Contacts of the helix formed by residues 287 - 300 (chain D) in PDB entry 1Z6T
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 287 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283D GLU* 5.1 3.6 + - - -
285D SER* 3.8 3.1 + - - -
286D LEU* 1.3 82.3 - - - +
288D LYS* 1.3 65.7 + - - -
289D GLU 3.3 2.9 - - - -
290D LYS* 3.3 7.7 + - - +
291D GLY* 3.0 19.9 + - - -
314D ILE* 5.3 0.6 - - - +
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Residues in contact with LYS 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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286D LEU 3.9 0.6 + - - -
287D GLY* 1.3 71.3 - - - -
289D GLU* 1.3 69.6 + - + +
291D GLY* 3.3 1.6 + - - -
292D LEU* 2.9 37.1 + - + +
314D ILE* 3.9 23.6 - - + +
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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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287D GLY 3.3 0.8 - - - -
288D LYS* 1.3 90.1 - - + +
290D LYS* 1.3 60.8 + - + +
292D LEU* 3.4 19.7 + - - +
293D GLU* 2.9 27.9 + - - +
303D LYS* 3.1 44.7 + - - +
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Residues in contact with LYS 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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127D VAL* 3.8 11.8 - - + +
128D THR* 2.8 51.5 + - - +
129D ARG* 5.4 1.8 - - + +
286D LEU* 3.6 30.5 - - + -
287D GLY* 3.3 7.2 + - - +
289D GLU* 1.3 76.7 - - + +
291D GLY* 1.3 59.9 + - - +
293D GLU* 2.7 31.2 + - - +
294D ILE* 3.0 32.2 + - - +
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Residues in contact with GLY 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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286D LEU* 3.8 13.5 - - - +
287D GLY 3.0 14.2 + - - -
288D LYS 3.7 3.4 - - - -
290D LYS* 1.3 74.5 - - - +
292D LEU* 1.3 62.7 + - - +
294D ILE* 3.1 5.8 + - - +
295D LEU 3.1 17.3 + - - -
314D ILE* 3.5 20.1 - - - +
324D VAL* 3.5 16.6 - - - +
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Residues in contact with LEU 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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288D LYS* 2.9 20.5 + - + +
289D GLU* 3.5 34.1 - - - +
291D GLY* 1.3 74.6 - - - +
293D GLU* 1.3 57.4 + - - +
295D LEU* 3.2 7.1 + - + +
296D SER* 2.9 28.9 + - - -
303D LYS* 3.8 15.5 - - + +
306D LEU* 3.7 21.5 - - + +
310D ALA* 3.9 12.1 - - + -
311D HIS* 3.6 35.4 - - + +
314D ILE* 3.8 19.6 - - + +
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Residues in contact with GLU 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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126D PHE 5.2 0.2 - - - +
127D VAL* 3.7 19.3 - - + +
128D THR* 5.1 1.0 + - - -
289D GLU 2.9 15.9 + - - +
290D LYS* 2.7 45.7 + - - +
291D GLY 3.2 0.4 - - - -
292D LEU* 1.3 74.7 - - - +
294D ILE* 1.3 64.2 + - - +
296D SER* 2.7 26.5 + - - +
297D LEU* 3.1 21.9 + - + +
303D LYS* 4.0 18.5 + - - +
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Residues in contact with ILE 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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125D VAL* 3.8 7.4 - - + +
127D VAL* 3.5 23.3 - - + -
286D LEU* 3.4 32.8 - - + -
290D LYS 3.0 13.7 + - - +
291D GLY 3.1 7.2 + - - +
293D GLU* 1.3 75.7 - - - +
295D LEU* 1.3 61.2 + - - +
297D LEU* 3.3 4.2 + - - +
298D PHE* 3.1 46.9 + - + -
321D PRO* 4.4 10.3 - - + +
324D VAL* 3.9 18.2 - - + +
325D SER* 3.8 10.5 - - - +
903D ADP 3.9 24.9 - - + +
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Residues in contact with LEU 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 GLY 3.1 14.3 + - - +
292D LEU* 3.5 9.0 - - + +
294D ILE* 1.3 77.6 - - - +
296D SER* 1.3 57.2 + - - +
298D PHE* 3.2 6.5 + - - +
299D VAL* 2.9 34.8 + - + +
306D LEU* 4.5 5.4 - - + -
310D ALA* 4.0 19.7 - - + +
313D ILE* 4.4 8.7 - - + -
314D ILE* 3.7 22.9 - - + -
324D VAL* 3.8 13.5 - - + +
327D ILE* 4.5 5.2 - - + -
328D GLY* 3.6 31.2 - - - +
331D LEU* 4.1 9.2 - - + -
338D TRP* 4.1 24.9 - - + -
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Residues in contact with SER 296 (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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292D LEU 2.9 13.4 + - - -
293D GLU* 2.7 28.4 + - - +
295D LEU* 1.3 74.8 - - - +
297D LEU* 1.3 62.5 + - - +
299D VAL* 3.9 7.9 - - - -
300D ASN* 2.8 24.6 + - - -
301D MET 3.0 31.4 + - - +
303D LYS* 4.1 21.3 + - - +
306D LEU* 4.0 7.8 - - - +
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Residues in contact with LEU 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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125D VAL* 3.6 25.7 - - + +
126D PHE 3.6 25.1 - - - +
127D VAL* 3.8 19.5 - - + -
293D GLU* 3.1 20.9 + - + +
294D ILE 3.7 0.2 - - - +
295D LEU 3.2 0.4 - - - -
296D SER* 1.3 83.5 + - - +
298D PHE* 1.3 67.7 + - - +
300D ASN* 3.6 9.5 + - - +
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Residues in contact with PHE 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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124D VAL* 3.7 26.7 - - + -
125D VAL* 3.6 27.6 - - + -
294D ILE* 3.1 32.4 + - + -
295D LEU 3.6 7.0 - - - +
297D LEU* 1.3 78.7 - - - +
299D VAL* 1.3 60.0 + - - +
300D ASN* 3.6 2.3 + - - +
325D SER* 3.4 36.8 - - - -
328D GLY* 3.4 25.6 - - - +
329D ALA* 3.5 30.1 - - + -
332D ARG* 3.2 48.6 - - - +
420D ASN 4.5 1.1 - - - -
422D SER* 4.2 2.5 - - - -
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Residues in contact with VAL 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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295D LEU 2.9 23.2 + - - +
296D SER 3.8 1.8 - - - +
298D PHE* 1.3 77.1 - - - +
300D ASN* 1.3 73.5 + - - +
301D MET* 3.3 40.6 - - + +
306D LEU* 3.7 17.5 - - + -
328D GLY* 4.1 3.8 - - - +
331D LEU* 3.8 32.8 - - + +
332D ARG* 3.9 14.1 - - - +
338D TRP* 4.0 10.3 - - + -
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Residues in contact with ASN 300 (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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296D SER 2.8 10.8 + - - -
297D LEU* 3.6 7.5 + - - +
298D PHE 3.3 4.8 - - - +
299D VAL* 1.3 82.5 - - - +
301D MET* 1.3 57.8 + - - +
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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