Contacts of the helix formed by residues 191 - 205 (chain B) in PDB entry 3DL2
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 GLY 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A TRP* 5.6 1.3 - - - -
189B GLY* 3.5 3.4 - - - -
190B GLY* 1.3 79.9 - - - +
192B GLU* 1.3 67.0 + - - -
193B LEU 3.2 3.4 - - - -
194B GLY 3.0 2.9 + - - +
195B ILE* 3.0 21.4 + - - +
252B THR* 5.4 0.4 + - - -
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Residues in contact with GLU 192 (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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192A GLU* 4.2 22.4 - - - +
386A ARG* 4.0 25.2 - - + +
387A SER* 5.0 3.7 + - - -
388A TRP* 3.9 26.9 + - + +
191B GLY* 1.3 71.4 - - - +
193B LEU* 1.3 57.9 + - - +
195B ILE* 3.4 8.1 + - - +
196B ALA* 2.9 29.8 + - - +
387B SER* 4.0 22.2 + - - +
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Residues in contact with LEU 193 (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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191B GLY 3.2 0.8 - - - -
192B GLU* 1.3 79.0 - - - +
194B GLY* 1.3 64.1 + - - +
196B ALA* 3.3 1.1 + - - +
197B CYS* 3.0 29.7 + - - -
252B THR* 3.8 33.4 - - + +
254B ASN* 5.2 4.3 - - - +
292B ALA* 3.9 28.3 - - + +
387B SER* 3.6 35.7 + - - +
390B VAL* 3.7 26.0 - - + -
391B GLY 4.0 5.8 - - - +
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Residues in contact with GLY 194 (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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187B VAL* 3.6 11.8 - - - +
189B GLY 3.3 26.0 - - - -
191B GLY* 3.0 7.5 + - - +
193B LEU* 1.3 77.6 - - - +
195B ILE* 1.3 53.0 + - - +
197B CYS 3.5 0.2 + - - -
198B THR* 2.8 36.6 + - - -
212B LEU* 4.3 2.5 - - - -
252B THR* 3.5 14.3 + - - -
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Residues in contact with ILE 195 (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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388A TRP* 3.7 63.3 - - + -
190B GLY 3.8 13.0 - - - +
191B GLY 3.0 18.6 + - - +
192B GLU* 3.6 8.3 - - - +
194B GLY* 1.3 74.1 - - - +
196B ALA* 1.3 59.6 + - - +
198B THR* 3.2 5.1 + - - -
199B LEU* 2.9 44.1 + - + +
212B LEU* 4.0 11.9 - - + -
223B THR* 4.5 4.0 - - + -
226B LEU* 4.0 28.3 - - + -
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Residues in contact with ALA 196 (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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199A LEU* 4.8 7.1 - - + +
192B GLU 2.9 17.8 + - - +
193B LEU 3.6 4.0 - - - +
195B ILE* 1.3 77.8 - - - +
197B CYS* 1.3 55.9 + - - +
199B LEU* 4.0 5.9 - - - +
200B ALA* 3.0 31.9 + - - +
387B SER* 3.5 32.3 - - - +
388B TRP* 4.0 10.9 - - + +
391B GLY* 4.0 6.0 - - - -
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Residues in contact with CYS 197 (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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187B VAL* 4.2 15.5 - - + -
193B LEU* 3.0 26.2 + - - +
194B GLY 3.7 4.5 - - - +
196B ALA* 1.3 75.1 - - - +
198B THR* 1.3 57.8 + - - +
200B ALA* 3.4 1.0 + - - +
201B ILE* 2.9 40.2 + - + +
250B ILE* 4.5 1.6 - - + -
252B THR* 3.9 19.5 - - - -
391B GLY* 4.0 16.6 - - - -
394B VAL* 3.8 36.6 - - + -
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Residues in contact with THR 198 (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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187B VAL* 3.9 7.4 - - - +
194B GLY 2.8 21.4 + - - -
195B ILE* 3.5 8.1 - - - -
197B CYS* 1.3 76.4 - - - +
199B LEU* 1.3 55.5 + - - +
201B ILE* 3.5 1.4 + - - +
202B SER* 2.7 43.8 + - - +
210B LEU* 3.8 28.1 - - + +
212B LEU* 3.6 19.6 - - + +
226B LEU* 4.1 24.2 - - + -
231B LEU* 4.8 4.7 - - + -
234B VAL* 4.3 9.9 - - + -
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Residues in contact with LEU 199 (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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196A ALA* 4.7 9.9 - - + +
199A LEU* 4.1 27.3 - - + +
200A ALA* 4.3 8.1 - - - +
203A ALA* 4.1 15.0 - - + +
388A TRP* 5.1 8.7 - - + +
392A LEU* 4.0 30.3 - - + -
195B ILE* 2.9 38.7 + - + +
196B ALA* 4.1 4.7 - - - +
198B THR* 1.3 70.6 - - - +
200B ALA* 1.3 56.4 + - - +
202B SER* 3.7 2.8 - - - -
203B ALA* 2.8 36.5 + - - +
226B LEU* 4.5 5.4 - - + -
229B PHE* 5.0 0.2 - - + -
231B LEU* 4.2 20.9 - - + -
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Residues in contact with ALA 200 (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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199A LEU* 4.3 13.6 - - + +
229A PHE* 3.5 14.0 - - + -
196B ALA 3.0 19.7 + - - +
197B CYS 3.8 0.9 - - - +
199B LEU* 1.3 75.8 - - - +
201B ILE* 1.3 61.6 + - - +
203B ALA* 3.4 2.1 + - - +
204B LYS* 3.4 17.2 + - - +
391B GLY 3.7 21.5 - - - +
392B LEU* 3.9 21.8 - - + -
395B ALA* 3.7 9.6 - - + -
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 4.3 8.7 - - + -
187B VAL* 4.5 1.3 - - + -
197B CYS* 2.9 26.4 + - + +
198B THR 3.9 2.5 - - - +
200B ALA* 1.3 74.8 - - - +
202B SER* 1.3 63.0 + - - +
204B LYS* 3.5 2.1 + - - -
205B GLY 3.2 2.8 + - - -
206B ILE* 3.1 37.9 + - + +
207B ALA* 3.7 26.0 + - + +
210B LEU* 3.7 28.5 - - + -
250B ILE* 3.8 29.6 - - + -
394B VAL* 5.1 0.7 - - + -
395B ALA* 3.7 23.3 - - + -
398B VAL* 4.4 11.2 - - + -
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Residues in contact with SER 202 (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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202A SER 4.8 0.3 - - - +
203A ALA* 3.8 28.5 - - - +
198B THR* 2.7 23.8 + - - +
199B LEU 3.8 3.6 - - - -
201B ILE* 1.3 75.0 - - - +
203B ALA* 1.3 64.8 + - - +
205B GLY* 3.0 15.0 + - - +
207B ALA* 5.9 1.1 - - - +
210B LEU* 4.8 3.3 - - - +
231B LEU* 4.0 10.9 - - - +
234B VAL* 3.8 22.9 - - - +
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Residues in contact with ALA 203 (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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199A LEU* 4.1 13.9 - - + +
202A SER* 3.8 25.9 - - - +
203A ALA* 3.6 15.4 - - - +
231A LEU* 3.8 24.1 - - + +
232A PRO* 5.3 5.2 - - - +
199B LEU 2.8 22.1 + - - +
200B ALA 3.7 5.2 - - - +
201B ILE 3.4 0.4 - - - -
202B SER* 1.3 73.7 - - - +
204B LYS* 1.3 58.7 + - - +
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Residues in contact with LYS 204 (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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229A PHE* 2.9 39.2 + - + -
230A ASN 2.7 33.3 + - - -
231A LEU* 3.6 18.6 - - + +
232A PRO* 3.9 10.8 - - + +
200B ALA 3.4 5.9 + - - +
201B ILE 3.5 0.2 + - - -
202B SER 3.2 0.6 - - - -
203B ALA* 1.3 77.7 - - - +
205B GLY* 1.3 62.9 + - - +
206B ILE* 3.5 28.3 + - + +
396B ASP* 5.7 4.5 - - - +
399B ASP* 4.5 13.5 - - - +
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Residues in contact with GLY 205 (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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201B ILE 3.2 1.5 + - - -
202B SER* 3.0 17.7 + - - -
203B ALA 3.4 0.4 - - - -
204B LYS* 1.3 79.2 - - - +
206B ILE* 1.3 63.0 + - - +
207B ALA 3.4 9.5 + - - +
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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