Contacts of the helix formed by residues 317 - 327 (chain B) in PDB entry 4K9P
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 ASP 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B ALA* 5.2 8.8 - - + +
181B SER* 3.8 5.9 + - - +
182B SER* 3.6 21.7 + - - -
183B VAL* 3.0 32.7 + - - +
214B ALA* 5.6 2.8 - - - +
300B CYS* 4.8 4.3 - - - -
316B ALA* 1.3 73.2 - - - +
318B ILE* 1.3 60.9 + - - +
319B GLY* 3.0 9.8 + - - -
320B ALA* 2.7 29.6 + - + +
321B MET* 2.9 31.9 + - - +
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Residues in contact with ILE 318 (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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210B ASP* 3.9 27.4 - - + +
211B VAL* 3.8 36.8 - - + -
214B ALA* 4.1 3.8 - - + +
216B ALA* 4.2 8.1 - - + -
273B ILE* 4.0 8.1 - - + -
274B GLY* 3.8 10.8 - - - +
298B VAL* 3.6 31.9 - - + +
299B THR* 4.2 0.4 - - - -
300B CYS* 4.2 23.9 - - + +
316B ALA 3.5 3.3 + - - +
317B ASP* 1.3 72.3 + - - +
319B GLY* 1.3 56.5 + - - +
321B MET* 4.6 3.1 - - - -
322B ALA* 2.8 39.0 + - + +
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Residues in contact with GLY 319 (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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214B ALA* 3.7 23.0 - - - +
216B ALA* 4.4 7.4 - - - -
219B ASP* 4.4 2.8 - - - +
317B ASP* 3.0 8.9 + - - -
318B ILE* 1.3 80.6 - - - +
320B ALA* 1.3 61.0 + - - +
322B ALA* 3.9 1.7 - - - +
323B SER* 3.1 22.2 + - - -
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Residues in contact with ALA 320 (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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186A ASN* 4.5 19.1 - - + -
182B SER* 4.5 4.9 - - - +
183B VAL 3.7 21.1 - - - +
184B ARG* 4.0 12.9 - - + +
317B ASP* 2.7 17.7 + - + +
319B GLY* 1.3 69.2 - - - +
321B MET* 1.3 61.2 + - - +
323B SER* 3.4 4.8 + - - -
324B ALA* 2.9 31.3 + - - +
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Residues in contact with MET 321 (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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184B ARG* 3.9 7.0 - - + -
185B LEU* 3.5 32.5 - - + -
190B LEU* 4.5 10.3 - - + -
193B LEU* 4.1 26.5 - - + -
273B ILE* 6.2 0.7 - - + -
298B VAL* 3.9 28.5 - - + -
314B ILE* 4.2 17.0 - - + -
316B ALA* 3.5 25.6 - - + -
317B ASP 2.9 13.0 + - - +
318B ILE* 3.9 2.0 - - - +
320B ALA* 1.3 76.6 - - - +
322B ALA* 1.3 63.6 + - - +
324B ALA* 3.3 4.0 + - - +
325B LEU* 3.0 40.5 + - + +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA* 3.7 24.5 - - + -
219B ASP* 3.7 11.4 - - + +
220B CYS* 4.3 14.6 - - - -
223B LEU* 5.4 3.5 - - - +
273B ILE* 5.2 10.7 - - + +
318B ILE* 2.8 26.4 + - + +
319B GLY 3.9 0.7 - - - +
321B MET* 1.3 72.6 - - - +
323B SER* 1.3 58.6 + - - +
325B LEU* 4.1 5.1 - - - +
326B ALA* 3.0 32.1 + - - +
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Residues in contact with SER 323 (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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219B ASP* 3.5 23.1 + - - -
319B GLY 3.1 18.4 + - - -
320B ALA* 3.8 5.4 - - - -
322B ALA* 1.3 76.4 - - - +
324B ALA* 1.3 64.0 + - - +
326B ALA* 3.8 0.3 - - - +
327B ASN* 3.0 38.6 + - - +
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Residues in contact with ALA 324 (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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184B ARG* 5.1 11.2 - - + +
190B LEU* 4.2 25.8 - - + -
320B ALA 2.9 18.4 + - - +
321B MET* 3.7 6.3 - - - +
323B SER* 1.3 78.5 + - - +
325B LEU* 1.3 61.5 + - - +
327B ASN* 3.4 2.8 + - - +
328B LEU* 3.1 32.7 + - + +
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Residues in contact with LEU 325 (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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190B LEU* 4.0 11.0 - - + -
193B LEU* 3.9 30.1 - - + -
194B VAL* 3.8 26.5 - - + -
197B LEU* 4.0 20.9 - - + -
223B LEU* 4.6 14.6 - - + -
271B LEU* 4.4 18.6 - - + -
273B ILE* 5.1 4.7 - - + -
298B VAL* 5.1 3.4 - - + -
321B MET* 3.0 29.2 + - + +
322B ALA* 4.2 3.1 - - - +
324B ALA* 1.3 74.2 - - - +
326B ALA* 1.3 66.5 + - - +
328B LEU* 3.0 12.7 + - - -
329B VAL* 3.0 21.2 + - + +
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Residues in contact with ALA 326 (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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219B ASP* 3.2 36.1 - - + +
222B MET* 3.3 27.1 - - + +
223B LEU* 4.1 16.5 - - + +
226B ARG* 4.5 4.5 + - - +
322B ALA 3.0 20.3 + - - +
323B SER 3.8 4.5 - - - +
325B LEU* 1.3 77.4 - - - +
327B ASN* 1.3 60.3 + - - +
328B LEU 3.7 0.3 + - - -
329B VAL* 3.8 10.5 - - - +
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Residues in contact with ASN 327 (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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219B ASP* 4.6 5.3 + - - -
222B MET* 3.4 23.4 - - - +
226B ARG* 6.0 0.7 - - - -
323B SER* 3.0 35.8 + - - +
324B ALA* 3.7 2.9 - - - +
325B LEU 3.1 0.6 - - - -
326B ALA* 1.3 79.9 - - - +
328B LEU* 1.3 65.2 + - + +
329B VAL 4.8 2.5 - - - +
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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