Contacts of the helix formed by residues 287 - 300 (chain A) in PDB entry 1ZEB
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 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A GLU* 3.7 2.9 - - - -
280A ARG* 3.5 34.3 - - - +
286A PRO* 1.3 76.5 - - - +
288A LEU* 1.3 64.8 + - - +
289A MET* 3.3 10.2 + - - +
290A GLU* 3.0 34.1 + - - +
291A MET* 2.9 23.3 + - - +
333A MET* 3.6 20.3 - - - +
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Residues in contact with LEU 288 (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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146A VAL* 3.8 23.8 - - + -
147A THR* 4.3 2.5 - - - -
148A THR* 3.9 18.0 - - + +
277A GLU* 5.0 0.4 + - - -
287A SER* 1.3 72.7 - - - +
289A MET* 1.3 53.3 + - - +
291A MET* 3.3 16.2 + - + +
292A THR* 2.6 39.8 + - + +
310A VAL* 4.0 9.4 - - + -
311A GLU 3.4 27.8 - - - +
312A GLY* 3.7 19.7 - - - +
330A GLU 5.6 0.7 - - - +
333A MET* 3.9 16.0 - - + +
334A PHE* 4.1 24.0 - - + +
337A ALA* 4.1 8.3 - - + -
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Residues in contact with MET 289 (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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287A SER* 3.2 9.5 + - - +
288A LEU* 1.3 77.9 - - - +
290A GLU* 1.3 66.4 + - + +
292A THR* 3.3 3.6 + - - -
293A GLU* 3.0 29.0 + - - +
333A MET* 3.7 19.8 - - + -
336A ASP* 3.7 29.4 - - + +
337A ALA* 3.8 13.6 - - - +
339A GLU* 6.1 0.4 - - - +
340A ARG* 3.5 32.3 - - + +
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Residues in contact with GLU 290 (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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250A ARG* 2.9 45.6 + - - -
253A LEU* 4.8 1.7 - - + +
280A ARG* 3.9 8.0 + - - -
286A PRO* 3.2 9.8 - - + +
287A SER* 3.0 36.3 + - - +
289A MET* 1.3 86.7 - - + +
291A MET* 1.3 57.7 + - - +
293A GLU* 3.4 8.1 + - - +
294A ALA* 2.9 29.5 + - - +
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.7 12.6 - - + -
147A THR 3.6 20.9 - - - +
148A THR* 4.4 3.4 - - + -
200A LEU* 3.3 27.3 - - + +
201A GLY 4.1 3.1 - - - -
253A LEU* 4.3 2.5 - - + -
269A PHE* 3.9 30.3 - - + -
274A MET* 3.8 19.7 - - + +
286A PRO* 3.4 23.3 - - + -
287A SER 2.9 10.0 + - - +
288A LEU* 3.7 31.0 - - + +
290A GLU* 1.3 77.3 - - - +
292A THR* 1.3 56.9 + - - +
294A ALA* 3.3 3.7 + - - -
295A ALA* 2.9 25.8 + - - +
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Residues in contact with THR 292 (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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39A PHE* 5.1 0.6 - - + -
146A VAL* 4.2 3.1 - - + -
288A LEU* 2.6 33.3 + - + +
289A MET 3.3 4.0 + - - +
291A MET* 1.3 75.3 - - - +
293A GLU* 1.3 58.9 + - - +
295A ALA* 3.3 7.3 + - - +
296A LEU* 2.9 41.6 + - - +
308A LEU* 4.6 2.4 - - - +
310A VAL* 3.5 42.8 - - + +
337A ALA* 3.7 23.7 + - + -
340A ARG* 5.2 1.2 - - - +
341A ALA* 4.3 6.1 + - - +
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Residues in contact with GLU 293 (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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289A MET* 3.0 14.1 + - - +
290A GLU* 3.7 10.3 - - - +
292A THR* 1.3 74.7 + - - +
294A ALA* 1.3 59.5 + - - +
296A LEU* 3.2 1.6 + - - +
297A ARG* 2.9 63.0 + - + +
340A ARG* 2.9 46.5 + - + +
344A LEU* 3.6 23.8 - - + +
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Residues in contact with ALA 294 (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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200A LEU* 4.1 2.7 - - + -
253A LEU* 3.8 37.9 - - + -
257A SER* 3.9 22.5 - - - +
265A LEU* 5.1 4.3 - - + +
290A GLU 2.9 15.1 + - - +
291A MET 3.3 8.0 + - - +
293A GLU* 1.3 76.5 - - - +
295A ALA* 1.3 63.0 + - - +
297A ARG* 3.4 12.9 + - - +
298A LEU* 3.5 12.3 + - - +
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Residues in contact with ALA 295 (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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146A VAL* 3.7 24.2 - - + -
198A VAL* 3.9 22.4 - - + -
200A LEU* 4.1 0.4 - - - +
291A MET 2.9 17.0 + - - +
292A THR 3.5 5.2 - - - +
293A GLU 3.2 0.2 - - - -
294A ALA* 1.3 76.7 - - - +
296A LEU* 1.3 52.7 + - - +
298A LEU* 3.2 3.1 + - - +
299A LEU* 2.8 41.9 + - + +
308A LEU* 4.0 14.1 - - + -
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Residues in contact with LEU 296 (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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37A ILE* 4.4 1.3 - - + -
292A THR* 2.9 24.0 + - - +
293A GLU* 3.2 5.6 + - - +
295A ALA* 1.3 74.3 - - - +
297A ARG* 1.3 57.6 + - - +
299A LEU* 4.5 2.9 - - + +
300A SER* 2.8 40.8 + - - -
306A PHE* 3.6 31.9 - - + -
308A LEU* 3.5 26.7 - - + -
341A ALA* 3.7 35.4 - - + -
344A LEU* 4.1 24.7 - - + +
345A THR* 4.1 12.6 - - + -
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Residues in contact with ARG 297 (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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254A MET* 4.5 7.3 + - - +
257A SER* 3.0 46.5 + - - +
258A LEU* 3.8 30.8 - - + +
293A GLU* 2.9 49.8 + - + +
294A ALA* 3.5 9.4 - - - +
295A ALA 3.2 0.2 - - - -
296A LEU* 1.3 77.5 - - - +
298A LEU* 1.3 59.2 + - - +
300A SER* 3.4 8.8 + - - -
301A ARG* 2.8 31.9 + - - +
344A LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 298 (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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142A SER* 5.3 1.2 + - - -
197A ASP* 5.5 1.8 - - + -
198A VAL* 3.6 19.7 - - + -
256A ALA 5.7 2.2 - - - +
257A SER* 5.4 4.5 - - - +
262A VAL* 3.0 33.4 - - + +
263A THR* 3.8 18.2 - - - +
265A LEU* 3.4 44.9 - - + +
294A ALA 3.5 7.7 + - - +
295A ALA 3.2 6.9 + - - +
297A ARG* 1.3 78.3 - - + +
299A LEU* 1.3 64.5 + - - +
301A ARG* 3.3 35.3 + - + +
302A ASN 4.6 0.5 + - - -
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Residues in contact with LEU 299 (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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142A SER* 3.6 26.1 - - - -
143A VAL 3.7 22.0 - - - +
144A GLY* 3.8 21.5 - - - +
197A ASP* 4.0 3.8 - - + -
198A VAL* 3.9 15.0 - - + -
295A ALA* 2.8 28.5 + - + +
296A LEU* 4.3 2.5 - - - +
298A LEU* 1.3 73.0 - - - +
300A SER* 1.3 61.4 + - - +
301A ARG 3.1 1.5 + - - -
302A ASN* 3.5 17.0 + - - +
305A GLY 4.5 0.2 - - - +
306A PHE* 3.8 31.5 - - + +
307A PHE 4.2 0.4 - - - +
308A LEU* 3.9 29.6 - - + -
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Residues in contact with SER 300 (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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34A LYS* 5.3 5.2 + - - -
296A LEU* 2.8 25.9 + - - -
297A ARG* 3.4 9.9 + - - -
299A LEU* 1.3 75.7 - - - +
301A ARG* 1.3 65.4 + - - +
302A ASN 3.3 6.4 + - - +
306A PHE* 4.2 19.7 - - - -
344A LEU 5.9 3.1 - - - -
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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