Contacts of the helix formed by residues 255 - 272 (chain A) in PDB entry 4Y5U
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 ALA 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ARG* 1.3 80.2 - - - +
256A SER* 1.3 68.1 + - - +
257A LEU 3.1 0.9 - - - -
258A THR* 3.0 14.1 + - - +
259A GLY* 3.3 8.1 + - - -
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Residues in contact with SER 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ARG 3.5 14.0 + - - -
255A ALA* 1.3 77.1 - - - +
257A LEU* 1.3 68.1 + - - +
259A GLY* 2.9 5.9 + - - -
260A ARG* 2.6 41.0 + - - +
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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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184A GLN* 3.5 38.4 - - + +
187A THR* 4.6 12.1 - - + -
242A VAL* 5.2 16.2 - - + -
254A ARG* 4.3 18.8 - - + +
255A ALA 3.1 0.2 - - - -
256A SER* 1.3 89.3 - - - +
258A THR* 1.3 60.1 + - - +
260A ARG* 3.4 28.9 - - - +
261A LEU* 2.8 39.2 + - + +
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Residues in contact with THR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLN* 3.1 31.4 - - - +
242A VAL* 4.5 12.1 - - + +
254A ARG* 2.9 25.0 + - - +
255A ALA* 3.0 15.0 - - - +
257A LEU* 1.3 75.1 - - - +
259A GLY* 1.3 55.2 + - - -
261A LEU* 3.8 0.9 - - - +
262A ASP* 2.9 35.6 + - - +
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Residues in contact with GLY 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 ALA 3.3 7.9 + - - -
256A SER 2.9 7.6 + - - -
258A THR* 1.3 78.6 - - - +
260A ARG* 1.3 54.5 + - - +
262A ASP* 3.4 6.9 - - - +
263A GLU* 2.6 34.5 + - - +
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Residues in contact with ARG 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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184A GLN 4.8 3.4 + - - -
185A GLU 4.9 2.6 - - - +
187A THR* 2.3 35.8 + - - -
188A GLY* 4.0 10.3 - - - +
191A GLU* 3.3 38.8 + - - +
256A SER* 2.6 20.8 + - - +
257A LEU* 3.4 29.8 - - + +
259A GLY* 1.3 73.4 - - - +
261A LEU* 1.3 61.5 + - + +
263A GLU* 3.3 8.5 + - - +
264A VAL* 3.0 28.4 + - - +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A THR* 4.2 25.1 - - + +
190A LEU* 3.6 28.3 - - + -
191A GLU* 6.1 0.2 - - + -
235A TYR* 2.8 32.9 - - + +
238A LEU* 3.6 31.0 - - + +
239A GLN* 2.8 30.7 - - - +
242A VAL* 5.6 3.4 - - + -
257A LEU* 2.8 19.8 + - + +
258A THR 3.9 0.7 - - - +
260A ARG* 1.3 77.5 - - + +
262A ASP* 1.3 63.1 + - - +
263A GLU 3.2 0.2 - - - -
264A VAL* 3.3 5.6 + - + +
265A LEU 3.3 10.6 + - - -
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Residues in contact with ASP 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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235A TYR* 2.9 24.3 + - - -
239A GLN* 4.8 4.7 - - - +
258A THR* 2.9 22.2 + - - +
259A GLY* 3.5 8.1 - - - +
261A LEU* 1.3 75.6 - - - +
263A GLU* 1.3 60.9 + - - +
265A LEU* 3.9 6.5 + - - +
266A ARG* 3.4 23.6 + - - +
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Residues in contact with GLU 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 GLY 2.6 19.6 + - - +
260A ARG* 3.5 9.4 - - - +
261A LEU 3.2 0.4 - - - -
262A ASP* 1.3 73.4 - - - +
264A VAL* 1.3 63.3 + - - +
265A LEU 3.2 0.2 - - - -
266A ARG* 3.4 38.8 + - - +
267A THR* 3.2 33.3 + - + +
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Residues in contact with VAL 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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190A LEU* 3.9 31.9 - - + -
191A GLU* 3.7 38.8 - - + +
194A LYS* 4.2 20.0 - - + +
231A LEU* 5.5 2.2 - - + +
235A TYR* 4.7 7.9 - - + -
260A ARG 3.0 16.2 + - - +
261A LEU* 3.3 13.6 + - + +
263A GLU* 1.3 75.2 - - - +
265A LEU* 1.3 64.2 + - - +
267A THR* 3.3 17.1 + - - -
268A LEU* 3.4 15.4 + - + +
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Residues in contact with LEU 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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232A VAL* 4.4 14.4 - - + -
235A TYR* 3.9 42.2 - - + +
261A LEU 3.3 12.3 + - - +
262A ASP* 4.2 6.7 - - - +
263A GLU 3.2 0.2 - - - -
264A VAL* 1.3 80.5 - - - +
266A ARG* 1.3 65.2 + - - +
268A LEU* 4.0 5.5 - - + +
269A VAL* 3.2 29.5 + - + +
297A LEU* 5.4 0.7 - - + -
301A PHE* 4.0 27.8 - - + -
394A LEU* 4.4 19.3 - - + -
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Residues in contact with ARG 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 ASP 3.4 15.1 + - - +
263A GLU* 3.4 40.2 + - - +
265A LEU* 1.3 81.3 - - - +
267A THR* 1.3 67.5 + - - +
269A VAL* 3.5 3.2 + - - +
270A THR* 2.8 57.6 + - - +
401A ILE* 5.1 15.2 - - + +
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Residues in contact with THR 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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194A LYS* 3.1 32.5 - - - +
198A LEU* 4.9 6.5 - - - -
263A GLU* 3.2 34.3 + - + +
264A VAL 3.3 4.2 + - - -
266A ARG* 1.3 86.3 - - + +
268A LEU* 1.3 55.3 + - - +
270A THR* 3.2 8.5 + - - -
271A SER* 2.2 40.8 + - - -
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Residues in contact with LEU 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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194A LYS* 4.1 19.1 - - + -
197A VAL* 4.4 13.9 - - + -
198A LEU* 4.4 8.7 - - + -
201A ILE* 5.7 1.1 - - + +
228A CYS* 4.0 29.2 - - + +
231A LEU* 4.5 16.6 - - + -
232A VAL* 4.0 17.9 - - + +
264A VAL* 3.4 17.8 + - + +
265A LEU* 4.0 7.4 - - + +
266A ARG 3.3 0.2 - - - -
267A THR* 1.3 78.0 + - - +
269A VAL* 1.3 64.5 + - - +
271A SER* 3.4 4.4 + - - -
272A CYS* 3.0 24.0 + - - +
297A LEU* 3.7 22.4 - - + -
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Residues in contact with VAL 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 LEU* 3.2 22.2 + - + +
266A ARG* 3.9 4.0 - - - +
267A THR 3.4 0.2 - - - -
268A LEU* 1.3 76.2 - - - +
270A THR* 1.3 58.9 + - - +
272A CYS* 3.0 25.7 + - - +
273A PHE 3.7 2.4 + - - -
295A PHE* 3.7 13.3 - - + -
297A LEU* 3.8 19.7 - - + -
301A PHE* 4.4 17.9 - - + -
392A PHE* 3.8 30.5 - - + -
394A LEU* 4.4 9.2 - - + -
401A ILE* 4.3 13.5 - - + -
403A LEU* 4.0 10.8 - - + +
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Residues in contact with THR 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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266A ARG* 2.8 41.1 + - - +
267A THR* 3.2 12.0 + - - -
269A VAL* 1.3 74.0 - - + +
271A SER* 1.3 63.2 + - - +
272A CYS 3.2 0.4 + - - -
273A PHE* 4.0 13.3 + - - +
401A ILE* 4.6 20.0 - - + -
402A GLN 5.2 4.0 - - - +
403A LEU* 4.1 11.3 - - + +
404A GLN 4.8 6.4 + - - +
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.5 34.6 - - - +
201A ILE* 3.9 20.6 - - - +
267A THR* 2.2 29.7 + - - -
268A LEU 3.7 4.0 - - - -
270A THR* 1.3 76.1 + - - +
272A CYS* 1.3 60.1 + - - +
273A PHE 3.4 1.3 - - - -
274A LEU* 3.4 19.7 - - - +
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Residues in contact with CYS 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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201A ILE* 5.2 1.3 - - - -
228A CYS* 3.8 16.6 - - - -
268A LEU 3.0 14.9 + - - +
269A VAL* 3.0 17.0 + - - +
271A SER* 1.3 76.2 - - - +
273A PHE* 1.3 57.9 + - - +
274A LEU* 3.6 7.9 + - - +
294A ARG 3.4 5.2 - - - +
295A PHE* 3.7 14.4 - - + -
296A LEU* 3.3 51.7 + - - +
297A LEU* 3.6 23.3 - - - -
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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