Contacts of the helix formed by residues 286 - 299 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D SER* 3.1 13.0 + - - -
97D GLU* 3.2 12.6 - - - -
98D GLN* 4.8 0.9 - - - -
281D ILE* 3.4 19.3 + - - -
285D GLY* 1.3 80.6 - - - +
287D LEU* 1.3 60.2 + - - -
288D MSE 3.5 1.8 - - - -
289D GLU 4.1 0.9 - - - -
290D THR* 2.8 30.5 + - - -
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLU* 2.7 15.5 + - - +
98D GLN* 4.6 9.6 - - + +
101D TRP* 4.4 9.2 - - + -
112D VAL* 4.1 19.7 - - + -
116D PHE* 3.8 15.0 - - + -
281D ILE* 4.0 19.9 - - + +
286D GLY* 1.3 69.1 - - - +
288D MSE 1.3 58.7 + - - +
290D THR* 3.3 5.2 + - - -
291D LYS* 2.8 27.4 + - - +
317D ALA* 3.4 24.2 - - + +
320D GLN* 4.5 3.4 - - + -
321D LEU* 3.9 28.5 - - + +
366D LEU* 3.7 30.1 - - + -
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Residues in contact with MSE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ILE* 6.0 0.4 - - + -
69D GLU* 3.6 13.0 - - - +
97D GLU* 2.8 17.6 + - - +
101D TRP* 3.8 26.5 - - + +
116D PHE* 3.4 37.8 - - + -
287D LEU* 1.3 72.0 - - - +
289D GLU* 1.3 61.8 + - - +
291D LYS* 3.1 22.3 + - + +
292D LYS* 2.8 62.8 + - - +
115G LEU 4.8 0.7 - - - +
116G PHE* 4.2 13.2 - - - +
288G MSE 4.8 11.4 - - + +
291G LYS* 4.3 10.8 - - - -
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Residues in contact with GLU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D TRP* 3.5 23.1 - - + +
97D GLU* 3.9 2.2 + - - -
261D THR* 3.5 6.6 - - - -
262D ARG* 2.8 66.2 + - - +
263D PHE* 5.7 0.3 - - - -
284D ALA 3.4 24.0 - - - +
285D GLY* 3.7 26.7 - - - +
286D GLY 3.8 0.2 + - - -
287D LEU 3.3 0.4 - - - -
288D MSE 1.3 77.3 - - - +
290D THR* 1.3 58.4 + - - +
292D LYS* 3.2 12.8 + - - +
293D ILE* 2.9 31.8 + - + +
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Residues in contact with THR 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D PRO* 3.9 26.0 - - + +
281D ILE* 3.6 17.6 - - + -
284D ALA* 3.6 20.3 - - - +
286D GLY 2.8 24.3 + - - -
287D LEU 3.7 3.8 - - - -
289D GLU* 1.3 72.3 - - - +
291D LYS* 1.3 65.9 + - - +
293D ILE* 3.2 9.3 + - - +
294D CYS* 2.9 24.0 + - - -
321D LEU* 3.4 29.2 - - + -
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Residues in contact with LYS 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D PHE* 3.3 50.0 + - + -
287D LEU 2.8 14.5 + - - +
288D MSE 3.1 21.7 + - - +
290D THR* 1.3 75.4 - - - +
292D LYS* 1.3 58.2 + - + +
294D CYS* 3.3 5.8 + - - +
295D ALA* 3.0 27.9 + - - +
321D LEU* 3.9 13.2 - - + +
324D ASN* 2.7 23.9 + - - +
325D ILE* 4.8 7.7 - - + +
69G GLU* 3.5 18.6 + - - -
288G MSE 3.6 24.2 - - - -
292G LYS* 4.3 9.8 - - - +
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Residues in contact with LYS 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU* 3.2 32.2 + - - -
72D TRP* 6.4 0.2 - - - -
262D ARG* 3.8 38.7 - - - +
288D MSE 2.8 42.1 + - + +
289D GLU* 3.4 13.3 + - - +
291D LYS* 1.3 77.7 - - + +
293D ILE* 1.3 60.2 + - - +
295D ALA* 3.5 7.2 + - - +
296D MSE 3.1 28.3 + - - +
291G LYS* 4.2 11.6 - - - +
292G LYS* 5.8 7.2 - - + +
295G ALA* 3.7 28.2 - - + +
298G GLU* 5.0 3.6 + - - -
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Residues in contact with ILE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D THR* 3.7 18.8 - - - -
262D ARG* 3.9 19.7 - - + +
265D PHE* 3.6 49.6 - - + -
269D PHE* 3.6 2.0 - - + -
277D ILE* 3.8 17.5 - - + -
279D PRO* 4.8 4.9 - - + -
284D ALA* 4.0 17.7 - - + +
289D GLU 2.9 20.3 + - - +
290D THR* 3.2 11.0 + - + +
292D LYS* 1.3 76.3 - - - +
294D CYS* 1.3 59.8 + - - +
296D MSE 3.2 10.0 + - - +
297D ALA* 2.9 25.5 + - - +
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Residues in contact with CYS 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D ILE* 4.6 0.7 - - - -
279D PRO* 4.5 4.7 - - - -
290D THR* 2.9 39.0 + - - +
291D LYS 3.3 4.9 + - - +
293D ILE* 1.3 77.4 - - - +
295D ALA* 1.3 62.2 + - - +
297D ALA* 3.2 6.8 + - - -
298D GLU* 3.2 9.4 + - - +
304D VAL* 3.7 31.2 - - + -
321D LEU* 4.5 1.1 - - - -
325D ILE* 3.9 25.1 - - + -
327D ASN* 3.0 36.9 + - - +
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D LYS* 3.0 17.7 + - + +
292D LYS* 3.7 6.7 - - - +
293D ILE 3.3 0.2 - - - -
294D CYS* 1.3 73.6 - - - +
296D MSE 1.3 66.7 + - + +
298D GLU* 3.4 12.0 + - - +
299D ALA 3.8 1.9 + - - -
262G ARG* 2.9 43.3 + - - +
292G LYS* 3.8 33.4 - - + +
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Residues in contact with MSE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ARG* 3.2 55.6 - - + +
265D PHE* 4.3 0.9 - - + -
266D ARG* 5.5 2.7 - - - -
269D PHE* 3.4 31.6 - - + -
292D LYS 3.1 16.1 + - - +
293D ILE* 3.2 14.3 + - + +
295D ALA* 1.3 74.5 - - - +
297D ALA* 1.3 63.1 + - - +
299D ALA* 2.9 26.6 + - - +
300D TYR* 3.4 11.2 - - + -
295G ALA* 6.3 0.2 - - + -
296G MSE 3.4 46.4 - - + +
299G ALA* 4.8 6.7 - - - -
300G TYR* 5.9 3.1 - - - -
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D PHE* 3.7 17.9 - - + -
277D ILE* 3.6 25.6 - - + -
293D ILE 2.9 13.9 + - - +
294D CYS 3.3 10.5 - - - +
296D MSE 1.3 77.6 - - - +
298D GLU* 1.3 56.3 + - - +
300D TYR* 2.9 17.9 + - - +
302D MSE 3.2 26.7 + - + +
327D ASN* 3.7 11.7 - - - +
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Residues in contact with GLU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ARG* 2.8 35.9 + - - +
294D CYS 3.2 14.9 + - - +
295D ALA* 3.5 11.7 - - - +
296D MSE 3.1 0.8 - - - -
297D ALA* 1.3 76.0 - - - +
299D ALA* 1.3 61.3 + - - +
300D TYR 3.0 1.3 + - - -
301D ASN 3.3 2.3 + - - -
302D MSE 4.4 2.7 - - - -
326D THR* 2.7 32.8 + - - +
327D ASN* 3.5 23.6 - - + +
262G ARG* 2.8 29.8 + - - +
263G PHE* 3.6 14.3 - - + -
292G LYS* 4.8 4.7 + - - -
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Residues in contact with ALA 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ASP* 3.5 5.9 - - - +
295D ALA 3.8 0.8 + - - +
296D MSE 2.9 16.1 + - - +
298D GLU* 1.3 79.0 - - - +
300D TYR* 1.3 66.8 + - + +
301D ASN 3.5 0.7 - - - -
262G ARG* 4.5 17.7 - - + +
263G PHE* 3.5 26.9 - - + -
266G ARG* 2.8 33.7 + - + -
296G MSE 4.9 4.0 - - - -
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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