Contacts of the helix formed by residues 253 - 262 (chain A) in PDB entry 1Z59
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 THR 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ASP 5.1 0.4 - - - +
252A TYR* 1.3 77.0 - - - +
254A ILE* 1.3 66.3 + - - +
255A LYS* 4.1 1.9 - - - +
256A GLU* 3.0 37.5 + - - +
257A PHE* 2.8 21.1 + - - +
281A PRO 3.3 16.2 + - - -
282A ASN* 3.5 30.0 + - + +
283A LYS 3.2 9.2 - - - -
284A LYS* 4.2 13.2 - - - +
285A VAL* 4.3 1.3 - - - -
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Residues in contact with ILE 254 (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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252A TYR 4.0 0.4 + - - -
253A THR* 1.3 70.5 - - - +
255A LYS* 1.3 63.3 + - - +
257A PHE* 3.2 10.9 + - + +
258A LEU* 3.0 31.8 + - + +
274A LEU* 3.6 19.5 - - + -
279A LEU* 4.1 25.1 - - + -
280A LYS 3.2 25.6 - - - +
281A PRO 3.8 0.2 + - - -
283A LYS* 2.9 36.5 + - + +
284A LYS 4.6 0.2 - - - -
285A VAL* 4.1 17.8 - - + +
288A LEU* 3.6 32.5 - - + -
292A GLU* 5.4 0.2 - - - +
296A LEU* 5.8 1.3 - - + -
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Residues in contact with LYS 255 (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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253A THR* 3.2 3.5 - - - +
254A ILE* 1.3 78.4 - - - +
256A GLU* 1.3 66.7 + - + +
258A LEU* 3.0 14.8 + - - +
259A VAL* 3.2 25.9 + - + +
267A ASP* 2.5 39.7 + - - +
270A ALA* 4.3 8.0 - - + +
271A ASP* 3.3 28.6 + - - +
274A LEU* 3.8 23.9 - - + +
281A PRO* 3.3 26.2 + - + +
282A ASN* 5.5 1.3 - - - +
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ASP 4.2 2.9 - - - +
252A TYR* 3.4 26.2 - - + -
253A THR* 3.0 42.6 + - - +
255A LYS* 1.3 81.1 - - + +
257A PHE* 1.3 61.6 + - - +
259A VAL* 4.7 2.9 - - - -
260A ASN* 2.9 42.0 + - - +
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Residues in contact with PHE 257 (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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241A ILE* 4.5 12.3 - - + -
244A LEU* 4.2 20.4 - - + -
245A ILE* 4.0 25.6 - - + -
248A LEU* 4.1 16.8 - - + -
252A TYR* 3.8 11.1 - - + -
253A THR 2.8 12.2 + - - +
254A ILE* 3.3 10.1 - - + +
256A GLU* 1.3 76.3 - - - +
258A LEU* 1.3 75.4 + - + +
261A GLU* 3.0 55.0 + - + +
262A PHE* 3.5 31.0 - + - -
285A VAL* 3.8 27.6 - - + -
288A LEU* 5.8 1.3 - - + -
296A LEU* 4.8 5.8 - - + -
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Residues in contact with LEU 258 (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 ILE* 3.0 19.2 + - + +
255A LYS 3.0 6.2 + - - +
257A PHE* 1.3 91.2 - - + +
259A VAL* 1.3 61.5 + - - +
262A PHE* 3.6 22.2 + - + -
265A ILE* 3.6 27.4 - - + +
270A ALA* 4.2 7.9 - - + +
273A ILE* 3.7 28.3 - - + -
274A LEU* 4.0 29.2 - - + -
296A LEU* 4.1 19.7 - - + -
300A PHE* 4.0 27.1 - - + -
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Residues in contact with VAL 259 (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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255A LYS* 3.2 30.4 + - + +
256A GLU* 4.7 1.6 - - - -
258A LEU* 1.3 77.3 - - - +
260A ASN* 1.3 82.0 + - - +
261A GLU 3.6 0.2 - - - -
262A PHE 3.9 9.7 - - - +
265A ILE 3.4 23.0 - - - +
266A GLY* 4.5 7.9 - - - +
267A ASP* 4.8 2.7 - - - +
270A ALA* 3.8 20.9 - - + -
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Residues in contact with ASN 260 (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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230A LYS* 4.2 15.8 - - - +
252A TYR* 3.9 28.1 + - + +
256A GLU* 2.9 36.8 + - - +
259A VAL* 1.3 95.4 - - - +
261A GLU* 1.3 66.5 + - - +
262A PHE 3.6 1.5 + - - +
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Residues in contact with GLU 261 (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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230A LYS* 3.8 15.6 - - - +
231A PRO* 3.3 23.7 - - - +
244A LEU* 4.1 25.1 - - + +
248A LEU* 3.9 20.8 - - + +
252A TYR* 4.1 14.2 + - + -
257A PHE* 3.0 45.0 + - + +
260A ASN* 1.3 82.3 - - - +
262A PHE* 1.3 69.8 + - + +
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Residues in contact with PHE 262 (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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230A LYS* 3.8 10.4 - - - +
231A PRO* 3.5 17.7 - - + +
233A PRO* 4.5 9.6 - - + -
236A VAL* 4.0 16.6 - - + -
241A ILE* 3.7 22.4 - - + -
244A LEU* 4.1 15.9 - - + -
257A PHE* 3.5 38.8 - + - -
258A LEU* 3.6 30.3 + - + +
259A VAL 3.9 12.8 - - - +
260A ASN 3.6 0.7 - - - -
261A GLU* 1.3 84.7 - - + +
263A GLN* 1.3 69.8 + - - +
264A SER 4.1 0.5 + - - -
265A ILE* 3.9 16.5 + - + +
300A PHE* 3.9 21.1 - + - -
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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