Contacts of the helix formed by residues 255 - 262 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212I ALA* 3.4 49.8 - - + +
215I ILE* 4.5 10.5 - - + +
216I ARG* 3.5 33.3 - - + +
219I VAL* 5.5 1.2 - - - +
250I LEU* 4.2 9.4 - - + -
251I GLY 3.7 5.6 - - - +
252I TYR* 3.1 17.3 + - + +
253I GLU 3.3 0.2 - - - -
254I ASP* 1.4 83.9 - - - +
256I ILE* 1.4 70.9 + - + +
257I PRO* 3.6 1.6 - - - -
258I GLU* 3.4 11.2 + - - +
259I ALA* 3.2 19.6 + - - +
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Residues in contact with ILE 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I ILE* 4.5 17.5 - - + -
252I TYR* 2.7 40.4 + - + +
253I GLU* 5.4 0.4 - - - -
255I VAL* 1.4 68.5 - - + +
257I PRO* 1.4 67.7 - - + +
259I ALA* 3.0 15.6 + - - +
260I ASP* 3.0 25.7 + - - +
266I ARG* 3.9 23.8 - - - +
286I THR* 3.4 29.2 - - + +
287I ILE* 3.7 19.7 - - - +
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Residues in contact with PRO 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253I GLU* 3.2 30.3 - - + +
254I ASP 4.7 0.9 - - - -
255I VAL 3.7 2.7 - - - +
256I ILE* 1.4 92.3 - - + +
258I GLU* 1.3 54.8 + - - +
260I ASP* 3.2 10.5 + - + +
261I ARG* 2.9 50.6 + - - +
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Residues in contact with GLU 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216I ARG* 3.8 17.2 + - - +
219I VAL* 4.3 13.9 - - + +
220I ARG* 2.8 53.1 + - - +
254I ASP 4.5 6.4 + - - +
255I VAL* 3.4 12.4 + - - +
256I ILE 3.3 0.4 - - - -
257I PRO* 1.3 78.1 - - - +
259I ALA* 1.4 56.6 + - - +
261I ARG* 3.4 28.3 + - - +
262I GLU* 3.0 35.8 + - + +
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Residues in contact with ALA 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I ILE* 4.7 4.5 - - + -
219I VAL* 3.9 26.4 - - + +
255I VAL 3.2 11.1 + - - +
256I ILE* 3.0 12.4 + - - +
258I GLU* 1.4 72.8 - - - +
260I ASP* 1.3 62.9 + - - +
262I GLU* 3.5 0.9 + - - -
263I GLY 3.3 3.8 + - - -
264I VAL* 2.9 32.4 + - + +
266I ARG* 3.9 28.7 - - - +
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Residues in contact with ASP 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I ILE* 3.0 27.2 + - - +
257I PRO* 3.5 11.2 - - + +
259I ALA* 1.3 74.6 - - - +
261I ARG* 1.4 58.5 + - + +
263I GLY* 2.9 21.1 + - - -
264I VAL 4.9 1.6 - - - +
266I ARG* 2.8 31.7 + - - +
289I SER* 4.9 1.7 + - - -
290I LYS* 5.0 13.7 + - - -
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Residues in contact with ARG 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257I PRO* 2.9 27.3 + - - +
258I GLU* 3.4 44.2 - - - +
260I ASP* 1.4 74.8 - - + +
262I GLU* 1.3 66.7 + - + +
263I GLY 3.2 0.9 + - - -
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Residues in contact with GLU 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I VAL* 4.2 22.5 - - + +
223I PHE* 5.1 4.8 - - + +
235I LYS* 3.3 39.2 + - - +
258I GLU* 3.0 27.3 + - + +
259I ALA 3.5 3.8 + - - +
260I ASP 3.3 0.4 - - - -
261I ARG* 1.3 81.3 - - + +
263I GLY* 1.3 60.7 + - - +
264I VAL* 3.5 6.7 - - + -
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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