Contacts of the helix formed by residues 286 - 299 (chain A) in PDB entry 2POZ
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 GLY 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A SER* 3.1 13.7 + - - -
97A GLU* 3.4 12.6 - - - -
98A GLN* 4.9 0.4 - - - -
281A ILE* 3.3 19.3 + - - +
285A GLY* 1.3 79.9 - - - +
287A LEU* 1.3 60.2 + - - -
288A MSE 3.6 1.1 - - - -
289A GLU 4.1 0.4 - - - -
290A THR* 2.7 36.0 + - - -
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Residues in contact with LEU 287 (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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97A GLU* 2.8 13.4 + - - +
98A GLN* 4.3 16.9 - - + +
101A TRP* 4.3 11.7 - - + -
112A VAL* 4.2 18.4 - - + -
116A PHE* 4.0 13.5 - - + -
281A ILE* 3.7 23.3 - - + -
286A GLY* 1.3 69.0 - - - -
288A MSE 1.3 61.1 + - - +
290A THR* 3.4 4.2 + - - -
291A LYS* 2.9 26.9 + - - +
317A ALA* 3.5 22.0 - - + +
320A GLN* 4.5 2.5 - - + -
321A LEU* 3.8 22.0 - - + +
366A LEU* 3.6 31.4 - - + -
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Residues in contact with MSE 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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69A GLU* 3.9 9.4 - - - +
97A GLU* 2.8 19.4 + - - +
101A TRP* 3.6 24.9 - - + +
116A PHE* 3.8 28.8 - - + -
287A LEU* 1.3 71.6 - - - +
289A GLU* 1.3 58.4 + - - +
291A LYS* 3.0 22.9 + - + +
292A LYS* 2.8 62.6 + - - +
115E LEU 4.8 0.7 - - - +
116E PHE* 3.8 25.1 - - - +
288E MSE 4.7 10.5 - - + +
291E LYS* 4.0 11.9 - - - -
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Residues in contact with GLU 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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72A TRP* 3.9 21.5 - - + +
97A GLU* 3.9 2.6 + - - -
261A THR* 3.5 6.4 - - - -
262A ARG* 2.7 67.6 + - - +
263A PHE* 5.6 0.2 - - - -
284A ALA 3.4 23.6 - - - +
285A GLY* 3.7 26.0 - - - +
286A GLY 3.8 0.2 + - - -
288A MSE 1.3 78.4 - - - +
290A THR* 1.3 58.2 + - - +
292A LYS* 3.2 12.3 + - - +
293A ILE* 2.9 32.3 + - + +
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Residues in contact with THR 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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279A PRO* 3.8 29.4 - - + +
281A ILE* 3.7 18.0 - - + +
284A ALA* 3.6 19.2 - - - +
286A GLY 2.7 24.0 + - - -
287A LEU 3.8 3.8 - - - -
288A MSE 3.2 0.2 - - - -
289A GLU* 1.3 74.0 - - - +
291A LYS* 1.3 60.6 + - - +
293A ILE* 3.2 7.4 + - - +
294A CYS* 2.8 29.5 + - - -
321A LEU* 3.6 25.4 - - + -
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Residues in contact with LYS 291 (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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116A PHE* 3.4 43.7 + - + -
287A LEU 2.9 14.7 + - - +
288A MSE 3.4 21.1 - - - +
290A THR* 1.3 75.3 - - - +
292A LYS* 1.3 59.2 + - - +
294A CYS* 3.3 5.2 + - - +
295A ALA* 2.9 27.8 + - + +
321A LEU* 3.7 14.5 - - + +
324A ASN* 2.6 24.5 + - - +
325A ILE* 4.7 8.7 - - + +
69E GLU* 3.0 25.9 + - - -
288E MSE 4.0 20.4 - - - -
292E LYS* 4.2 10.1 - - - +
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Residues in contact with LYS 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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69A GLU* 2.8 39.0 + - - -
262A ARG* 3.9 36.8 - - - +
288A MSE 2.8 36.8 + - - +
289A GLU* 3.4 15.0 + - - +
291A LYS* 1.3 73.4 - - + +
293A ILE* 1.3 64.7 + - - +
295A ALA* 3.2 8.5 + - - +
296A MSE 3.0 27.3 + - + +
291E LYS* 4.2 11.1 - - - +
292E LYS* 5.8 6.7 - - + +
295E ALA* 3.7 28.7 - - + +
298E GLU* 4.9 3.8 + - - -
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Residues in contact with ILE 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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261A THR* 3.5 19.7 - - - -
262A ARG* 3.7 24.7 - - + +
265A PHE* 3.5 48.9 - - + -
269A PHE* 3.6 1.1 - - + -
277A ILE* 3.7 18.6 - - + -
279A PRO* 4.7 5.4 - - + -
284A ALA* 4.1 17.7 - - + +
289A GLU 2.9 19.5 + - - +
290A THR* 3.2 11.4 + - + +
292A LYS* 1.3 77.0 - - - +
294A CYS* 1.3 56.6 + - - +
296A MSE 3.2 7.3 + - - +
297A ALA* 2.9 26.0 + - - +
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Residues in contact with CYS 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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277A ILE* 4.8 0.7 - - - -
279A PRO* 4.7 3.8 - - - -
290A THR* 2.8 37.8 + - - +
291A LYS 3.6 4.5 - - - +
293A ILE* 1.3 73.6 - - - +
295A ALA* 1.3 66.2 + - - +
297A ALA* 3.2 7.0 + - - -
298A GLU* 3.1 7.8 + - - +
304A VAL* 3.8 30.7 - - + -
321A LEU* 4.5 1.8 - - - -
325A ILE* 3.9 26.9 - - + -
327A ASN* 3.1 37.8 + - - +
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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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291A LYS 2.9 14.2 + - - +
292A LYS* 3.2 10.1 + - - +
294A CYS* 1.3 75.8 - - - +
296A MSE 1.3 62.8 + - - +
298A GLU* 3.3 12.7 + - - +
299A ALA 3.7 2.6 + - - -
262E ARG* 3.0 42.1 + - - +
292E LYS* 3.8 34.3 - - + +
296E MSE 4.5 0.8 - - + +
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Residues in contact with MSE 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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262A ARG* 3.8 42.0 - - + +
266A ARG* 4.6 7.9 - - + -
269A PHE* 3.4 35.9 - - + -
292A LYS* 3.0 14.8 + - + +
293A ILE* 3.5 4.9 - - - +
295A ALA* 1.3 73.7 - - - +
297A ALA* 1.3 66.5 + - - +
299A ALA* 2.9 20.3 + - - +
300A TYR* 3.3 15.4 - - + -
292E LYS 5.5 0.4 - - - +
295E ALA* 6.4 0.2 - - + -
296E MSE 3.6 54.5 - - + +
299E ALA* 4.6 9.4 - - + -
300E TYR* 4.7 9.4 - - + +
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Residues in contact with ALA 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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269A PHE* 3.6 16.4 - - + -
277A ILE* 3.7 25.1 - - + -
293A ILE 2.9 13.6 + - - +
294A CYS 3.2 10.5 + - - +
296A MSE 1.3 78.0 - - - +
298A GLU* 1.3 57.1 + - - +
300A TYR* 2.8 19.8 + - - +
302A MSE 3.2 27.0 + - + +
304A VAL* 4.6 0.2 - - + -
327A ASN* 3.8 10.8 - - - +
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Residues in contact with GLU 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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294A CYS 3.1 5.6 + - - +
295A ALA* 3.4 11.9 - - - +
296A MSE 3.1 0.2 - - - -
297A ALA* 1.3 71.5 - - - +
299A ALA* 1.3 60.4 + - - +
300A TYR 3.0 6.0 + - - -
301A ASN 3.3 2.1 + - - -
302A MSE 4.3 2.5 - - - -
326A THR* 2.3 37.8 + - - +
327A ASN* 3.4 32.9 + - + +
174D ARG* 5.7 1.6 - - - +
175D ARG* 2.8 37.0 + - - +
262E ARG* 2.9 28.1 + - - +
263E PHE* 3.7 13.8 - - + -
292E LYS* 5.5 1.0 + - - -
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Residues in contact with ALA 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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295A ALA 3.7 3.2 + - - +
296A MSE 2.9 16.6 + - - +
298A GLU* 1.3 76.9 - - - +
300A TYR* 1.3 65.9 + - + +
301A ASN 3.5 0.4 - - - -
238D ASP* 3.5 7.0 - - - +
262E ARG* 4.5 18.2 - - + +
263E PHE* 3.5 29.5 - - + -
266E ARG* 2.9 30.3 + - + -
296E MSE 4.7 3.8 - - - -
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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