Contacts of the helix formed by residues 255 - 265 (chain R) in PDB entry 5GJQ
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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225R TYR* 5.6 0.7 - - - +
253R LEU* 4.5 1.5 - - + +
254R PRO* 1.3 80.1 - - + +
256R VAL* 1.3 70.0 + - - +
257R ARG* 4.1 4.9 - - - +
258R GLN* 3.0 21.4 + - - +
259R TYR* 3.1 10.7 + - - +
274R SER* 4.2 5.2 - - - -
277R VAL* 5.2 10.8 - - + -
278R VAL* 4.4 15.3 - - + -
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Residues in contact with VAL 256 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220R VAL* 6.4 0.4 - - + -
221R THR* 4.5 23.6 - - + -
224R VAL* 4.8 6.1 - - + -
225R TYR* 2.8 41.5 + - + +
250R LEU* 3.9 17.0 - - + -
253R LEU* 4.8 6.3 - - + -
255R ALA* 1.3 74.4 - - - +
257R ARG* 1.3 64.4 + - - +
259R TYR* 1.9 56.4 + - + -
278R VAL* 4.0 5.3 - - - +
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Residues in contact with ARG 257 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224R VAL* 5.6 0.2 - - - -
250R LEU* 2.7 59.2 - - + +
253R LEU 4.5 0.4 - - - -
254R PRO* 4.1 24.0 - - + -
255R ALA 3.2 0.4 - - - +
256R VAL* 1.3 80.7 - - - +
258R GLN* 1.3 79.8 + - + +
260R LEU* 2.9 5.8 + - - +
261R PHE* 2.8 38.9 + - + +
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Residues in contact with GLN 258 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254R PRO* 4.0 19.0 + - + +
255R ALA* 3.2 17.5 - - - +
257R ARG* 1.3 85.3 - - + +
259R TYR* 1.3 55.8 + - - +
261R PHE* 4.2 6.9 - - - +
262R SER* 3.2 24.6 + - - -
274R SER* 3.5 19.2 + - - +
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Residues in contact with TYR 259 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224R VAL* 3.5 4.0 + - + -
225R TYR* 3.4 29.3 + + - -
228R MET* 2.7 39.9 - - + +
255R ALA 3.1 4.4 + - - +
256R VAL* 1.9 46.5 + - + +
258R GLN* 1.3 75.5 - - - +
260R LEU* 1.3 93.2 + - + -
262R SER* 3.0 16.5 + - - -
263R LEU 3.0 10.9 + - - -
271R PHE* 3.3 29.3 - + + +
274R SER* 3.5 27.1 - - - +
275R LEU* 4.8 15.7 - - + -
278R VAL* 5.3 5.6 - - + -
295R TYR* 3.6 15.7 + + - -
299R MET* 5.0 2.7 - - + -
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Residues in contact with LEU 260 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224R VAL* 4.4 10.5 - - + -
228R MET* 3.5 23.8 - - + -
236R LEU* 3.6 20.2 - - + -
240R VAL* 4.5 8.1 - - + -
241R ILE* 2.5 39.9 - - + -
250R LEU* 3.9 25.1 - - + -
256R VAL 2.8 1.1 + - - +
257R ARG* 3.4 8.5 - - - +
259R TYR* 1.3 107.6 - - + +
261R PHE* 1.3 67.9 + - + +
263R LEU* 3.4 2.4 + - - +
264R TYR* 3.2 16.4 + - + +
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Residues in contact with PHE 261 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241R ILE* 4.0 33.4 - - + -
247R LEU* 5.2 14.1 - - + -
250R LEU* 4.8 13.5 - - + -
257R ARG* 2.8 38.4 + - + +
258R GLN* 4.2 6.3 - - - +
260R LEU* 1.3 77.8 - - + +
262R SER* 1.3 65.6 + - - +
264R TYR* 3.4 7.0 + + - +
265R GLU* 3.0 31.4 + - + +
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Residues in contact with SER 262 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258R GLN 3.2 18.1 + - - -
259R TYR 3.0 7.9 + - - -
261R PHE* 1.3 79.2 - - - +
263R LEU* 1.3 60.1 + - - +
265R GLU* 5.0 0.2 - - - -
266R CYS* 3.6 1.0 + - - -
267R ARG* 2.6 65.4 + - - +
268R TYR 3.9 0.5 + - - -
270R VAL* 3.3 8.6 - - - +
271R PHE* 2.8 28.4 + - - +
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Residues in contact with LEU 263 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228R MET* 2.9 35.9 - - + +
236R LEU* 4.7 9.6 - - + -
259R TYR 3.0 1.4 + - - -
260R LEU 3.4 3.6 - - - +
262R SER* 1.3 72.8 - - - +
264R TYR* 1.3 57.7 + - - +
265R GLU 2.8 2.2 + - - -
266R CYS* 2.7 29.8 + - - -
268R TYR* 4.3 6.4 - - + -
271R PHE* 2.2 45.2 - - + -
299R MET* 4.4 7.4 - - + -
302R HIS* 5.5 7.9 - - + -
303R ALA* 4.5 22.0 - - + +
306R GLN* 3.5 36.7 + - - +
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Residues in contact with TYR 264 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367Q GLN* 5.1 6.9 + - - -
371Q ASP* 5.3 2.3 + - - -
233R ARG* 2.7 67.6 + - + +
236R LEU* 4.9 6.5 - - + -
237R ARG* 2.6 46.8 - - + +
241R ILE* 3.7 41.1 - - + -
242R LYS* 5.6 2.3 - - - -
260R LEU* 3.2 15.2 + - + +
261R PHE* 3.9 8.5 - + - +
263R LEU* 1.3 81.6 - - - +
265R GLU* 1.3 58.7 + - + +
266R CYS* 3.7 1.2 + - - -
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Residues in contact with GLU 265 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261R PHE* 3.0 18.6 + - + +
262R SER* 4.5 2.0 - - - +
263R LEU 2.8 6.3 + - - -
264R TYR* 1.3 76.1 - - + +
266R CYS* 1.3 72.5 + - - +
267R ARG* 4.7 7.2 - - + +
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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