Contacts of the helix formed by residues 260 - 274 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482I PRO* 5.6 5.4 - - + -
483I SER* 4.9 17.6 - - - +
258L ASP 3.8 1.2 + - - -
259L ALA* 1.3 69.9 - - - +
261L MET* 1.3 65.9 + - - +
262L ASP* 3.9 15.3 + - - +
263L ASN* 3.1 32.7 + - + +
264L ALA* 3.0 19.8 + - - +
417L ARG* 4.9 7.0 - - + +
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Residues in contact with MET 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255L VAL* 3.7 24.2 - - + -
256L MET 5.0 4.3 - - - +
257L PRO 5.5 3.1 - - - +
259L ALA* 3.1 12.0 + - - +
260L ASP* 1.3 73.8 + - - +
262L ASP* 1.3 58.5 + - - +
264L ALA* 3.1 6.1 + - - +
265L VAL* 2.8 37.9 + - + +
293L ALA* 3.7 36.6 - - + +
296L ALA* 4.2 24.5 - - + +
297L LEU* 3.9 26.9 - - - -
300L LYS* 4.4 16.4 - - + +
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Residues in contact with ASP 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260L ASP* 3.2 15.0 + - - +
261L MET* 1.3 77.1 - - - +
263L ASN* 1.3 57.6 + - - +
265L VAL* 3.9 4.1 - - - +
266L ASN* 2.9 32.0 + - - +
300L LYS* 2.4 41.6 + - - +
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Residues in contact with ASN 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480I ARG* 3.8 20.8 + - - +
482I PRO* 4.4 17.8 - - + +
260L ASP* 3.1 28.7 + - + +
262L ASP* 1.3 75.9 - - - +
264L ALA* 1.3 66.3 + - - +
266L ASN* 4.5 7.9 + - - -
267L GLN* 3.1 48.2 + - - +
415L PHE* 5.1 3.8 - - - -
437L ASN* 5.3 1.8 + - - +
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Residues in contact with ALA 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255L VAL* 4.8 11.7 - - + -
259L ALA* 5.4 0.2 - - + -
260L ASP 3.0 13.8 + - - +
261L MET* 3.1 16.1 + - - +
263L ASN* 1.3 75.3 - - - +
265L VAL* 1.3 58.2 + - + +
267L GLN* 3.1 5.4 + - - +
268L LEU* 2.8 37.6 + - + +
297L LEU* 5.3 0.2 - - + -
415L PHE* 4.1 40.2 - - + -
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Residues in contact with VAL 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261L MET* 2.8 24.0 + - + +
262L ASP* 3.9 4.0 - - - +
264L ALA* 1.3 71.4 - - - +
266L ASN* 1.3 67.3 + - - +
268L LEU* 3.0 18.0 + - - +
269L LEU* 3.1 13.3 + - - +
297L LEU* 3.9 25.4 - - + +
300L LYS* 3.6 44.4 - - + +
301L MET* 4.0 21.6 - - + +
304L ALA* 4.2 11.2 - - + -
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Residues in contact with ASN 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L ASP 2.9 19.6 + - - +
263L ASN* 4.1 8.6 + - - +
265L VAL* 1.3 78.9 - - - +
267L GLN* 1.3 64.2 + - - +
269L LEU* 3.6 26.3 - - - +
270L GLY 4.1 2.1 + - - -
304L ALA* 6.1 0.2 - - - -
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Residues in contact with GLN 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480I ARG* 3.9 13.4 + - - +
263L ASN* 3.1 40.0 + - - +
264L ALA 3.1 4.8 + - - +
266L ASN* 1.3 79.8 - - + +
268L LEU* 1.3 58.8 + - - +
270L GLY* 3.7 2.2 + - - +
271L ALA* 3.2 26.0 + - - +
415L PHE* 3.8 9.5 - - + -
437L ASN 3.4 22.6 + - - +
438L ILE* 5.1 4.3 - - - +
439L PRO* 3.5 30.5 - - + +
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Residues in contact with LEU 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L ALA* 4.5 1.3 - - + -
255L VAL* 4.7 4.5 - - + -
264L ALA* 2.8 20.7 + - + +
265L VAL* 3.0 6.7 + - - +
267L GLN* 1.3 74.3 - - - +
269L LEU* 1.3 60.6 + - - +
271L ALA* 3.7 1.8 - - + -
272L ALA* 2.9 32.9 + - - +
283L LEU* 3.8 44.9 - - + +
286L ALA* 4.4 15.0 - - + -
297L LEU* 4.0 27.1 - - + -
301L MET* 4.4 3.8 - - - -
388L LEU* 4.3 20.9 - - + +
415L PHE* 4.1 21.1 - - + -
439L PRO* 4.7 0.2 - - + -
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Residues in contact with LEU 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265L VAL 3.1 11.2 + - - +
266L ASN* 3.6 23.8 - - - +
267L GLN 3.3 0.4 - - - -
268L LEU* 1.3 74.6 - - - +
270L GLY* 1.3 58.2 + - - +
273L PHE* 2.9 49.0 + - + +
274L GLY 3.6 0.2 + - - -
301L MET* 3.4 27.3 - - + +
304L ALA* 3.8 21.1 - - + +
305L MET 4.2 7.9 - - - +
307L LYS* 6.3 1.3 - - + -
308L LEU* 3.8 33.7 - - + -
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Residues in contact with GLY 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266L ASN 4.1 3.2 + - - -
267L GLN 3.7 5.0 + - - -
268L LEU 3.4 0.2 - - - -
269L LEU* 1.3 80.9 - - - +
271L ALA* 1.3 51.6 + - - +
274L GLY* 3.0 17.2 + - - -
279L ARG* 2.7 30.5 + - - -
440L LEU* 4.9 3.1 - - - -
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Residues in contact with ALA 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267L GLN 3.2 18.8 + - - +
268L LEU* 3.8 6.5 - - - +
269L LEU 3.2 0.6 - - - -
270L GLY* 1.3 79.5 - - - +
272L ALA* 1.3 57.3 + - - +
274L GLY 5.1 0.3 - - - +
279L ARG* 4.0 6.6 + - - -
282L ALA* 3.3 11.6 - - - +
283L LEU* 3.0 38.8 + - + -
439L PRO* 3.7 19.7 - - + -
440L LEU* 4.2 17.3 - - + +
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Residues in contact with ALA 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268L LEU 2.9 16.9 + - - +
271L ALA* 1.3 78.7 - - - +
273L PHE* 1.3 70.2 + - + +
274L GLY 3.7 0.7 - - - -
277L GLY* 3.4 21.9 - - - -
282L ALA* 4.8 2.9 - - - +
283L LEU 3.2 24.0 - - - +
284L SER* 5.5 0.4 - - - +
385L GLY 4.2 5.4 - - - +
386L PRO* 4.3 0.2 - - - +
387L VAL 4.5 3.1 + - - +
388L LEU* 3.7 31.0 - - + +
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Residues in contact with PHE 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269L LEU* 2.9 36.4 + - + +
272L ALA* 1.3 83.2 - - + +
274L GLY* 1.3 67.4 + - - +
276L SER* 3.1 13.7 + - - -
277L GLY 3.9 3.6 - - - +
301L MET* 4.0 14.6 - - + -
305L MET* 3.7 35.7 - - + -
308L LEU* 4.1 10.1 - - + -
320L PHE* 3.3 34.1 - - + -
366L GLY* 4.2 4.7 - - - -
367L THR 3.4 15.3 - - - -
386L PRO* 3.4 34.5 - - + -
388L LEU* 3.7 27.1 - - + -
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Residues in contact with GLY 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L ASP* 4.5 4.9 - - - -
269L LEU 3.6 2.2 + - - -
270L GLY* 3.0 25.8 + - - -
271L ALA 5.1 0.3 - - - +
272L ALA 3.7 1.1 - - - +
273L PHE* 1.3 77.1 - - - +
275L SER* 1.3 69.7 + - - -
277L GLY* 3.0 14.7 + - - -
279L ARG* 3.4 18.5 + - - -
319L ASP 5.4 2.2 - - - -
320L PHE* 5.1 1.6 - - - -
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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