Contacts of the helix formed by residues 256 - 264 (chain B) in PDB entry 4K9N
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 GLY 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B PRO* 2.9 6.1 + - - +
255B ALA* 1.3 78.0 - - - +
257B ILE* 1.3 66.3 + - - +
258B ALA 3.4 2.0 - - - -
259B ALA* 3.9 1.5 - - - +
260B ILE* 3.0 27.4 + - - +
280B TYR* 3.5 6.8 - - - -
282B GLN* 3.8 7.8 - - - +
284B ASP* 3.5 24.5 - - - -
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Residues in contact with ILE 257 (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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256B GLY* 1.3 71.4 - - - +
258B ALA* 1.3 64.9 + - - +
260B ILE* 3.9 1.7 - - - +
261B SER* 3.2 18.0 + - - -
280B TYR* 3.5 37.2 + - + +
282B GLN 5.2 0.6 + - - -
284B ASP* 3.4 15.5 + - - +
285B PRO* 5.0 7.4 - - + -
286B GLY 3.7 20.9 - - - +
287B GLN 3.4 23.3 - - - +
288B TYR* 3.9 31.4 - - + +
102D ALA 5.9 1.3 - - - +
103D MET* 4.3 22.0 - - + -
106D VAL* 5.9 1.3 - - + -
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Residues in contact with ALA 258 (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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257B ILE* 1.3 74.5 - - - +
259B ALA* 1.3 67.5 + - - +
261B SER* 3.1 9.3 + - - -
262B GLN* 3.0 25.3 + - - +
284B ASP* 3.0 21.1 + - - +
285B PRO 3.5 23.1 - - - +
286B GLY* 4.3 5.6 - - - -
287B GLN 4.4 1.3 - - - +
290B LYS* 5.5 0.3 - - - -
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Residues in contact with ALA 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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254B PRO* 4.0 29.4 - - + -
256B GLY* 3.9 6.1 - - - +
257B ILE 3.4 0.4 - - - -
258B ALA* 1.3 75.9 - - - +
260B ILE* 1.3 57.7 + - - +
262B GLN* 3.4 7.1 + - - +
263B LEU* 3.0 32.8 + - - +
282B GLN* 5.9 0.4 - - - +
284B ASP* 3.1 18.4 + - - +
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Residues in contact with ILE 260 (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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235B PRO* 3.9 26.9 - - + -
253B MET* 4.0 21.5 - - + -
254B PRO 3.2 26.9 - - - +
256B GLY 3.0 17.0 + - - +
257B ILE 4.0 2.9 - - - +
259B ALA* 1.3 75.7 - - - +
261B SER* 1.3 66.5 + - - +
263B LEU* 3.2 7.1 + - + +
264B LEU* 3.0 42.5 + - + +
278B PHE* 3.8 21.3 - - + -
280B TYR* 3.8 20.4 - - + +
288B TYR 5.1 2.9 - - - +
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Residues in contact with SER 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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257B ILE 3.2 5.6 + - - -
258B ALA* 3.1 14.4 + - - -
260B ILE* 1.3 77.5 - - - +
262B GLN* 1.3 56.8 + - - +
264B LEU* 3.4 6.9 + - - +
265B GLU 3.0 22.2 + - - -
287B GLN* 2.8 34.5 + - - +
288B TYR 3.5 18.6 + - - -
289B LEU* 3.8 10.1 - - - +
290B LYS* 3.4 24.5 + - - +
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Residues in contact with GLN 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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258B ALA 3.0 18.6 + - - +
259B ALA* 3.6 7.2 - - - +
261B SER* 1.3 77.0 + - - +
263B LEU* 1.3 66.9 + - + +
265B GLU* 3.0 37.3 + - - +
290B LYS* 3.8 22.7 + - - +
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Residues in contact with LEU 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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232B TRP* 3.9 41.8 - - + +
253B MET* 4.2 18.2 - - + -
254B PRO* 3.6 31.9 - - + -
259B ALA 3.0 14.7 + - - +
260B ILE* 3.4 10.5 - - - +
262B GLN* 1.3 78.4 - - + +
264B LEU* 1.3 64.0 + - + +
265B GLU 3.5 2.4 + - - +
267B HIS* 3.9 11.4 + - - -
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Residues in contact with LEU 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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204B ALA* 4.5 3.1 - - + -
206B VAL* 4.5 0.7 - - + -
232B TRP* 4.4 18.8 - - + -
253B MET* 3.9 22.4 - - + -
260B ILE* 3.0 36.2 + - + +
261B SER* 3.6 5.4 - - - +
263B LEU* 1.3 77.0 - - - +
265B GLU* 1.3 68.2 + - - +
267B HIS* 3.0 21.5 + - - +
270B VAL* 3.9 42.2 - - + -
278B PHE* 4.7 8.3 - - + -
289B LEU* 4.3 18.6 - - + -
293B THR* 3.2 15.2 + - + -
295B LEU* 5.1 0.2 - - + -
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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