Contacts of the helix formed by residues 266 - 279 (chain A) in PDB entry 4ZSL
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 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 3.8 17.6 - - - +
264A GLY 3.4 1.0 + - - -
265A LYS* 1.3 86.3 + - - +
267A TYR* 1.3 57.6 + - - +
268A VAL* 3.4 7.6 + - - +
269A HIS* 2.8 36.4 + - - +
270A GLN* 2.9 30.7 + - - +
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Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 3.7 26.9 - - + -
225A ARG* 4.6 3.0 - - - +
228A ARG* 5.7 1.1 - - - -
233A MET* 2.7 58.8 + - + +
234A LEU* 4.1 2.9 - - - +
266A ASN* 1.3 75.2 - - - +
268A VAL* 1.3 76.1 + - + +
270A GLN* 3.3 13.1 + - - +
271A LEU* 3.4 30.3 + - + +
294A VAL* 3.4 37.8 - - + +
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASN* 3.4 5.2 + - - +
267A TYR* 1.3 88.5 - - + +
269A HIS* 1.4 60.0 + - - +
271A LEU* 3.1 11.1 + - + +
272A GLN* 2.9 42.9 + - - +
294A VAL* 6.3 0.2 - - + -
297A TYR* 3.6 38.8 - - + -
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Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PRO 4.5 2.2 - - - -
264A GLY* 3.7 2.8 - - - -
265A LYS* 2.9 43.7 + - + +
266A ASN* 2.8 28.2 + - - +
268A VAL* 1.4 71.9 - - - +
270A GLN* 1.4 56.5 + - - +
272A GLN* 3.3 29.7 + - + +
273A LEU* 3.0 61.1 + - + +
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 3.2 42.3 + - + +
226A TRP* 3.5 6.5 + - - +
228A ARG 5.5 1.4 + - - +
233A MET* 3.8 17.7 - - + -
246A TRP* 6.2 0.2 - - - +
262A PHE* 3.0 37.0 + - - +
264A GLY* 2.9 30.0 + - - -
266A ASN 2.9 19.1 + - - +
267A TYR 3.4 6.7 - - - +
268A VAL 3.2 0.2 - - - -
269A HIS* 1.4 75.5 - - - +
271A LEU* 1.4 60.4 + - - +
273A LEU* 3.3 5.5 + - - +
274A ILE* 3.1 40.2 + - + +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PRO* 5.9 2.0 - - + -
233A MET* 3.9 26.7 - - + -
234A LEU* 3.9 24.0 - - + -
267A TYR* 3.4 39.4 + - + +
268A VAL* 3.1 9.7 + - + +
270A GLN* 1.4 71.4 - - - +
272A GLN* 1.3 60.0 + - - +
274A ILE* 3.3 13.2 + - + +
275A MET* 2.9 50.0 + - + +
294A VAL* 3.8 18.6 - - + -
297A TYR* 5.3 9.4 - - + -
298A ILE* 5.0 5.4 - - + -
330A PHE* 6.4 1.6 - - + -
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 2.9 29.4 + - - +
269A HIS* 3.4 34.0 + - + +
271A LEU* 1.3 75.7 - - - +
273A LEU* 1.4 58.4 + - + +
275A MET* 3.2 8.5 + - - +
276A MET* 2.9 36.7 + - + +
297A TYR* 3.2 24.0 + - + +
301A LEU* 5.4 6.5 - - + -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU 5.5 0.4 - - - +
262A PHE* 3.4 25.8 - - + -
263A PRO* 3.5 26.0 - - + +
264A GLY* 3.4 35.2 - - - +
269A HIS* 3.0 39.9 + - + +
270A GLN 3.7 4.0 - - - +
271A LEU 3.3 0.2 - - - -
272A GLN* 1.4 72.2 - - + +
274A ILE* 1.3 66.3 + - - +
276A MET* 3.3 24.1 + - + +
277A VAL* 3.7 2.6 + - - +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG 4.7 9.9 - - - +
230A PRO* 4.9 7.2 - - + -
233A MET* 5.1 3.4 - - + -
246A TRP* 3.8 32.1 - - + +
262A PHE* 3.7 29.4 - - + -
270A GLN* 3.1 34.3 + - + +
271A LEU* 3.3 18.8 + - + +
273A LEU* 1.3 74.5 - - - +
275A MET* 1.4 58.9 + - - +
277A VAL* 3.2 4.7 + - - +
278A LEU* 2.9 33.2 + - + +
330A PHE* 3.7 27.6 - - + -
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Residues in contact with MET 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 5.8 2.0 - - + -
271A LEU* 2.9 36.8 + - + +
272A GLN* 3.7 5.8 - - - +
274A ILE* 1.4 73.5 - - - +
276A MET* 1.4 59.6 + - - +
279A GLY* 2.9 47.1 + - - +
280A THR* 4.9 3.8 - - - +
281A PRO* 3.7 23.8 - - + -
297A TYR* 5.7 2.7 - - + -
298A ILE* 3.6 37.0 - - + -
301A LEU* 4.3 23.3 - - + -
304A ARG* 3.6 11.5 + - + -
330A PHE* 4.0 13.5 - - + -
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Residues in contact with MET 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLN* 2.9 22.3 + - + +
273A LEU* 3.5 18.8 - - + +
274A ILE 3.3 1.0 - - - -
275A MET* 1.4 76.3 - - - +
277A VAL* 1.3 60.8 + - + +
304A ARG* 2.8 65.3 + - - +
307A VAL* 3.4 7.1 - - - +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU* 5.1 2.0 - - + -
262A PHE* 4.0 22.2 - - + -
273A LEU 3.7 2.2 + - - +
274A ILE 3.2 2.0 + - - -
275A MET 3.2 0.2 - - - -
276A MET* 1.3 82.6 - - + +
278A LEU* 1.3 64.3 + - + +
279A GLY 3.3 1.8 - - - -
305A GLN 5.2 0.2 - - - -
306A PRO* 3.4 1.6 - - - +
307A VAL* 2.7 40.4 + - + +
309A TRP* 3.5 40.6 - - + -
312A VAL* 3.8 31.0 - - + -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.7 33.0 - - + -
262A PHE* 3.9 22.2 - - + -
274A ILE* 2.9 26.3 + - + +
277A VAL* 1.3 82.9 - - + +
279A GLY* 1.3 59.5 + - - +
280A THR 4.9 1.0 - - - +
306A PRO* 3.4 23.5 - - - +
309A TRP* 4.1 14.1 - - + -
328A LEU* 3.8 15.9 - - + +
329A ARG* 4.3 0.4 - - - -
330A PHE* 3.6 43.0 - - + +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A MET* 2.9 27.2 + - - +
277A VAL 3.3 3.2 + - - -
278A LEU* 1.3 79.9 - - - +
280A THR* 1.3 66.2 + - - -
304A ARG* 3.3 16.2 - - - -
305A GLN 3.8 14.3 + - - -
306A PRO* 4.1 0.7 - - - -
330A PHE* 3.2 16.8 - - - -
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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