6 + - - +
265K VAL* 2.9 44.0 + - + +
293K ALA* 3.9 27.8 - - + +
296K ALA* 4.3 22.9 - - + +
297K LEU* 3.9 28.0 - - - -
300K LYS* 4.4 16.4 - - + +
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Residues in contact with ASP 262 (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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260K ASP* 3.3 14.1 + - - +
261K MET* 1.3 78.1 - - - +
263K ASN* 1.3 62.5 + - - +
265K VAL* 3.9 4.0 - - - +
266K ASN* 3.0 26.1 + - - +
300K LYS* 2.7 37.9 + - - +
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Residues in contact with ASN 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480J ARG* 3.7 19.0 - - - +
482J PRO* 3.6 28.7 - - + +
260K ASP* 3.7 27.5 + - + +
262K ASP* 1.3 77.0 - - - +
264K ALA* 1.3 67.4 + - - +
266K ASN* 4.0 6.5 - - - +
267K GLN* 2.9 54.7 + - - +
415K PHE* 4.8 4.9 - - - -
437K ASN* 4.7 1.7 - - - +
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Residues in contact with ALA 264 (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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255K VAL* 4.9 5.4 - - + -
259K ALA* 5.4 0.2 - - + -
260K ASP 3.2 13.3 + - - +
261K MET* 3.2 20.2 + - - +
263K ASN* 1.3 80.2 + - - +
265K VAL* 1.3 58.9 + - + +
267K GLN* 3.4 1.6 + - - +
268K LEU* 2.8 40.2 + - + +
297K LEU* 5.4 0.2 - - + -
415K PHE* 4.0 39.8 - - + -
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Residues in contact with VAL 265 (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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261K MET* 2.9 25.1 + - + +
262K ASP* 3.9 4.5 - - - +
264K ALA* 1.3 73.7 - - - +
266K ASN* 1.3 66.3 + - - +
268K LEU* 3.2 8.2 + - - +
269K LEU* 3.1 22.7 + - - +
297K LEU* 4.0 24.9 - - + +
300K LYS* 3.8 28.5 - - + +
301K MET* 3.7 33.7 - - + +
304K ALA* 4.3 13.0 - - + -
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Residues in contact with ASN 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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262K ASP 3.0 18.0 + - - +
263K ASN* 4.0 7.7 - - - +
265K VAL* 1.3 78.2 - - - +
267K GLN* 1.3 66.9 + - + +
269K LEU* 3.3 29.8 + - - +
270K GLY 4.0 2.1 + - - -
304K ALA* 6.1 0.2 - - - -
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Residues in contact with GLN 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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480J ARG* 3.3 22.5 + - - +
263K ASN* 2.9 45.3 + - - +
264K ALA 3.9 2.9 - - - +
266K ASN* 1.3 79.9 - - + +
268K LEU* 1.3 60.0 + - - +
270K GLY* 3.7 2.4 + - - -
271K ALA* 3.3 22.3 + - - +
415K PHE* 3.8 12.4 - - + -
437K ASN 3.1 24.1 + - - +
438K ILE* 4.9 2.8 - - - +
439K PRO* 3.7 25.6 - - + +
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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
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253K ALA* 4.4 1.6 - - + -
255K VAL* 4.7 4.3 - - + -
264K ALA 2.8 28.7 + - - +
265K VAL* 3.2 6.7 + - - +
267K GLN* 1.3 69.2 - - - +
269K LEU* 1.3 64.1 + - - +
271K ALA* 3.9 3.6 - - + -
272K ALA* 3.2 26.3 + - - +
273K PHE* 4.3 2.3 - - - -
283K LEU* 3.9 46.0 - - + +
286K ALA* 4.3 17.9 - - + -
297K LEU* 4.0 26.7 - - + -
301K MET* 4.6 9.0 - - - -
388K LEU* 4.3 10.1 - - + +
415K PHE* 4.2 20.2 - - + -
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Residues in contact with LEU 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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265K VAL 3.1 10.7 + - - +
266K ASN* 3.4 26.5 - - - +
267K GLN 3.3 0.6 - - - -
268K LEU* 1.3 75.2 - - - +
270K GLY* 1.3 60.7 + - - +
273K PHE* 3.0 43.3 + - + +
274K GLY 3.6 0.2 + - - -
301K MET* 3.3 26.7 - - + -
304K ALA* 4.0 31.2 - - + +
305K MET* 4.5 0.2 - - - -
308K LEU* 3.8 33.6 - - + +
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Residues in contact with GLY 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 ASN 4.0 2.6 + - - -
267K GLN 3.7 4.9 + - - -
269K LEU* 1.3 78.5 - - - +
271K ALA* 1.3 56.7 + - - +
274K GLY* 2.7 29.0 + - - -
279K ARG* 3.0 16.8 + - - -
440K LEU* 5.1 2.5 - - - -
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Residues in contact with ALA 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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267K GLN 3.3 17.8 + - - +
268K LEU* 4.1 5.8 - - - -
269K LEU 3.2 0.4 - - - -
270K GLY* 1.3 78.7 - - - +
272K ALA* 1.3 60.0 + - - +
274K GLY 4.8 0.5 + - - +
279K ARG* 4.2 5.4 + - - -
282K ALA* 3.4 10.7 - - - +
283K LEU* 2.9 33.1 + - + -
439K PRO* 3.6 26.9 - - + -
440K LEU* 4.2 18.1 - - + +
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Residues in contact with ALA 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* 3.2 16.6 + - + +
271K ALA* 1.3 80.6 - - - +
273K PHE* 1.3 71.3 + - + +
274K GLY 3.7 0.4 - - - -
277K GLY* 3.3 22.9 - - - -
282K ALA* 4.7 2.1 - - - +
283K LEU 3.2 24.0 - - - +
385K GLY 4.2 4.7 - - - +
386K PRO* 4.3 0.5 - - - +
387K VAL 4.6 5.5 + - - +
388K LEU* 4.0 24.9 - - + -
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Residues in contact with PHE 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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268K LEU 4.3 1.8 - - - -
269K LEU* 3.0 33.6 + - + +
272K ALA* 1.3 84.8 - - + +
274K GLY* 1.3 66.7 + - - +
276K SER* 3.2 8.0 + - - -
277K GLY 3.9 4.5 - - - +
301K MET* 4.0 23.8 - - + -
305K MET* 3.8 23.1 - - + -
308K LEU* 4.3 9.4 - - + -
320K PHE* 3.1 38.3 - - + -
366K GLY* 4.1 5.4 - - - -
367K THR 3.8 22.2 - - - -
386K PRO* 3.8 28.9 - - + -
387K VAL 4.1 1.8 - - - -
388K LEU* 3.8 24.0 - - + -
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Residues in contact with GLY 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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96K ASP* 4.8 4.0 - - - -
269K LEU 3.6 0.8 + - - -
270K GLY* 2.7 32.9 + - - -
271K ALA 5.1 0.5 - - - +
272K ALA 3.7 0.9 - - - +
273K PHE* 1.3 72.0 - - - +
275K SER* 1.3 68.7 + - - -
276K SER 3.0 1.4 + - - -
277K GLY* 3.1 12.6 + - - -
278K GLU 4.2 0.3 + - - -
279K ARG* 3.7 17.3 + - - +
282K ALA* 5.7 0.2 - - - +
319K ASP 5.2 3.4 - - - -
320K PHE* 4.9 2.5 - - - -
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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