Contacts of the helix formed by residues 255 - 262 (chain L) in PDB entry 3Q3G
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 VAL 255 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212L ALA* 3.2 38.6 - - + +
215L ILE* 3.5 21.8 - - + -
216L ARG* 3.4 31.9 - - + +
219L VAL* 5.5 1.0 - - - +
250L LEU* 4.0 13.0 - - + -
251L GLY 3.7 13.2 - - - +
252L TYR* 3.0 6.5 + - + +
253L GLU 3.3 0.2 - - - -
254L ASP* 1.3 84.2 - - - +
256L ILE* 1.4 65.5 + - + +
257L PRO* 3.6 2.0 - - - -
258L GLU* 3.5 11.6 + - - +
259L ALA* 3.3 18.2 + - - +
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Residues in contact with ILE 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L ILE* 4.5 20.0 - - + -
252L TYR* 2.8 39.2 + - + +
253L GLU* 5.3 0.4 - - - -
255L VAL* 1.4 69.0 - - + +
257L PRO* 1.4 67.9 - - + +
259L ALA* 3.0 15.8 + - - +
260L ASP* 3.0 19.1 + - - +
266L ARG* 3.2 33.4 - - - +
286L THR* 3.4 30.7 - - + +
287L ILE* 3.7 20.0 - - - +
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Residues in contact with PRO 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L GLU* 3.2 30.3 - - + +
254L ASP 4.6 0.7 - - - -
255L VAL 3.7 3.1 - - - +
256L ILE* 1.4 93.1 - - + +
258L GLU* 1.3 54.0 + - - +
260L ASP* 3.2 11.0 + - + +
261L ARG* 2.9 49.8 + - - +
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Residues in contact with GLU 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L ARG* 3.8 16.6 + - - +
219L VAL* 4.3 12.6 - - + +
220L ARG* 2.8 53.6 + - - +
254L ASP 4.5 7.5 + - - +
255L VAL* 3.5 12.1 + - - +
256L ILE 3.3 0.4 - - - -
257L PRO* 1.3 77.9 - - - +
259L ALA* 1.4 56.0 + - - +
261L ARG* 3.4 27.4 + - - +
262L GLU* 3.1 35.7 + - + +
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Residues in contact with ALA 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L ILE* 4.7 5.6 - - + -
219L VAL* 3.9 27.9 - - + +
255L VAL 3.3 9.2 + - - +
256L ILE* 3.0 11.7 + - - +
258L GLU* 1.4 74.6 - - - +
260L ASP* 1.3 59.2 + - - +
262L GLU 3.5 0.5 + - - -
263L GLY 3.3 3.8 + - - -
264L VAL* 2.8 35.3 + - + +
266L ARG* 3.9 28.7 - - - +
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Residues in contact with ASP 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256L ILE* 3.0 17.4 + - - +
257L PRO* 3.2 11.3 + - + +
259L ALA* 1.3 75.7 - - - +
261L ARG* 1.4 57.6 + - + +
263L GLY* 2.9 21.1 + - - -
264L VAL 4.7 1.3 - - - +
266L ARG* 2.8 40.7 + - - +
289L SER* 4.9 1.9 + - - -
290L LYS* 5.0 12.8 + - - -
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Residues in contact with ARG 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257L PRO* 2.9 27.3 + - - +
258L GLU* 3.4 44.1 - - - +
260L ASP* 1.4 74.7 - - + +
262L GLU* 1.3 66.2 + - + +
263L GLY 3.2 0.9 + - - -
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Residues in contact with GLU 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L VAL* 4.2 17.3 - - + -
235L LYS* 3.3 29.1 + - - +
258L GLU* 3.1 26.7 + - + +
259L ALA 3.5 3.3 + - - +
260L ASP 3.3 0.4 - - - -
261L ARG* 1.3 80.8 - - + +
263L GLY* 1.3 61.6 + - - +
264L VAL* 3.5 4.7 - - + -
615L EDO 2.6 41.3 + - - +
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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