Contacts of the helix formed by residues 250 - 267 (chain A) in PDB entry 4WNF
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A TYR* 3.0 30.7 + - + +
248A LEU* 3.1 29.8 - - - +
249A GLY* 1.3 72.3 - - - +
251A PHE* 1.3 58.7 + - - +
252A GLU 3.5 2.2 - - - -
253A THR* 3.2 23.7 - - - +
254A ALA* 2.9 27.0 + - - +
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Residues in contact with PHE 251 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ILE* 4.6 30.3 - - + -
249A GLY* 2.5 41.5 + - - -
250A GLU* 1.3 69.0 - - - +
252A GLU* 1.3 57.0 + - - +
254A ALA* 3.5 5.4 - - - +
255A SER* 2.6 37.0 + - - -
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Residues in contact with GLU 252 (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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250A GLU 3.5 0.4 - - - -
251A PHE* 1.3 77.0 - - - +
253A THR* 1.3 64.6 + - - +
255A SER* 3.4 17.3 - - - -
256A GLU* 3.4 15.1 + - - +
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Residues in contact with THR 253 (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 TYR* 3.7 35.4 - - + -
250A GLU* 3.2 32.1 + - - +
251A PHE 3.2 0.2 - - - -
252A GLU* 1.3 74.8 - - - +
254A ALA* 1.3 66.2 + - - +
256A GLU* 2.9 18.7 + - - +
257A TYR* 3.2 20.8 + - + -
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Residues in contact with ALA 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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242A GLY* 3.6 21.1 - - - +
245A TYR* 4.2 3.8 - - + +
246A ILE* 3.5 34.8 - - + +
250A GLU 2.9 20.2 + - - +
251A PHE* 3.5 6.5 - - - +
253A THR* 1.3 72.0 - - - +
255A SER* 1.3 64.8 + - - +
256A GLU 3.1 0.2 + - - -
257A TYR* 3.1 3.3 + - - +
258A TYR* 2.8 27.5 + - - +
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Residues in contact with SER 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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251A PHE 2.6 21.5 + - - -
252A GLU* 3.4 12.8 - - - -
254A ALA* 1.3 73.5 - - - +
256A GLU* 1.3 59.4 + - - +
258A TYR* 3.5 6.5 + - - +
259A LYS* 2.9 36.7 + - - +
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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
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252A GLU 3.5 13.7 - - - +
253A THR* 2.9 10.7 + - - +
255A SER* 1.3 76.8 - - - +
257A TYR* 1.3 61.7 + - + +
258A TYR 3.1 1.1 - - - -
259A LYS* 2.9 13.9 + - - +
260A LYS* 2.8 37.6 + - + +
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Residues in contact with TYR 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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219A GLU* 4.4 12.8 + - - +
222A LEU* 5.1 5.0 - - + +
238A TYR* 3.5 52.5 - + - +
241A LEU* 4.3 20.1 - - + +
242A GLY* 4.0 8.3 - - - +
245A TYR* 3.5 39.5 + + - -
253A THR* 3.2 17.3 + - + +
254A ALA 3.1 6.3 + - - +
256A GLU* 1.3 77.7 - - + +
258A TYR* 1.3 55.5 - - - +
260A LYS* 3.4 14.5 + - + +
261A THR* 2.6 32.4 + - - -
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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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238A TYR 5.5 0.4 - - - -
239A SER* 6.1 0.7 - - - +
242A GLY* 4.9 4.8 - - - -
254A ALA 2.8 18.2 + - - +
255A SER* 3.5 6.5 - - - +
257A TYR* 1.3 74.2 - - - +
259A LYS* 1.3 64.6 + - - +
261A THR* 3.0 19.1 + - - -
262A LEU* 3.0 23.8 + - + +
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Residues in contact with LYS 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 SER* 2.9 33.7 + - - +
256A GLU* 2.9 18.8 + - + +
258A TYR* 1.3 74.0 - - - +
260A LYS* 1.3 52.0 + - + +
261A THR 3.2 0.3 + - - -
262A LEU* 3.2 11.0 + - + +
263A LEU* 2.6 39.8 + - + +
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Residues in contact with LYS 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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238A TYR* 3.5 48.5 + - + -
256A GLU* 2.8 25.4 + - + +
257A TYR* 3.5 17.9 - - + +
259A LYS* 1.3 73.4 - - + +
261A THR* 1.3 53.2 + - - +
263A LEU* 3.5 8.1 - - - +
264A LEU* 2.7 35.7 + - - +
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Residues in contact with THR 261 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A ARG* 3.5 37.9 - - + +
238A TYR* 3.3 15.5 - - - +
239A SER* 3.4 20.8 + - - -
257A TYR 2.6 22.7 + - - -
258A TYR* 3.0 12.9 + - - -
260A LYS* 1.3 74.0 - - - +
262A LEU* 1.3 69.5 + - + +
264A LEU* 3.1 13.9 + - - +
265A ALA* 3.3 15.6 + - - +
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Residues in contact with LEU 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 19.0 + - + +
259A LYS* 3.7 8.3 - - - +
261A THR* 1.3 82.2 - - + +
263A LEU* 1.3 62.8 + - - +
264A LEU 3.2 1.0 + - - -
265A ALA* 3.7 3.4 + - - +
266A ARG* 3.5 23.9 + - - +
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A LYS* 2.6 24.1 + - + +
260A LYS* 3.5 11.2 - - - +
262A LEU* 1.3 73.7 - - - +
264A LEU* 1.3 60.4 + - - +
266A ARG* 3.4 18.6 - - - +
267A GLN* 3.5 12.0 - - - +
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Residues in contact with LEU 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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231A LYS* 5.6 2.0 - - + +
234A GLU* 5.7 1.8 - - + -
235A ARG* 4.8 17.0 - - + +
238A TYR* 4.8 10.5 - - + -
260A LYS 2.7 20.6 + - - +
261A THR* 3.1 9.4 + - - +
263A LEU* 1.3 70.2 - - - +
265A ALA* 1.3 57.7 + - - +
266A ARG 3.0 1.6 - - - -
267A GLN* 2.8 37.6 + - - +
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Residues in contact with ALA 265 (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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235A ARG* 4.1 29.6 - - - +
261A THR 3.3 10.1 + - - +
262A LEU* 3.7 4.2 + - - +
264A LEU* 1.3 77.2 - - - +
266A ARG* 1.3 64.4 + - - +
267A GLN 4.6 1.4 - - - -
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Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LEU 3.5 14.6 + - - +
263A LEU* 3.4 15.9 - - - +
264A LEU 3.0 0.2 - - - -
265A ALA* 1.3 81.9 - - - +
267A GLN* 1.3 67.2 + - + +
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Residues in contact with GLN 267 (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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263A LEU 3.5 17.3 - - - +
264A LEU* 2.8 19.9 + - - +
265A ALA 4.6 1.8 - - - -
266A ARG* 1.3 83.0 - - + +
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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