Contacts of the helix formed by residues 264 - 275 (chain A) in PDB entry 5AJQ
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 SER 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLU* 2.4 37.9 + - - -
263A TRP* 1.3 78.2 - - - +
265A VAL* 1.3 64.0 + - - +
266A GLU* 3.4 17.8 + - - +
267A PHE* 3.1 15.6 + - - +
268A ARG* 3.3 21.9 + - - +
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Residues in contact with VAL 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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264A SER* 1.3 73.1 - - - +
266A GLU* 1.3 68.0 + - - +
268A ARG* 3.7 25.4 - - + +
269A ASP* 2.9 30.7 + - + +
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Residues in contact with GLU 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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131A GLU* 5.1 0.2 - - - +
135A GLN* 6.1 0.2 - - - +
264A SER* 3.2 19.8 - - - +
265A VAL* 1.3 82.6 + - - +
267A PHE* 1.3 60.0 + - - +
269A ASP* 4.5 1.3 - - - -
270A PHE* 2.8 31.5 + - - +
291A HIS* 3.3 9.2 - - + -
292A PRO* 3.9 28.9 - - + +
293A PHE* 4.1 20.6 - - + +
89B ASP* 5.0 10.5 - - - +
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Residues in contact with PHE 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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131A GLU* 3.7 8.3 - - + +
134A ILE* 3.9 24.0 - - + -
227A LEU* 4.0 30.3 - - + -
231A ALA* 4.2 5.6 - - + -
257A LEU* 3.9 13.9 - - + -
263A TRP* 3.5 45.3 - + + -
264A SER* 3.1 20.3 + - - +
265A VAL 3.4 0.2 - - - -
266A GLU* 1.3 75.9 - - - +
268A ARG* 1.3 56.9 + - - +
270A PHE* 3.2 2.7 + - + +
271A LEU* 3.0 45.9 + - + +
293A PHE* 3.4 38.3 - + + -
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Residues in contact with ARG 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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257A LEU* 3.9 23.8 - - + +
260A PRO* 3.5 42.8 + - - +
261A SER* 5.7 0.8 - - - +
263A TRP* 3.6 16.7 + - + -
264A SER* 3.3 14.8 + - - +
265A VAL* 3.7 31.9 - - + +
267A PHE* 1.3 76.2 - - - +
269A ASP* 1.3 58.0 + - - +
271A LEU* 3.5 7.0 + - - +
272A LYS* 3.0 27.8 + - - +
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Residues in contact with ASP 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 VAL* 2.9 24.1 + - + +
266A GLU* 3.8 4.0 - - - +
268A ARG* 1.3 74.4 - - - +
270A PHE* 1.3 66.2 + - - +
272A LYS* 3.3 27.6 + - - +
273A ILE* 3.1 30.9 + - - +
291A HIS* 2.8 26.5 + - + +
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Residues in contact with PHE 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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138A CYS* 3.4 21.3 - - - -
142A LEU* 4.0 10.8 - - + -
223A LEU* 4.5 6.3 - - + -
224A GLY* 5.7 0.2 - - - -
227A LEU* 3.4 33.4 - - + -
266A GLU 2.8 18.7 + - - +
267A PHE* 3.4 5.2 - + - +
269A ASP* 1.3 76.4 - - - +
271A LEU* 1.3 61.0 + - + +
273A ILE* 3.3 7.3 + - - +
274A ALA* 2.9 36.1 + - + +
288A LEU* 3.8 43.7 - - + -
291A HIS* 3.6 30.7 - + + -
293A PHE* 3.9 18.4 - + + -
294A VAL* 4.4 3.8 - - + -
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Residues in contact with LEU 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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224A GLY* 3.3 38.4 - - - +
227A LEU* 4.0 16.6 - - + -
228A ILE* 3.7 18.6 - - + -
255A PRO 5.5 2.0 - - - +
256A THR* 5.5 2.5 - - - -
257A LEU* 3.6 41.5 - - + +
267A PHE* 3.0 27.9 + - + +
268A ARG* 3.8 5.2 - - - +
270A PHE* 1.3 76.0 - - - +
272A LYS* 1.3 55.3 + - - +
274A ALA* 4.6 1.1 - - - -
275A LEU* 2.8 49.9 + - + +
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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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254A PRO* 6.5 0.4 - - - -
256A THR* 6.5 0.9 - - - -
268A ARG 3.0 17.3 + - - +
269A ASP* 3.6 26.8 + - - +
270A PHE 3.3 0.2 - - - -
271A LEU* 1.3 77.4 - - - +
273A ILE* 1.3 69.3 + - + +
275A LEU* 3.9 14.1 + - - +
276A ASP* 4.3 2.4 + - - +
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Residues in contact with ILE 273 (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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269A ASP* 3.1 26.0 + - - +
270A PHE 3.3 11.2 - - - +
272A LYS* 1.3 82.7 - - + +
274A ALA* 1.3 68.4 + - - +
276A ASP* 3.6 13.2 - - - +
283A PRO* 3.1 26.5 - - + +
287A GLN 6.0 0.4 - - - +
288A LEU* 3.7 21.1 - - + -
291A HIS* 3.6 28.5 - - + -
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Residues in contact with ALA 274 (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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220A ILE* 4.2 14.5 - - + +
221A TRP* 4.2 3.6 - - - -
223A LEU* 6.0 0.4 - - + -
224A GLY* 4.7 9.0 - - - +
270A PHE* 2.9 28.5 + - + +
271A LEU* 4.0 3.6 - - - +
273A ILE* 1.3 77.7 - - - +
275A LEU* 1.3 60.4 + - - +
276A ASP 3.1 6.3 + - - -
282A ARG* 3.2 24.3 + - - +
283A PRO* 4.2 10.1 - - - -
288A LEU* 4.2 20.9 - - + -
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Residues in contact with LEU 275 (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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221A TRP* 3.3 53.2 - - + +
224A GLY* 3.7 16.8 - - - -
225A ILE* 3.9 7.2 - - + -
228A ILE* 3.8 21.3 - - + -
254A PRO* 3.1 32.6 - - + +
255A PRO* 3.4 30.1 - - + +
271A LEU* 2.8 35.2 + - + +
272A LYS* 3.9 8.9 - - - +
274A ALA* 1.3 69.0 - - - +
276A ASP* 1.3 58.8 + - - +
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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