Contacts of the helix formed by residues 253 - 264 (chain A) in PDB entry 3JW8
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 ASP 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A VAL* 5.5 0.9 - - - +
160A LEU* 3.9 20.6 + - + +
161A ALA 5.5 0.2 - - - +
162A ASN* 5.7 1.0 - - - +
163A PRO* 3.7 34.7 - - + +
245A GLN* 4.4 1.0 + - - -
249A ASP 3.8 13.6 - - - +
250A ARG 5.2 0.6 - - - -
251A LEU 3.8 3.0 + - - -
252A CYS* 1.3 74.8 - - - +
254A SER* 1.3 70.2 + - - +
255A LYS* 3.0 34.9 + - - +
256A GLY* 3.0 16.5 + - - -
257A ALA 4.1 1.7 + - - -
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Residues in contact with SER 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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245A GLN* 3.6 19.2 - - - +
246A GLY 3.8 19.0 + - - -
247A SER* 4.3 17.3 + - - -
249A ASP 4.6 3.2 + - - -
252A CYS 3.4 3.0 + - - -
253A ASP* 1.3 75.8 + - - +
255A LYS* 1.4 63.4 + - - +
257A ALA* 2.9 16.3 + - - +
258A TYR* 3.3 27.8 - - - -
273A ILE* 4.9 2.0 - - - -
262B GLU* 5.5 3.3 + - - +
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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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160A LEU* 3.8 23.6 - - + -
253A ASP* 3.0 18.4 + - - +
254A SER* 1.4 77.5 + - - +
256A GLY* 1.3 62.0 + - - +
258A TYR* 3.2 13.5 + - - +
259A LEU* 3.0 22.6 + - + +
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Residues in contact with GLY 256 (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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159A VAL* 3.3 32.0 - - - +
160A LEU* 3.8 21.4 - - - +
253A ASP 3.0 11.3 + - - -
255A LYS* 1.3 78.5 - - - +
257A ALA* 1.3 56.9 + - - +
259A LEU* 3.3 5.9 + - - +
260A LEU* 2.9 25.6 + - - +
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Residues in contact with ALA 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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157A PRO* 5.9 0.7 - - + -
159A VAL* 4.0 3.0 - - - +
243A LEU* 3.3 32.0 - - + +
245A GLN* 3.6 37.6 + - + +
253A ASP 4.1 1.2 + - - -
254A SER 2.9 12.7 + - - +
256A GLY* 1.3 77.0 - - - +
258A TYR* 1.4 61.0 + - + +
260A LEU* 3.4 1.9 + - - -
261A MSE 3.2 21.3 + - - +
271A LEU* 4.3 6.7 - - + -
273A ILE* 5.1 2.5 - - + -
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Residues in contact with TYR 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 SER* 3.3 42.3 + - - -
255A LYS* 3.2 11.1 + - - +
257A ALA* 1.4 72.7 - - - +
259A LEU* 1.3 65.2 + - - +
261A MSE 3.3 8.3 + - - +
262A GLU* 3.0 24.0 + - - +
271A LEU* 3.8 21.8 - - + -
273A ILE* 3.4 27.8 - - + +
258B TYR* 3.7 36.2 - + + -
261B MSE 3.6 15.3 + - + -
262B GLU* 3.4 41.4 + - + +
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Residues in contact with LEU 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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159A VAL* 5.2 9.9 - - + +
160A LEU* 4.4 21.5 - - + -
231A GLU* 5.3 10.3 - - + -
234A LEU* 4.5 10.1 - - + -
255A LYS* 3.0 15.7 + - + +
256A GLY* 3.5 9.6 - - - +
258A TYR* 1.3 78.0 - - - +
260A LEU* 1.3 56.8 + - - +
262A GLU* 3.2 11.5 + - - +
263A LEU* 2.9 65.5 + - + +
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Residues in contact with LEU 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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139A ILE* 4.3 4.3 - - + -
154A LEU* 3.7 28.0 - - + -
157A PRO* 4.3 0.9 - - + -
159A VAL* 4.2 21.3 - - + +
234A LEU* 3.4 37.9 - - + +
237A LEU* 4.0 16.8 - - + -
241A PHE* 4.1 9.4 - - + -
243A LEU* 3.8 23.8 - - + -
256A GLY 2.9 15.9 + - - +
257A ALA* 3.6 5.6 - - - +
258A TYR 3.4 0.2 - - - -
259A LEU* 1.3 77.4 - - - +
261A MSE 1.3 60.9 + - - +
264A ALA* 3.1 33.2 + - + +
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Residues in contact with MSE 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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241A PHE* 4.0 20.0 - - - -
243A LEU* 3.9 4.3 - - + -
257A ALA 3.2 16.7 + - - +
258A TYR* 3.3 8.0 + - - +
260A LEU* 1.3 75.6 - - - +
262A GLU* 1.3 55.7 + - - +
269A LYS* 2.6 57.7 + - + +
270A THR 3.9 10.8 - - - -
271A LEU* 3.7 34.1 - - + +
258B TYR* 3.6 18.1 + - + +
271B LEU* 3.6 26.2 - - + +
273B ILE* 3.7 28.6 - - + +
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Residues in contact with GLU 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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258A TYR 3.0 15.2 + - - +
259A LEU* 3.8 13.4 - - - +
260A LEU 3.2 0.2 - - - -
261A MSE 1.3 81.2 - - - +
263A LEU* 1.3 74.5 + - + +
265A LYS* 5.2 1.0 + - - -
269A LYS* 4.0 5.6 + - - -
247B SER* 5.8 2.2 - - - -
254B SER* 5.3 1.9 + - - +
255B LYS* 3.6 27.6 + - - -
258B TYR* 3.4 24.9 - - + +
273B ILE* 5.9 0.4 - - - -
275B GLU* 4.1 9.9 - - - +
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Residues in contact with LEU 263 (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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231A GLU* 5.3 11.7 - - + +
234A LEU* 3.5 31.2 - - + +
235A PRO* 3.9 8.9 - - + +
259A LEU* 2.9 50.7 + - + +
262A GLU* 1.3 86.3 - - + +
264A ALA* 1.3 66.6 + - - +
265A LYS* 3.0 24.4 + - - +
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Residues in contact with ALA 264 (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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234A LEU* 3.6 12.5 - - + +
237A LEU* 4.2 10.3 - - + +
241A PHE* 3.7 29.4 - - + -
260A LEU* 3.1 28.5 + - + +
263A LEU* 1.3 78.7 - - - +
265A LYS* 1.4 59.8 + - - +
266A SER* 3.3 3.1 - - - +
269A LYS* 2.7 30.3 + - + -
275B GLU* 3.7 4.9 - - - +
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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