Contacts of the helix formed by residues 320 - 334 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202H ILE* 3.8 4.7 - - - +
203H LYS 2.7 22.9 + - - -
204H LYS 3.4 10.5 - - - -
206H GLY 3.6 3.7 + - - -
259H GLY* 3.6 7.3 - - - -
260H GLY 2.8 27.6 + - - -
319H GLY* 1.3 71.2 - - - -
321H PRO* 1.3 70.7 - - - +
323H ASP* 3.0 26.0 + - - +
324H VAL* 2.9 21.4 + - - +
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Residues in contact with PRO 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H ILE* 4.0 4.5 - - + +
203H LYS 3.7 9.0 - - - +
204H LYS* 3.5 24.0 - - + +
292H GLY 3.6 23.6 - - - +
294H MET* 3.8 30.2 - - + +
319H GLY 3.5 4.0 - - - +
320H SER* 1.3 82.3 - - - +
322H ASP* 1.3 57.4 + - - +
325H LEU* 2.9 40.7 + - + +
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Residues in contact with ASP 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H LYS* 2.8 64.2 + - - +
205H LYS* 3.7 35.3 + - + +
321H PRO* 1.3 77.3 - - - +
323H ASP* 1.3 57.3 + - - +
325H LEU* 4.0 8.4 - - - +
326H GLU* 3.0 28.2 + - - +
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Residues in contact with ASP 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205H LYS* 3.6 9.5 + - - -
206H GLY* 2.7 31.7 + - - -
226H TYR* 3.6 17.4 + - - +
230H LYS* 5.0 0.2 + - - -
240H TYR* 2.5 37.2 + - - -
260H GLY* 3.6 6.6 - - - +
261H ILE* 3.7 18.3 - - + +
320H SER* 3.0 18.3 + - - +
322H ASP* 1.3 74.5 - - - +
324H VAL* 1.3 60.2 + - - +
326H GLU* 3.2 7.7 + - - +
327H PHE 3.0 23.7 + - - -
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Residues in contact with VAL 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H ILE* 4.0 12.8 - - + -
294H MET* 3.7 33.0 - - + +
296H THR* 3.8 28.7 - - + -
317H ILE* 4.1 4.9 - - + +
318H LEU* 3.6 10.1 - - - +
319H GLY 3.5 28.9 - - - +
320H SER 2.9 19.3 + - - +
321H PRO 4.1 0.7 - - - +
323H ASP* 1.3 75.7 - - - +
325H LEU* 1.3 57.2 + - - +
327H PHE* 3.2 4.8 + - - +
328H LEU* 3.0 30.4 + - + +
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Residues in contact with LEU 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294H MET* 3.7 30.7 - - + -
321H PRO* 2.9 30.3 + - + +
322H ASP* 4.0 9.0 - - - +
324H VAL* 1.3 75.7 - - - +
326H GLU* 1.3 58.0 + - - +
328H LEU* 3.3 15.6 + - + +
329H LYS* 2.9 27.0 + - - +
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Residues in contact with GLU 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205H LYS* 2.9 26.7 + - - -
226H TYR* 3.7 11.1 - - + -
229H ARG* 4.7 12.2 + - - +
230H LYS* 2.8 32.7 + - - -
322H ASP 3.0 16.2 + - - +
323H ASP* 3.2 6.7 + - - +
325H LEU* 1.3 73.6 - - - +
327H PHE* 1.3 65.4 + - - +
329H LYS* 3.2 26.1 + - - +
330H VAL* 3.1 23.9 + - + +
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Residues in contact with PHE 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H ALA* 4.5 4.7 - - + -
223H VAL* 4.2 29.8 - - + -
226H TYR* 3.7 32.0 - + + -
261H ILE* 4.1 10.3 - - + -
263H LEU* 3.9 20.4 - - + -
265H PRO* 5.1 1.6 - - + -
296H THR* 4.8 0.4 - - + -
298H GLY* 4.5 6.5 - - - -
317H ILE* 3.6 42.0 - - + -
323H ASP 3.0 12.8 + - - +
324H VAL 3.5 7.6 - - - +
326H GLU* 1.3 75.4 - - - +
328H LEU* 1.3 61.6 + - + +
330H VAL* 3.2 4.2 + - - +
331H TYR* 2.8 60.0 + + + +
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Residues in contact with LEU 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294H MET* 4.7 6.1 - - + -
296H THR* 3.7 36.1 - - + +
298H GLY* 3.7 27.1 - - - +
324H VAL* 3.0 21.9 + - + +
325H LEU* 3.5 28.5 - - + +
327H PHE* 1.3 77.0 - - + +
329H LYS* 1.3 59.5 + - - +
331H TYR* 3.7 5.0 - - + +
332H GLU* 2.9 35.1 + - + +
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Residues in contact with LYS 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229H ARG* 4.6 15.7 - - - +
325H LEU 2.9 12.4 + - - +
326H GLU* 3.2 28.3 + - - +
328H LEU* 1.3 75.5 - - - +
330H VAL* 1.3 63.0 + - + +
332H GLU* 3.6 5.2 + - - +
333H LYS* 3.2 21.4 + - + +
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Residues in contact with VAL 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H ALA* 3.4 26.7 - - - +
225H GLU* 3.8 28.0 - - + -
226H TYR* 3.9 19.7 - - + +
229H ARG* 3.9 32.1 - - - +
326H GLU* 3.1 16.4 + - + +
327H PHE 3.2 5.8 + - - +
329H LYS* 1.3 76.4 - - + +
331H TYR* 1.3 65.2 + - - +
333H LYS* 3.2 20.3 + - + +
334H HIS* 3.3 10.7 + - - +
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Residues in contact with TYR 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220H ASP* 4.8 15.5 - - - -
222H ALA* 3.8 16.8 - - + +
223H VAL* 6.3 0.4 - - + -
266H ALA* 6.2 3.5 - - + +
297H THR 5.1 2.9 + - - -
298H GLY* 3.2 36.3 - - - +
299H LYS* 3.6 29.9 - - + +
327H PHE* 2.8 44.8 + + + +
328H LEU* 3.7 8.3 - - + +
330H VAL* 1.3 76.8 - - - +
332H GLU* 1.3 67.3 + - + +
334H HIS* 3.2 14.6 + - - +
335H SER* 3.2 30.6 + - - -
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Residues in contact with GLU 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H LEU* 2.9 18.7 + - + +
329H LYS* 3.8 6.5 - - - +
331H TYR* 1.3 75.6 - - + +
333H LYS* 1.3 65.3 + - - +
334H HIS 3.1 2.9 + - - -
335H SER* 3.2 25.0 + - - +
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Residues in contact with LYS 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H GLU* 2.6 43.2 + - - +
229H ARG* 3.7 11.0 - - - +
329H LYS* 3.2 14.6 + - + +
330H VAL* 3.2 13.9 + - - +
332H GLU* 1.3 77.4 - - - +
334H HIS* 1.3 63.5 + - + +
335H SER 3.6 0.6 - - - +
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Residues in contact with HIS 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220H ASP* 5.0 2.5 - - - +
221H PRO* 3.7 42.1 + - + +
222H ALA* 3.6 18.5 - - + +
225H GLU* 2.8 34.0 + - + -
330H VAL 3.3 16.6 + - - -
331H TYR 3.2 8.8 + - - +
332H GLU 3.1 0.6 - - - -
333H LYS* 1.3 89.6 - - + +
335H SER* 1.3 59.5 + - - +
336H ALA 3.8 1.9 + - - -
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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