Contacts of the helix formed by residues 258 - 264 (chain B) in PDB entry 6APL
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 ARG 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B PRO* 3.7 33.4 - - - +
256B GLY* 3.4 23.9 + - - +
257B ASP* 1.3 74.1 - - - +
259B PRO* 1.3 68.2 - - - +
260B HIS* 3.2 6.1 - - + +
261B ALA* 3.0 31.1 + - + +
262B TYR* 3.6 10.8 + - - -
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Residues in contact with PRO 259 (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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239B MSE 4.3 8.7 - - - -
242B SER* 3.8 21.3 - - - +
243B ALA* 3.6 28.3 - - + +
246B GLY* 5.5 2.5 - - - -
247B VAL 3.2 30.3 - - - +
248B PRO* 3.8 2.2 - - + -
249B VAL 4.8 0.4 - - - +
257B ASP 3.4 9.6 - - - +
258B ARG* 1.3 84.0 - - - +
260B HIS* 1.3 53.9 + - + +
262B TYR* 3.0 10.1 + - + -
263B PHE* 2.8 46.8 + - + +
272B PHE* 6.0 0.2 - - + -
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Residues in contact with HIS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLN* 4.8 0.5 + - - -
246B GLY* 3.7 30.3 + - - -
247B VAL 6.2 0.2 - - - -
258B ARG* 3.2 5.8 - - + -
259B PRO* 1.3 80.2 - - + +
261B ALA* 1.3 59.1 + - - +
264B GLY* 2.7 51.6 + - - +
265B PRO* 3.1 26.6 + - + +
266B GLU 4.7 0.8 + - - -
267B ALA* 3.9 19.5 - - + -
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Residues in contact with ALA 261 (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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218B SER* 5.2 7.6 - - - -
221B GLN* 4.4 7.1 + - - -
258B ARG* 3.0 23.3 + - + +
260B HIS* 1.3 77.9 - - - +
262B TYR* 1.3 65.1 + - + +
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Residues in contact with TYR 262 (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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204B MSE 4.2 14.8 - - - -
205B LYS* 3.5 24.2 - - + +
208B LEU* 3.5 31.8 - - + +
218B SER* 5.5 0.7 - - - +
219B VAL* 3.2 27.3 + - + +
221B GLN* 3.6 9.9 + - - +
239B MSE 4.0 25.1 - - + -
257B ASP* 3.2 41.8 + - + -
258B ARG 3.6 11.3 + - - -
259B PRO* 3.0 7.0 + - + +
261B ALA* 1.3 83.1 - - + +
263B PHE* 1.3 78.7 + + + +
264B GLY 3.7 0.4 - - - -
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Residues in contact with PHE 263 (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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199B PHE* 3.8 23.3 - + - -
204B MSE 3.5 31.2 - - + -
219B VAL* 4.4 0.9 - - + -
221B GLN* 3.0 15.2 - - - +
227B TYR* 3.6 42.5 - + + -
229B PHE* 4.0 11.4 - + - -
239B MSE 4.2 18.4 - - + -
243B ALA* 3.9 21.1 - - + -
259B PRO* 2.8 26.2 + - + +
262B TYR* 1.3 91.0 - + + +
264B GLY* 1.3 61.2 + - - +
266B GLU 5.4 0.2 - - - -
271B LYS* 3.7 13.3 - - - +
272B PHE* 3.6 27.1 - + + -
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Residues in contact with GLY 264 (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 GLN* 3.5 14.7 + - - +
260B HIS* 2.7 45.3 + - - -
262B TYR 3.7 0.6 - - - -
263B PHE* 1.3 75.5 - - - +
265B PRO* 1.3 73.3 - - - +
266B GLU 3.4 6.5 + - - +
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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