Contacts of the helix formed by residues 256 - 267 (chain G) in PDB entry 4U7B
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 256 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216G ALA* 3.8 28.5 - - + -
252G PRO 3.3 10.7 + - - +
253G SER 3.8 7.1 + - - +
254G HIS 3.6 1.8 - - - -
255G THR* 1.3 83.4 - - - +
257G ARG* 1.3 67.7 + - - +
258G ALA* 3.6 3.6 - - + +
259G VAL* 3.7 5.0 + - + +
260G ARG* 3.4 17.5 + - - -
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Residues in contact with ARG 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G ALA* 1.3 71.9 - - - +
258G ALA* 1.3 68.9 + - - +
259G VAL 3.2 0.7 + - - -
260G ARG* 3.4 39.8 + - + +
261G ASP* 2.7 34.8 + - - +
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Residues in contact with ALA 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G ALA* 5.2 7.2 - - + +
217G ALA* 6.4 0.7 - - - -
220G GLN* 2.8 31.1 - - - +
256G ALA* 3.6 3.5 - - + +
257G ARG* 1.3 80.4 - - - +
259G VAL* 1.3 64.6 + - + +
261G ASP* 3.2 20.5 + - - +
262G THR* 3.3 3.5 + - - -
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Residues in contact with VAL 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216G ALA* 3.4 31.0 - - + +
219G TYR* 3.8 17.3 - - + -
220G GLN* 3.4 12.3 - - + +
223G LEU* 3.7 23.3 - - + -
253G SER 3.6 18.8 - - - +
254G HIS 4.0 16.4 - - - +
256G ALA* 3.7 8.2 + - + +
257G ARG 3.2 1.0 + - - -
258G ALA* 1.3 76.2 - - - +
260G ARG* 1.3 61.2 + - - +
262G THR* 2.9 21.4 + - - -
263G LEU* 3.1 16.9 + - + +
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Residues in contact with ARG 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LYS* 6.0 2.0 - - - +
254G HIS 5.4 4.3 - - - +
255G THR* 3.6 15.4 + - - +
256G ALA 3.4 14.6 + - - +
257G ARG* 3.5 46.7 - - + +
259G VAL* 1.3 79.2 - - - +
261G ASP* 1.3 58.3 + - - +
263G LEU* 3.5 17.4 + - + +
264G GLU* 3.0 29.6 + - - +
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Residues in contact with ASP 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257G ARG* 2.7 34.5 + - - +
258G ALA* 3.2 11.0 + - - +
260G ARG* 1.3 76.9 - - - +
262G THR* 1.3 59.0 + - - +
264G GLU* 3.2 20.5 + - - +
265G THR* 2.8 35.6 + - + +
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Residues in contact with THR 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G GLN* 2.7 45.0 + - + +
223G LEU* 4.8 8.1 - - + -
224G ILE* 4.2 20.2 - - + -
258G ALA 3.3 0.7 + - - -
259G VAL 2.9 8.2 + - - -
261G ASP* 1.3 74.6 - - - +
263G LEU* 1.3 60.0 + - - +
265G THR* 2.8 22.6 + - - +
266G LEU* 2.8 34.1 + - + +
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Residues in contact with LEU 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G TYR* 6.1 0.4 - - + -
223G LEU* 3.8 34.5 - - + -
246G PHE* 4.5 7.6 - - + -
248G HIS* 4.4 15.0 - - + +
254G HIS 5.2 1.8 - - - +
259G VAL* 3.1 22.1 + - + +
260G ARG* 3.7 20.0 - - + +
261G ASP 3.3 0.2 - - - -
262G THR* 1.3 76.1 - - - +
264G GLU* 1.3 57.4 + - - +
266G LEU* 3.3 5.8 + - + +
267G ASN 2.9 22.3 + - - -
268G TRP* 3.3 37.3 + - + +
270G VAL* 3.9 28.3 - - + -
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Residues in contact with GLU 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LYS 5.3 6.5 - - - +
145A ARG* 5.9 11.2 - - + -
260G ARG* 3.0 15.7 + - - +
261G ASP* 3.3 24.8 - - - +
263G LEU* 1.3 76.1 - - - +
265G THR* 1.3 59.2 + - + +
267G ASN* 3.2 21.5 + - - +
268G TRP 5.8 0.7 - - - -
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Residues in contact with THR 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G ASP* 2.8 21.5 + - + +
262G THR* 2.8 27.0 + - - +
264G GLU* 1.3 74.9 - - + +
266G LEU* 1.3 62.5 + - - +
267G ASN* 3.2 3.3 + - - +
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Residues in contact with LEU 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G LEU* 4.1 16.8 - - + +
224G ILE* 5.5 3.4 - - + -
227G ASN* 3.3 39.3 - - + +
237G TYR* 4.8 1.2 + - - -
241G GLN* 4.0 15.8 - - - +
262G THR* 2.8 36.3 + - + +
263G LEU* 3.6 8.3 - - + +
264G GLU 3.3 0.2 - - - -
265G THR* 1.3 76.5 - - - +
267G ASN* 1.3 69.7 + - - +
268G TRP* 3.4 48.0 + - + -
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Residues in contact with ASN 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ARG* 3.0 32.3 + - - +
242G HIS* 3.1 42.2 - - + +
263G LEU 2.9 6.1 + - - -
264G GLU* 3.2 14.9 + - - +
265G THR 3.2 4.9 - - - +
266G LEU* 1.3 81.7 - - - +
268G TRP* 1.3 61.3 + - - +
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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
------------------------------------------------------------
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