Contacts of the helix formed by residues 204 - 216 (chain D) in PDB entry 2VT4
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 ASN 204 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404C SOG 4.0 4.0 - - - +
181D TRP 3.0 24.3 + - - +
182D TRP* 3.0 16.8 + - - +
183D ARG 2.7 25.5 + - - +
184D ASP* 3.6 25.1 - - - +
203D THR* 1.3 79.5 + - - +
205D ARG* 1.3 60.2 + - - +
206D ALA* 3.4 12.6 - - - +
207D TYR* 2.8 29.5 + - - +
208D ALA* 2.9 26.0 + - - +
402D SOG 3.8 21.0 + - - +
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Residues in contact with ARG 205 (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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157C ARG* 4.2 21.8 - - - +
404C SOG 3.6 62.1 + - + +
203D THR 4.0 0.2 + - - -
204D ASN* 1.3 70.4 - - - +
206D ALA* 1.3 65.2 + - - +
208D ALA* 3.7 6.4 - - - +
209D ILE* 3.0 29.3 + - - +
314D VAL* 3.4 45.4 + - + +
315D PHE* 4.4 13.7 + - - +
316D ASN* 5.8 0.8 - - - +
317D ARG* 4.1 24.2 - - - +
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C VAL* 4.2 15.9 - - + -
164C THR* 3.5 25.4 - - - +
404C SOG 3.7 19.8 - - + +
204D ASN* 3.3 10.2 + - + +
205D ARG* 1.3 77.8 - - - +
207D TYR* 1.3 63.2 + - - +
209D ILE* 3.4 1.6 + - - +
210D ALA* 3.0 26.9 + - - +
402D SOG 4.1 17.0 - - + +
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Residues in contact with TYR 207 (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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122D VAL* 4.8 10.2 - - - +
172D VAL 5.7 0.9 - - - -
173D SER* 5.3 2.1 + - - -
176D PRO* 4.1 21.2 - - + +
177D ILE* 4.6 8.7 - - + +
181D TRP 3.8 12.1 - - - +
182D TRP* 3.7 25.6 - - + +
201D PHE* 3.7 31.5 - + - -
203D THR* 3.7 16.8 - - + -
204D ASN* 2.8 24.4 + - - +
206D ALA* 1.3 72.5 - - - +
208D ALA* 1.3 63.2 + - - +
210D ALA 3.2 0.3 + - - -
211D SER* 2.8 60.4 + - - -
400D P32 4.0 9.4 + - - -
402D SOG 3.9 28.6 - - + +
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Residues in contact with ALA 208 (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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203D THR* 3.5 11.7 - - - +
204D ASN 2.9 18.5 + - - +
205D ARG* 3.7 4.9 - - - +
207D TYR* 1.3 78.1 - - - +
209D ILE* 1.3 58.0 + - - +
211D SER* 3.8 0.9 + - - -
212D SER* 2.6 30.5 + - - -
310D ASN* 4.3 6.6 + - - +
314D VAL* 3.8 20.4 - - + -
400D P32 3.7 19.7 + - - +
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Residues in contact with ILE 209 (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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404C SOG 4.0 34.5 - - + -
205D ARG 3.0 18.5 + - - +
206D ALA 4.0 2.2 - - - +
208D ALA* 1.3 73.4 - - - +
210D ALA* 1.3 60.4 + - - +
212D SER* 3.3 5.1 + - - -
213D ILE* 2.9 49.7 + - + +
311D ILE* 5.7 11.4 - - + -
314D VAL* 3.6 34.8 - - + -
315D PHE* 5.1 7.2 - - + -
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Residues in contact with ALA 210 (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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164C THR* 3.9 12.1 - - + -
168C ILE* 3.8 27.8 - - + -
404C SOG 4.7 4.3 - - + -
206D ALA 3.0 17.8 + - - +
207D TYR 4.0 1.6 - - - +
209D ILE* 1.3 77.7 - - - +
211D SER* 1.3 65.8 + - - +
213D ILE* 3.3 7.0 + - - +
214D ILE* 3.0 30.9 + - - +
402D SOG 4.1 12.1 - - + -
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Residues in contact with SER 211 (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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122D VAL* 6.2 0.4 - - - -
172D VAL 5.4 3.8 - - - -
207D TYR* 2.8 53.0 + - - -
208D ALA 3.8 0.3 + - - -
210D ALA* 1.3 73.1 - - - +
212D SER* 1.3 57.4 + - - +
214D ILE* 4.6 0.2 - - - -
215D SER* 2.8 38.1 + - - -
400D P32 2.7 34.0 + - - -
402D SOG 4.3 15.1 - - - +
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Residues in contact with SER 212 (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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208D ALA 2.6 22.8 + - - -
209D ILE* 3.3 6.2 + - - -
210D ALA 3.1 0.4 - - - -
211D SER* 1.3 75.7 + - - +
213D ILE* 1.3 65.2 + - - +
214D ILE 3.1 1.3 - - - -
216D PHE* 3.1 20.7 + - - +
217D TYR* 3.1 24.4 + - - -
307D PHE* 4.1 22.1 - - - -
310D ASN* 3.7 17.9 + - - -
311D ILE* 5.5 5.8 - - - -
400D P32 4.0 7.5 + - - -
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Residues in contact with ILE 213 (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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404C SOG 5.0 7.9 - - + -
406C D10 6.1 0.4 - - + -
209D ILE* 2.9 40.1 + - + +
210D ALA* 3.3 7.2 + - - +
212D SER* 1.3 76.2 - - - +
214D ILE* 1.3 65.1 + - + +
217D TYR* 3.7 16.8 + - + -
218D ILE* 3.0 55.9 + - + +
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Residues in contact with ILE 214 (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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168C ILE* 3.8 43.5 - - + -
172C VAL* 6.0 1.3 - - + -
406C D10 3.7 48.7 - - + +
130D GLU* 4.7 4.3 - - - +
172D VAL* 3.9 34.3 - - + +
210D ALA* 3.0 19.8 + - + +
211D SER 4.2 1.6 - - - +
213D ILE* 1.3 86.2 - - + +
215D SER* 1.3 62.8 + - - +
219D PRO* 3.8 9.0 - - - +
402D SOG 3.9 17.5 - - + -
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Residues in contact with SER 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D VAL* 4.6 1.7 - - - +
125D VAL* 5.2 1.1 - - - +
126D THR* 3.1 35.8 + - - +
129D ILE* 3.2 25.5 - - - +
172D VAL* 3.9 18.0 + - - +
211D SER* 2.8 24.1 + - - -
214D ILE* 1.3 75.2 - - - +
216D PHE* 1.3 59.2 + - - +
219D PRO* 3.5 6.0 - - - +
400D P32 3.6 23.0 - - - -
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Residues in contact with PHE 216 (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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125D VAL* 4.7 6.7 - - + -
129D ILE* 4.2 4.8 - - + +
212D SER 3.1 10.2 + - - +
214D ILE 3.5 1.0 - - - -
215D SER* 1.3 80.0 - - - +
217D TYR* 1.3 78.7 + + - +
218D ILE 3.5 1.3 - - - -
219D PRO* 3.3 4.2 - - - +
220D LEU* 2.8 67.6 + - + +
299D PHE* 4.0 20.6 - + - -
300D THR* 5.2 2.2 - - - -
303D TRP* 3.7 16.2 - - + -
304D LEU* 3.9 23.1 - - + -
307D PHE* 3.3 57.4 - + + -
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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