Contacts of the helix formed by residues 255 - 272 (chain A) in PDB entry 1CEC
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 LYS 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A TYR* 3.1 9.4 + - - -
254A ASN* 1.3 76.3 - - - +
256A GLU* 1.3 69.0 + - - +
258A LEU* 3.1 6.3 + - - +
259A ARG* 2.9 43.8 + - - +
298A ASP* 4.0 31.3 + - + +
301A SER* 3.1 28.9 + - - +
302A LEU* 4.2 22.7 - - + +
305A GLU* 5.3 3.2 + - - -
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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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254A ASN* 3.1 22.6 + - - +
255A LYS* 1.3 88.8 + - - +
257A LEU* 1.3 61.5 + - - +
259A ARG* 3.5 18.2 + - - +
260A LYS* 3.0 23.6 + - - +
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Residues in contact with LEU 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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202A PRO* 3.7 18.8 - - + -
251A LEU* 4.1 25.6 - - + -
252A LYS 3.5 19.3 - - - +
253A LEU* 3.7 25.1 - - + -
254A ASN* 3.0 22.8 - - - +
256A GLU* 1.3 79.1 - - - +
258A LEU* 1.3 63.6 + - + +
260A LYS* 3.2 20.1 + - + +
261A ASP* 3.0 36.9 + - - +
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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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199A PHE* 3.7 19.5 - - + -
201A ASN* 3.5 26.5 - - + +
202A PRO* 4.1 11.9 - - + -
225A TYR* 3.5 20.4 - - + +
254A ASN 3.7 12.8 - - - +
255A LYS* 3.1 6.6 + - - +
257A LEU* 1.3 78.4 - - + +
259A ARG* 1.3 65.2 + - - +
261A ASP* 3.2 2.0 + - - -
262A LEU* 3.0 23.6 + - - +
295A TRP* 3.7 19.5 - - + +
298A ASP* 4.0 18.2 - - + -
299A TYR* 4.1 20.0 - - + +
302A LEU* 3.7 12.1 - - + -
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Residues in contact with ARG 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* 2.9 31.9 + - - +
256A GLU* 3.9 19.3 + - - +
258A LEU* 1.3 76.5 - - - +
260A LYS* 1.3 63.6 + - - +
262A LEU* 3.3 5.1 + - - +
263A LYS* 3.1 24.8 + - + +
302A LEU* 3.6 26.4 - - + +
305A GLU* 2.9 33.9 + - - -
306A TYR* 3.1 25.7 + - + +
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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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256A GLU 3.0 14.7 + - - +
257A LEU* 3.4 22.0 - - + +
258A LEU 3.2 0.2 - - - -
259A ARG* 1.3 77.7 - - - +
261A ASP* 1.3 73.8 + - - +
263A LYS* 3.2 22.2 + - + +
264A PRO* 3.7 3.6 - - - +
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Residues in contact with ASP 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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179A PRO* 4.0 17.7 - - - +
199A PHE* 3.7 20.4 - - + -
201A ASN* 3.2 34.5 + - - +
202A PRO* 5.4 0.3 - - - +
257A LEU* 3.0 31.1 + - - +
258A LEU* 3.7 4.1 - - - +
260A LYS* 1.3 91.2 + - - +
262A LEU* 1.3 57.5 + - - +
263A LYS 3.3 0.2 - - - -
264A PRO* 3.3 15.7 - - - +
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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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179A PRO* 5.5 1.1 - - + -
197A PHE* 3.5 38.8 - - + -
199A PHE* 4.2 7.6 - - + -
258A LEU 3.0 13.5 + - - +
259A ARG* 3.7 7.0 - - - +
260A LYS 3.2 0.2 - - - -
261A ASP* 1.3 75.3 - - - +
263A LYS* 1.3 65.9 + - - +
264A PRO* 3.3 2.5 - - - -
265A ALA* 3.1 18.4 + - + +
266A ILE* 3.4 18.3 + - + +
299A TYR* 3.9 18.4 - - + +
302A LEU* 3.9 31.0 - - + -
303A LEU* 4.5 9.0 - - + -
306A TYR* 4.2 18.4 - - + -
308A ILE* 4.9 3.6 - - + -
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Residues in contact with LYS 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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259A ARG* 3.1 15.0 + - + +
260A LYS* 3.3 17.0 - - + +
262A LEU* 1.3 76.5 - - - +
264A PRO* 1.3 66.1 - - + +
266A ILE* 3.1 27.3 + - + +
267A GLU* 2.9 56.7 + - - +
270A GLU* 4.5 10.9 + - - -
306A TYR* 5.5 8.3 + - + +
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Residues in contact with PRO 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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179A PRO* 3.6 20.3 - - + +
180A ASP* 3.8 24.0 - - + +
183A LYS* 6.1 0.4 - - - +
260A LYS 3.7 4.7 - - - +
261A ASP* 3.3 19.1 - - - +
262A LEU 3.3 1.3 - - - -
263A LYS* 1.3 94.8 - - + +
265A ALA* 1.3 60.5 + - - +
267A GLU* 3.5 15.1 + - - +
268A PHE* 3.1 23.2 + - - +
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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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179A PRO* 3.9 20.2 + - + +
182A LEU* 4.3 10.3 - - + -
197A PHE* 4.1 32.5 - - + -
262A LEU* 3.1 12.2 + - + +
264A PRO* 1.3 78.3 - - - +
266A ILE* 1.3 59.8 + - + +
268A PHE* 3.4 3.9 + - - +
269A ARG 3.0 22.7 + - - -
276A LEU* 3.4 19.1 - - + +
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Residues in contact with ILE 266 (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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262A LEU* 3.7 20.0 - - + +
263A LYS* 3.1 31.4 + - + +
265A ALA* 1.3 75.4 - - + +
267A GLU* 1.3 58.8 + - - +
269A ARG* 3.2 18.0 + - - +
270A GLU* 2.9 43.6 + - + +
276A LEU* 4.6 1.3 - - + -
306A TYR* 3.6 56.1 - - + -
308A ILE* 3.8 18.2 - - + -
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Residues in contact with GLU 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 LYS* 2.9 50.6 + - - +
264A PRO* 3.8 12.3 - - - +
266A ILE* 1.3 72.5 - - - +
268A PHE* 1.3 68.6 + - - +
270A GLU* 3.0 24.6 + - - +
271A LYS* 3.1 36.8 + - - +
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Residues in contact with PHE 268 (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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182A LEU* 3.4 43.7 - - + -
183A LYS* 3.8 24.2 - - + +
185A LEU* 5.2 2.7 - - + -
195A TYR* 3.7 36.3 - + + -
264A PRO 3.1 11.3 + - - +
265A ALA* 3.4 8.5 - - - +
267A GLU* 1.3 78.4 - - - +
269A ARG* 1.3 59.6 + - - +
271A LYS* 3.1 10.8 + - + +
272A LYS* 2.9 51.3 + - + +
274A CYS* 3.7 24.2 - - - -
276A LEU* 4.2 4.3 - - + -
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Residues in contact with ARG 269 (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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265A ALA 3.0 14.0 + - - +
266A ILE* 3.6 19.0 + - - +
268A PHE* 1.3 76.4 - - - +
270A GLU* 1.3 59.3 + - - +
273A LYS* 2.7 35.4 + - - -
274A CYS* 3.1 40.8 - - - +
275A LYS* 5.0 0.4 - - - +
276A LEU* 3.7 27.0 - - + +
306A TYR* 2.7 48.1 + - - +
307A ASP* 3.6 14.5 + - - +
308A ILE* 3.9 8.2 - - - +
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Residues in contact with GLU 270 (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 LYS* 4.5 11.5 + - - -
266A ILE* 2.9 30.4 + - + +
267A GLU* 3.0 19.6 + - - +
269A ARG* 1.3 78.9 - - - +
271A LYS* 1.3 63.9 + - + +
273A LYS* 4.0 11.3 - - - +
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Residues in contact with LYS 271 (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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267A GLU* 3.1 40.2 + - - +
268A PHE* 3.7 8.9 - - + +
270A GLU* 1.3 82.8 - - + +
272A LYS* 1.3 63.6 + - + +
273A LYS* 3.5 6.8 + - - +
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Residues in contact with LYS 272 (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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186A ALA 5.5 0.9 - - - -
187A ASP* 3.3 28.2 + - - +
188A ILE 3.4 35.2 + - - +
189A ASP* 5.2 0.8 - - - +
195A TYR* 3.8 22.2 + - + +
268A PHE* 2.9 39.3 + - + +
271A LYS* 1.3 73.1 - - + +
273A LYS* 1.3 69.9 + - - +
274A CYS* 3.2 18.1 + - + +
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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