Contacts of the helix formed by residues 317 - 329 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D ALA* 5.0 10.7 - - + +
181D SER* 3.7 10.4 + - - +
182D SER* 3.5 21.5 + - - -
183D VAL* 3.1 30.0 + - - +
214D ALA* 5.4 2.7 - - - +
300D CYS* 4.7 5.1 - - - +
316D ALA* 1.3 72.4 - - - +
318D ILE* 1.3 60.2 + - - +
319D GLY* 3.1 9.1 + - - -
320D ALA* 3.0 24.7 + - + -
321D MET* 3.0 31.6 + - - +
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Residues in contact with ILE 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ASP* 3.9 38.6 - - + +
211D VAL* 4.0 14.8 - - + -
214D ALA* 4.3 3.8 - - + +
216D ALA* 4.5 7.4 - - + -
273D ILE* 3.8 21.1 - - + -
274D GLY* 3.9 7.6 - - - +
298D VAL* 3.8 31.0 - - + +
299D THR 4.0 0.9 - - - -
300D CYS* 3.9 28.6 - - + +
316D ALA 3.9 3.8 - - - +
317D ASP* 1.3 74.0 + - - +
319D GLY* 1.3 54.8 + - - +
321D MET* 4.5 2.5 - - - -
322D ALA* 2.7 34.0 + - + +
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Residues in contact with GLY 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ALA* 3.8 22.6 - - - +
216D ALA* 4.4 8.5 - - - -
219D ASP* 4.4 2.6 - - - +
317D ASP* 3.1 8.4 + - - -
318D ILE* 1.3 78.3 - - - +
320D ALA* 1.3 61.2 + - - +
322D ALA* 4.0 0.9 - - - +
323D SER* 3.0 26.3 + - - -
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Residues in contact with ALA 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ASN* 4.4 13.7 - - + -
182D SER* 3.9 14.1 + - - +
183D VAL 3.7 23.6 - - - +
184D ARG* 4.1 14.9 - - + +
317D ASP* 3.0 12.7 + - - +
319D GLY* 1.3 74.8 - - - +
321D MET* 1.3 58.6 + - - +
323D SER* 3.7 4.7 - - - -
324D ALA* 3.0 28.6 + - - +
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Residues in contact with MET 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ARG* 3.8 6.5 - - + -
185D LEU* 3.6 31.2 - - + -
190D LEU* 4.5 11.4 - - + -
193D LEU* 4.3 18.6 - - + -
273D ILE* 6.1 0.7 - - + -
298D VAL* 3.9 39.7 - - + -
314D ILE* 4.0 16.4 - - + -
316D ALA* 3.6 19.5 - - + -
317D ASP 3.0 20.7 + - - +
318D ILE* 3.9 2.2 - - - +
320D ALA* 1.3 74.9 - - - +
322D ALA* 1.3 67.2 + - - +
324D ALA* 3.2 2.8 + - - +
325D LEU* 3.0 36.3 + - + +
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ALA* 3.7 24.9 - - + -
219D ASP* 4.0 11.1 - - + +
220D CYS* 4.4 14.6 - - - +
223D LEU* 5.5 2.6 - - + +
273D ILE* 5.2 9.8 - - + +
318D ILE* 2.7 25.4 + - + +
319D GLY 4.0 0.7 - - - +
321D MET* 1.3 73.3 - - - +
323D SER* 1.3 64.6 + - - +
325D LEU* 3.9 6.2 - - - +
326D ALA* 3.0 26.9 + - - +
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Residues in contact with SER 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ASP* 3.5 23.7 + - - -
319D GLY 3.0 18.7 + - - -
320D ALA* 3.7 5.6 - - - -
322D ALA* 1.3 79.7 - - - +
324D ALA* 1.3 61.2 + - - +
326D ALA* 3.6 1.0 + - - +
327D ASN* 3.0 40.4 + - - -
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ARG* 4.8 13.9 - - + +
190D LEU* 4.2 25.8 - - + -
320D ALA 3.0 19.3 + - - +
321D MET* 3.2 6.5 + - - +
323D SER* 1.3 75.9 - - - +
325D LEU* 1.3 64.3 + - - +
327D ASN* 3.2 5.2 + - - +
328D LEU* 3.1 33.4 + - + +
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Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D LEU* 3.9 26.2 - - + -
193D LEU* 3.9 22.0 - - + -
194D VAL* 4.1 14.8 - - + -
197D LEU* 4.2 9.4 - - + -
223D LEU* 3.9 18.6 - - + -
271D LEU* 4.1 27.4 - - + -
273D ILE* 4.6 9.2 - - + -
298D VAL* 5.0 3.4 - - + -
321D MET* 3.0 30.9 + - + +
322D ALA* 3.9 2.5 - - - +
324D ALA* 1.3 75.6 - - - +
326D ALA* 1.3 65.4 + - - +
328D LEU* 3.0 14.2 + - - -
329D VAL* 3.1 19.6 + - + +
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ASP* 3.3 34.5 - - + +
222D MET* 3.4 20.1 - - - +
223D LEU* 3.9 20.6 - - + +
226D ARG* 3.3 20.1 + - - +
322D ALA 3.0 16.8 + - - +
323D SER 3.9 3.8 - - - +
325D LEU* 1.3 77.0 - - - +
327D ASN* 1.3 59.4 + - - +
328D LEU 3.8 0.2 + - - -
329D VAL* 4.2 4.7 - - - +
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Residues in contact with ASN 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ASP* 5.2 4.2 + - - -
222D MET* 3.8 20.7 - - - +
226D ARG* 4.4 9.7 + - - +
323D SER* 3.0 33.5 + - - +
324D ALA* 3.2 4.8 + - - +
325D LEU 3.0 1.0 - - - -
326D ALA* 1.3 78.8 - - - +
328D LEU* 1.3 67.5 + - + +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ARG* 6.1 1.1 - - - +
190D LEU* 3.7 32.5 - - + -
191D ASP* 4.8 10.1 - - - +
194D VAL* 3.8 27.4 - - + +
198D ASN* 4.7 1.2 + - - -
324D ALA* 3.1 21.2 + - + +
325D LEU 3.0 2.5 + - - +
327D ASN* 1.3 85.5 - - + +
329D VAL* 1.3 66.1 + - - +
330D GLU* 3.7 2.9 + - - +
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Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D VAL* 4.2 14.8 - - + -
197D LEU* 4.1 30.1 - - + -
198D ASN* 3.7 7.6 - - - +
223D LEU* 3.7 26.0 - - + -
226D ARG* 3.4 41.1 + - + -
227D LEU* 4.4 9.6 - - + -
325D LEU* 3.1 18.1 + - - +
326D ALA 4.2 6.1 - - - +
328D LEU* 1.3 78.0 - - - +
330D GLU* 1.3 65.3 + - - +
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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
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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