Contacts of the helix formed by residues 293 - 305 (chain B) in PDB entry 1ZOO
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 GLU 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B LYS* 4.2 15.7 - - - +
291B THR* 2.8 30.7 + - - +
292B PHE* 1.3 75.8 - - - +
294B LYS* 1.3 81.5 + - - +
296B LYS* 3.0 42.2 + - + +
297B ASP* 3.4 6.1 - - - +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 3.8 22.5 - - + +
290B ASP* 2.8 47.2 + - - +
291B THR* 3.1 18.6 + - - +
292B PHE 3.0 0.6 - - - -
293B GLU* 1.3 97.4 - - - +
295B LEU* 1.3 54.2 + - - +
296B LYS 3.0 5.8 - - - -
297B ASP* 2.9 31.0 + - + +
298B LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS* 3.6 26.2 - - + +
150B ILE* 3.8 19.3 - - + +
153B PHE* 3.6 40.2 - - + -
156B ASP* 5.7 0.2 - - - +
237B ILE* 4.7 3.6 - - + -
259B ILE* 4.4 6.5 - - + -
261B ILE* 4.0 24.2 - - + -
289B LEU* 3.7 23.2 - - + +
292B PHE* 3.0 20.9 + - + +
294B LYS* 1.3 77.1 - - - +
296B LYS* 1.3 63.2 + - + +
298B LEU* 3.9 9.1 - - + +
299B PHE* 3.1 24.3 + - - +
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Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS* 4.7 26.3 - - + +
156B ASP* 5.9 2.9 - - - +
292B PHE 5.1 1.8 - - - +
293B GLU* 3.0 24.5 + - + +
295B LEU* 1.3 79.4 - - + +
297B ASP* 1.3 65.0 + - - +
299B PHE* 3.5 7.5 + - - +
300B THR* 3.1 25.2 + - - -
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 5.9 0.7 - - + -
293B GLU* 3.4 11.1 - - - +
294B LYS* 2.9 44.5 + - + +
296B LYS* 1.3 76.9 - - - +
298B LEU* 1.3 65.4 + - - +
300B THR* 2.9 11.8 + - - -
301B GLU* 2.9 36.0 + - + +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B PHE* 4.0 16.2 - - + -
259B ILE* 3.5 35.2 - - + -
287B LYS* 4.5 28.9 - - + -
289B LEU* 4.2 24.5 - - + -
294B LYS 2.9 16.6 + - - +
295B LEU* 3.9 8.1 - - + +
297B ASP* 1.3 73.9 - - - +
299B PHE* 1.3 56.1 + - - +
301B GLU* 3.3 25.3 + - + +
302B LEU* 2.9 32.4 + - + +
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B PHE* 4.1 9.1 - - + -
156B ASP* 3.4 61.5 - - + +
157B VAL* 3.9 11.0 - - + -
160B LYS* 4.1 8.5 - - + -
295B LEU 3.1 18.1 + - - +
296B LYS* 3.8 7.4 - - - +
297B ASP 3.2 0.2 - - - -
298B LEU* 1.3 72.5 - - - +
300B THR* 1.3 67.3 + - - +
302B LEU* 3.4 22.7 - - + +
303B GLN* 3.2 66.8 + - + +
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LYS 3.1 14.9 + - - -
297B ASP* 2.9 13.4 + - - -
299B PHE* 1.3 79.0 - - - +
301B GLU* 1.3 65.9 + - + +
303B GLN* 3.5 12.7 + - - -
304B LYS* 2.7 42.6 + - - +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 5.4 4.0 - - - +
297B ASP* 2.9 21.3 + - + +
298B LEU* 3.3 39.6 + - + +
300B THR* 1.3 79.0 - - + +
302B LEU* 1.3 62.7 + - - +
304B LYS* 3.1 26.5 + - - +
305B LYS* 4.0 8.1 + - - +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A VAL* 3.9 29.0 - - + +
153B PHE* 3.8 24.9 - - + -
157B VAL* 4.2 14.4 - - + -
160B LYS* 6.3 0.4 - - + -
161B LEU* 6.0 1.3 - - + -
298B LEU* 2.9 18.8 + - + +
299B PHE* 3.4 42.6 - - + +
301B GLU* 1.3 73.9 - - - +
303B GLN* 1.3 62.6 + - + +
305B LYS* 3.0 33.0 + - - +
306B ILE* 3.8 6.0 + - + +
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Residues in contact with GLN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ASN* 3.2 41.4 + - - +
164A THR* 3.3 19.5 - - + +
160B LYS* 3.3 32.1 - - + +
299B PHE* 3.2 55.5 + - + +
300B THR* 3.7 11.8 + - - +
301B GLU 3.2 0.8 - - - -
302B LEU* 1.3 73.3 - - + +
304B LYS* 1.3 57.1 + - - +
305B LYS 2.9 10.2 + - - -
306B ILE* 3.0 32.6 + - + +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ASN* 2.5 37.7 + - - +
164A THR 3.5 19.1 - - - +
165A SER* 2.6 36.8 + - - +
300B THR* 2.7 47.0 + - + +
301B GLU* 3.1 14.8 + - - +
303B GLN* 1.3 77.5 - - - +
305B LYS* 1.3 65.5 + - + +
306B ILE 3.4 0.9 - - - -
307B TYR* 3.4 9.5 + - - -
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY* 6.3 1.0 - - - -
307A TYR 3.3 1.9 - - - +
308A VAL* 3.3 6.1 - - + -
309A ILE* 2.9 46.1 + - + +
310A GLU 5.8 4.0 - - - -
301B GLU 4.2 9.9 - - - +
302B LEU* 3.0 17.8 + - - +
303B GLN 2.9 1.4 - - - -
304B LYS* 1.3 88.9 - - - +
306B ILE* 1.3 57.3 + - - +
307B TYR* 3.4 23.8 + - + +
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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