Contacts of the helix formed by residues 320 - 334 (chain D) in PDB entry 2VT5
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 SER 320 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D ILE* 3.4 5.8 - - - +
203D LYS 2.8 22.7 + - - -
204D LYS 3.5 9.6 - - - -
205D LYS* 3.9 0.7 - - - -
206D GLY 3.7 2.8 + - - -
259D GLY* 3.4 8.3 - - - -
260D GLY 3.0 25.5 + - - -
319D GLY* 1.3 73.1 - - - -
321D PRO* 1.3 69.7 - - - +
323D ASP* 3.2 25.2 + - - +
324D VAL* 3.0 20.6 + - - +
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Residues in contact with PRO 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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202D ILE* 4.2 2.9 - - + +
203D LYS 3.7 9.0 - - - +
204D LYS* 3.4 25.8 - - + +
292D GLY 3.6 24.0 - - - +
293D GLY* 4.2 0.2 - - - -
294D MET* 3.9 31.1 - - + +
319D GLY 3.6 2.6 - - - +
320D SER* 1.3 83.9 - - - +
322D ASP* 1.3 58.7 + - - +
324D VAL 4.5 0.2 - - - +
325D LEU* 2.9 41.3 + - + +
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Residues in contact with ASP 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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204D LYS* 2.9 62.4 + - - +
205D LYS* 3.7 32.1 + - + +
321D PRO* 1.3 73.4 - - - +
323D ASP* 1.3 57.1 + - - +
325D LEU* 4.1 8.9 - - - +
326D GLU* 3.1 28.9 + - - +
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Residues in contact with ASP 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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205D LYS* 3.7 9.4 + - - +
206D GLY* 2.9 29.8 + - - -
226D TYR* 3.6 16.6 + - - +
240D TYR* 2.6 37.8 + - - -
260D GLY* 3.7 6.1 - - - -
261D ILE* 4.0 16.6 - - + -
320D SER* 3.2 18.9 + - - +
321D PRO 3.2 0.6 - - - -
322D ASP* 1.3 75.0 - - - +
324D VAL* 1.3 59.8 + - - +
326D GLU* 3.3 6.7 + - - +
327D PHE* 2.8 28.4 + - - +
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Residues in contact with VAL 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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261D ILE* 4.1 13.2 - - + -
294D MET* 3.7 33.0 - - + +
296D THR* 3.6 29.6 - - + -
317D ILE* 4.1 5.8 - - + +
318D LEU* 3.7 12.6 - - - +
319D GLY* 3.7 27.4 - - - +
320D SER 3.0 16.9 + - - +
321D PRO 4.0 0.7 - - - +
323D ASP* 1.3 74.8 - - - +
325D LEU* 1.3 57.6 + - - +
327D PHE* 3.3 3.2 + - - +
328D LEU* 2.9 28.2 + - + +
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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
----------------------------------------------------------
294D MET* 3.7 27.1 - - + -
321D PRO* 2.9 24.9 + - + +
322D ASP* 4.1 9.0 - - - +
324D VAL* 1.3 73.8 - - - +
326D GLU* 1.3 61.1 + - - +
328D LEU* 3.3 13.5 + - + +
329D LYS* 2.9 27.4 + - - +
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Residues in contact with GLU 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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205D LYS* 3.3 26.7 + - - -
226D TYR* 3.9 9.8 - - + -
229D ARG* 4.7 13.2 + - - +
230D LYS* 2.8 32.7 + - - -
322D ASP 3.1 18.4 + - - +
323D ASP* 3.5 7.5 - - - +
324D VAL 3.3 0.2 - - - -
325D LEU* 1.3 74.7 - - - +
327D PHE* 1.3 65.1 + - - +
329D LYS* 3.3 26.2 + - - +
330D VAL* 3.2 23.8 + - + +
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Residues in contact with PHE 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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222D ALA 4.9 2.0 - - - -
223D VAL* 4.0 26.9 - - + -
226D TYR* 3.7 30.6 - + + -
261D ILE* 4.0 12.1 - - + -
263D LEU* 3.8 23.6 - - + -
265D PRO* 4.9 0.9 - - + -
296D THR* 4.6 0.9 - - + -
298D GLY* 4.5 1.6 - - - -
317D ILE* 3.6 43.5 - - + -
323D ASP 2.8 14.3 + - - +
324D VAL 3.3 8.5 + - - +
326D GLU* 1.3 77.3 - - - +
328D LEU* 1.3 69.4 + - + +
330D VAL* 3.2 4.9 + - - +
331D TYR* 2.8 56.7 + + + +
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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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294D MET* 4.2 19.1 - - + -
296D THR* 3.5 37.2 - - + +
298D GLY* 3.3 30.7 - - - +
324D VAL 2.9 20.1 + - - +
325D LEU* 3.3 13.2 + - + +
327D PHE* 1.3 80.9 - - + +
329D LYS* 1.3 53.3 + - - +
331D TYR* 3.4 5.7 - - + +
332D GLU* 2.8 37.6 + - - +
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Residues in contact with LYS 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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229D ARG* 4.6 14.6 - - - +
325D LEU 2.9 12.7 + - - +
326D GLU* 3.4 27.1 - - - +
328D LEU* 1.3 76.3 - - - +
330D VAL* 1.3 62.9 + - + +
332D GLU* 3.6 7.2 + - - +
333D LYS* 3.2 19.6 + - - +
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Residues in contact with VAL 330 (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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222D ALA* 3.5 26.9 - - - +
225D GLU* 3.9 27.4 - - + -
226D TYR* 4.0 21.1 - - + +
229D ARG* 3.8 31.6 - - - +
326D GLU* 3.2 15.7 + - + +
327D PHE* 3.2 6.6 + - + +
329D LYS* 1.3 74.8 - - + +
331D TYR* 1.3 66.7 + - - +
333D LYS* 3.2 21.1 + - + +
334D HIS* 3.3 11.6 + - + +
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Residues in contact with TYR 331 (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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220D ASP* 4.9 14.1 - - - -
222D ALA* 3.9 15.6 - - + +
223D VAL* 6.2 0.7 - - + -
266D ALA* 6.1 3.2 - - + +
297D THR 4.9 3.9 + - - -
298D GLY* 3.2 35.2 - - - -
299D LYS* 3.6 28.8 + - + +
317D ILE* 6.2 0.2 - - + -
327D PHE* 2.8 43.3 + + + +
328D LEU* 3.4 11.7 - - + +
330D VAL* 1.3 76.8 - - - +
332D GLU* 1.3 64.9 + - + +
334D HIS* 3.3 8.0 + - - +
335D SER* 3.2 34.3 + - - -
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Residues in contact with GLU 332 (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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328D LEU 2.8 16.6 + - - +
329D LYS* 3.8 7.2 - - - +
331D TYR* 1.3 75.7 - - + +
333D LYS* 1.3 61.7 + - - +
335D SER* 2.9 36.4 + - - +
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Residues in contact with LYS 333 (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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225D GLU* 2.8 44.2 + - - +
229D ARG* 3.8 11.6 - - - +
329D LYS 3.2 11.9 + - - +
330D VAL* 3.2 15.8 + - + +
332D GLU* 1.3 77.4 - - - +
334D HIS* 1.3 65.1 + - + +
335D SER 3.9 1.6 + - - +
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Residues in contact with HIS 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ASP* 4.9 3.6 - - - +
221D PRO* 3.5 34.8 + - + +
222D ALA* 3.6 27.2 - - + +
225D GLU* 3.1 29.6 + - + -
330D VAL* 3.3 13.4 + - + -
331D TYR 3.3 8.5 + - - +
332D GLU 3.1 0.2 - - - -
333D LYS* 1.3 87.6 - - + +
335D SER* 1.3 64.0 + - - +
336D ALA 3.5 1.4 + - - -
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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