Contacts of the helix formed by residues 264 - 275 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B GLU* 2.3 35.5 + - - -
263B TRP* 1.3 77.1 - - - +
265B VAL* 1.3 63.3 - - - +
266B GLU* 3.4 18.1 + - - +
267B PHE* 3.1 15.4 + - - +
268B ARG* 3.3 22.3 + - - +
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B SER* 1.3 72.1 - - - +
266B GLU* 1.3 68.2 + - - +
268B ARG* 3.7 25.0 - - + +
269B ASP* 2.9 32.7 + - + +
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLN* 6.1 0.2 - - - +
264B SER* 3.5 19.0 - - - +
265B VAL* 1.3 83.7 + - - +
267B PHE* 1.3 60.4 + - - +
269B ASP* 3.4 1.7 + - - -
270B PHE* 2.8 31.5 + - - +
291B HIS* 3.3 8.0 - - + -
292B PRO* 3.8 29.2 - - + +
293B PHE* 4.0 21.1 - - + +
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Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLU* 3.7 7.6 - - + +
134B ILE* 3.9 22.7 - - + -
227B LEU* 4.0 30.7 - - + -
231B ALA* 4.2 4.9 - - + -
257B LEU* 3.9 14.6 - - + -
263B TRP* 3.5 45.5 - + + -
264B SER* 3.1 19.5 + - - +
266B GLU* 1.3 73.4 - - - +
268B ARG* 1.3 59.7 + - - +
270B PHE* 3.2 3.0 + - + +
271B LEU* 3.0 45.8 + - + +
293B PHE* 3.4 38.3 - + + -
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B LEU* 3.9 26.2 - - + +
260B PRO* 3.6 42.9 + - - +
261B SER* 5.8 0.8 - - - +
263B TRP* 3.6 15.2 + - + -
264B SER 3.3 15.2 + - - +
265B VAL* 3.7 30.9 - - + +
267B PHE* 1.3 74.3 - - - +
269B ASP* 1.3 59.5 + - - +
271B LEU* 3.5 5.2 + - - +
272B LYS* 3.0 28.5 + - - +
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Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B VAL* 2.9 23.9 + - + +
266B GLU* 3.8 3.8 - - - +
268B ARG* 1.3 76.3 - - - +
270B PHE* 1.3 64.4 + - - +
272B LYS* 3.3 17.4 + - - +
273B ILE* 3.1 31.3 + - - +
291B HIS* 2.8 27.1 + - + +
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Residues in contact with PHE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B CYS* 3.4 21.5 - - - -
142B LEU* 4.0 10.5 - - + -
223B LEU* 4.5 5.2 - - + -
224B GLY* 5.7 0.2 - - - -
227B LEU* 3.4 32.5 - - + -
266B GLU 2.8 17.9 + - - +
267B PHE 3.4 5.2 - - - +
269B ASP* 1.3 76.6 - - - +
271B LEU* 1.3 60.2 + - - +
273B ILE* 3.3 7.7 + - - +
274B ALA* 2.9 36.3 + - + +
288B LEU* 3.8 44.2 - - + -
291B HIS* 3.6 29.8 - + + -
293B PHE* 3.9 17.9 - + + -
294B VAL* 4.5 4.0 - - + -
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B GLY* 3.3 38.1 - - - +
227B LEU* 4.1 16.6 - - + -
228B ILE* 3.7 18.8 - - + -
255B PRO 5.5 1.8 - - - +
256B THR* 5.4 2.2 - - - -
257B LEU* 3.6 42.0 - - + +
267B PHE* 3.0 26.8 + - + +
268B ARG* 3.8 5.4 - - - +
269B ASP 3.4 0.2 - - - -
270B PHE* 1.3 77.3 - - + +
272B LYS* 1.3 56.4 + - - +
274B ALA* 4.5 1.3 - - - +
275B LEU* 2.8 48.7 + - + +
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Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B PRO* 6.5 0.7 - - - -
256B THR* 6.5 1.1 - - + -
268B ARG 3.0 19.0 + - - +
269B ASP* 3.6 19.3 - - - +
270B PHE 3.3 0.2 - - - -
271B LEU* 1.3 76.6 - - - +
273B ILE* 1.3 66.7 + - + +
275B LEU* 3.9 14.0 + - - +
276B ASP* 4.4 2.8 + - - +
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ASP* 3.1 26.7 + - - +
270B PHE 3.3 10.8 - - - +
272B LYS* 1.3 83.6 - - + +
274B ALA* 1.3 65.9 + - - +
276B ASP* 3.6 13.8 - - - +
283B PRO* 3.1 27.5 - - + +
287B GLN 6.0 0.7 - - - +
288B LEU* 3.7 23.8 - - + -
291B HIS* 3.7 25.4 - - + -
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ILE* 4.2 14.5 - - + +
221B TRP* 4.2 3.6 - - - -
223B LEU* 6.0 0.4 - - + -
224B GLY* 4.7 9.0 - - - +
270B PHE* 2.9 28.7 + - + +
271B LEU* 4.0 3.6 - - - +
273B ILE* 1.3 78.2 - - - +
275B LEU* 1.3 59.4 + - - +
276B ASP 3.1 6.6 + - - -
282B ARG* 3.2 24.4 - - - +
283B PRO* 4.2 9.4 - - - -
288B LEU* 4.2 20.0 - - + -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B TRP* 3.3 51.8 - - + +
224B GLY* 3.7 17.7 - - - -
225B ILE* 3.9 7.9 - - + -
228B ILE* 3.8 20.9 - - + -
254B PRO* 3.1 32.1 - - + +
255B PRO* 3.4 30.5 - - + +
271B LEU* 2.8 34.1 + - + +
272B LYS* 4.0 9.2 - - - +
274B ALA* 1.3 69.6 - - - +
276B ASP* 1.3 58.0 + - - +
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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