Contacts of the helix formed by residues 203 - 224 (chain B) in PDB entry 6DVD
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 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP 4.7 7.6 - - - -
198B THR* 4.0 1.3 - - - -
202B ILE* 1.3 78.1 - - - +
204B PRO* 1.3 74.8 - - - +
205B ARG* 3.2 23.8 + - - +
206B ASP* 2.7 32.0 + - - -
207B ALA* 3.2 19.6 + - - +
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Residues in contact with PRO 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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16B ASP 3.9 14.1 - - - +
17B ASN* 4.0 0.2 - - - -
18B ARG* 3.5 24.5 - - - +
19B SER* 3.5 35.0 - - - +
21B PHE* 3.6 18.0 - - + -
196B VAL* 4.0 13.1 - - + +
198B THR* 3.7 17.7 - - + -
203B SER* 1.3 88.6 - - - +
205B ARG* 1.3 65.9 + - - +
207B ALA* 3.8 6.0 - - + +
208B LEU* 3.2 18.9 + - - +
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 5.2 7.9 - - + +
226A ASN* 5.7 6.4 - - + +
11B GLU* 3.2 36.8 + - - +
13B VAL* 3.3 32.3 - - - +
16B ASP 5.3 3.8 + - - -
19B SER* 5.1 1.0 + - - -
21B PHE* 4.0 8.9 - - + -
203B SER* 3.1 21.9 - - - +
204B PRO* 1.3 83.3 - - - +
206B ASP* 1.3 63.2 + - - +
208B LEU* 3.3 2.6 + - - +
209B ALA* 3.0 27.1 + - - +
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 5.7 9.0 - - - +
202B ILE* 4.7 16.8 - - + -
203B SER* 2.7 30.4 + - - +
205B ARG* 1.3 76.9 - - - +
207B ALA* 1.3 56.3 + - - +
209B ALA* 3.8 7.2 - - - +
210B SER* 2.7 35.4 + - - -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.2 14.4 - - + +
46B ILE* 3.6 11.7 - - + +
171B VAL* 3.7 29.6 - - + -
196B VAL* 5.1 1.8 - - + -
198B THR* 5.2 0.2 - - - +
202B ILE* 3.8 15.1 - - + +
203B SER 3.2 16.2 + - - +
204B PRO* 3.8 8.1 - - + +
206B ASP* 1.3 78.9 - - - +
208B LEU* 1.3 61.3 + - - +
210B SER* 3.3 4.9 + - - -
211B ALA 3.1 17.3 + - - -
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA* 3.7 24.4 - - + +
9B LEU* 4.0 21.3 - - + -
21B PHE* 3.6 43.7 - - + -
23B ILE* 5.9 1.6 - - + -
38B LEU* 4.2 19.3 - - + -
42B LEU* 3.7 17.4 - - + +
194B LEU* 4.2 17.5 - - + -
196B VAL* 5.8 1.6 - - + -
204B PRO 3.2 15.6 + - - +
205B ARG 3.7 3.8 - - - +
207B ALA* 1.3 78.0 - - - +
209B ALA* 1.3 61.4 + - - +
211B ALA* 3.2 2.3 + - + +
212B GLY* 3.0 18.0 + - - -
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Residues in contact with ALA 209 (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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222A ALA 3.4 17.2 + - - +
223A ARG* 4.0 14.4 - - + +
225A LEU* 4.0 24.2 - - + -
205B ARG 3.0 16.0 + - - +
206B ASP* 3.8 7.4 - - - +
208B LEU* 1.3 76.1 - - - +
210B SER* 1.3 62.4 + - - +
212B GLY* 3.3 1.4 + - - -
213B LYS* 3.3 22.9 + - - +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER 4.6 3.6 + - - -
46B ILE* 3.9 26.1 - - - +
47B PRO* 5.0 3.8 - - - +
206B ASP 2.7 21.2 + - - -
207B ALA* 3.5 8.7 - - - -
209B ALA* 1.3 73.7 - - - +
211B ALA* 1.3 60.8 + - - +
213B LYS* 3.5 9.0 + - - +
214B THR* 3.3 28.6 + - - +
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Residues in contact with ALA 211 (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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38B LEU* 4.6 9.2 - - + -
41B THR* 3.7 24.7 - - + +
42B LEU* 3.8 21.5 - - + +
45B SER 5.6 0.2 - - - -
46B ILE* 5.0 2.6 - - + +
207B ALA 3.1 12.9 + - - +
208B LEU* 3.2 8.5 + - - +
210B SER* 1.3 77.6 + - - +
212B GLY* 1.3 62.7 + - - +
214B THR* 3.1 18.2 + - - -
215B LEU* 3.1 20.7 + - - +
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Residues in contact with GLY 212 (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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219A PHE* 4.1 15.7 - - - +
222A ALA* 4.5 8.5 - - - +
223A ARG* 4.7 7.6 - - - -
38B LEU* 5.3 0.9 - - - -
208B LEU 3.0 14.3 + - - -
209B ALA 3.3 4.2 + - - -
210B SER 3.2 0.4 - - - -
211B ALA* 1.3 74.6 - - - +
213B LYS* 1.3 58.6 + - - +
215B LEU* 3.3 6.3 + - - +
216B VAL* 2.9 37.0 + - - +
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Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG* 4.4 22.7 - - - +
209B ALA 3.3 12.8 + - - +
210B SER* 4.0 10.1 - - - +
211B ALA 3.4 0.4 - - - -
212B GLY* 1.3 76.6 - - - +
214B THR* 1.3 60.8 + - + +
216B VAL* 3.3 4.1 + - - +
217B GLU* 3.0 51.4 + - + +
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.4 16.0 - - - +
45B SER* 4.4 22.8 + - - +
210B SER* 3.3 17.0 + - - +
211B ALA* 3.1 14.7 + - - -
213B LYS* 1.3 80.7 - - + +
215B LEU* 1.3 56.7 + - - +
217B GLU* 3.9 15.1 - - - +
218B LEU* 3.2 29.7 + - - +
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Residues in contact with LEU 215 (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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30A PHE* 4.1 15.3 - - + -
34A LEU* 4.5 2.7 - - + -
219A PHE* 3.5 39.9 - - + -
37B SER* 4.2 6.3 - - - +
38B LEU* 3.7 15.3 - - + -
41B THR* 3.2 31.2 - - + +
211B ALA 3.1 22.3 + - - +
212B GLY* 3.8 3.1 - - - +
214B THR* 1.3 77.3 + - - +
216B VAL* 1.3 60.7 + - - +
217B GLU 3.2 0.2 - - - -
218B LEU* 3.4 9.4 - - + +
219B PHE* 2.9 57.7 + - + -
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Residues in contact with VAL 216 (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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216A VAL* 3.5 46.2 - - + +
219A PHE* 4.1 6.3 - - + -
220A GLY* 4.0 20.4 - - - +
223A ARG* 4.5 16.2 - - - +
212B GLY 2.9 22.3 + - - +
213B LYS* 3.8 5.6 - - - +
215B LEU* 1.3 75.0 - - - +
217B GLU* 1.3 60.3 + - + +
220B GLY* 2.8 27.4 + - - -
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Residues in contact with GLU 217 (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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6A ARG* 3.7 29.1 + - - -
213B LYS* 3.0 38.8 + - + +
214B THR* 3.9 16.4 + - - +
216B VAL* 1.3 78.5 - - + +
218B LEU* 1.3 63.7 + - - +
220B GLY* 3.3 8.3 + - - -
221B LEU* 3.5 17.3 + - - +
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Residues in contact with LEU 218 (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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7A PRO* 4.2 19.5 - - + -
23A ILE* 4.4 15.8 - - + +
26A LEU* 3.8 17.5 - - + -
30A PHE* 3.7 21.8 - - + -
34A LEU* 3.6 37.2 - - + -
41B THR* 6.3 0.4 - - + -
214B THR* 3.2 20.2 + - - +
215B LEU* 3.1 12.2 + - + +
217B GLU* 1.3 76.1 - - - +
219B PHE* 1.3 66.6 + - + +
221B LEU* 3.1 27.7 + - + +
222B ALA* 4.2 0.7 + - - +
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Residues in contact with PHE 219 (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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34A LEU* 3.5 26.2 - - + -
37A SER* 4.2 13.2 - - - -
38A LEU* 3.6 34.3 - - + -
212A GLY* 3.9 9.4 - - - +
215A LEU* 3.5 24.0 - - + -
216A VAL* 3.4 21.2 - - + +
219A PHE* 3.3 40.8 - + - -
37B SER* 5.2 1.1 - - - -
215B LEU* 2.9 44.9 + - + +
218B LEU* 1.3 69.9 - - + +
220B GLY* 1.3 63.6 + - - +
221B LEU 3.2 0.2 - - - -
222B ALA* 3.2 10.1 + - + +
223B ARG* 3.1 16.6 + - - +
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Residues in contact with GLY 220 (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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216A VAL* 3.7 8.5 - - - -
216B VAL 2.8 20.8 + - - -
217B GLU* 3.7 4.7 - - - -
218B LEU 3.1 0.8 - - - -
219B PHE* 1.3 75.0 - - - +
221B LEU* 1.3 59.1 + - - +
223B ARG* 3.6 7.2 - - - +
224B GLU* 2.9 41.2 + - - +
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Residues in contact with LEU 221 (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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7A PRO* 3.5 45.5 - - + +
8A THR* 4.4 1.6 - - - +
9A LEU* 3.4 37.0 - - + +
23A ILE* 4.9 7.0 - - + -
217B GLU 3.5 10.5 + - - +
218B LEU* 3.1 21.2 + - + +
220B GLY* 1.3 78.4 - - - +
222B ALA* 1.3 60.7 + - - +
224B GLU* 3.7 26.8 + - - +
225B LEU* 4.0 6.4 - - - +
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Residues in contact with ALA 222 (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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9A LEU* 3.7 12.9 - - + +
23A ILE* 6.0 2.7 - - + +
38A LEU* 5.0 7.0 - - + -
208A LEU* 3.7 37.9 - - + +
209A ALA* 3.3 12.6 - - - -
212A GLY* 4.1 5.2 - - - -
218B LEU 4.2 0.8 + - - +
219B PHE* 3.2 13.2 + - - +
220B GLY 3.2 0.2 - - - -
221B LEU* 1.3 76.5 - - - +
223B ARG* 1.3 66.7 + - - +
225B LEU* 3.2 21.7 + - - +
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Residues in contact with ARG 223 (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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209A ALA* 4.2 11.1 - - - +
212A GLY* 4.1 1.0 - - - -
213A LYS* 3.9 44.3 - - + +
216A VAL* 4.0 29.2 - - - +
219B PHE 3.1 12.8 + - - +
220B GLY* 3.1 11.2 + - - +
222B ALA* 1.3 78.4 - - - +
224B GLU* 1.3 61.0 + - - +
225B LEU 3.0 5.9 + - - -
226B ASN 3.7 0.2 + - - -
227B VAL* 3.3 44.1 + - + +
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Residues in contact with GLU 224 (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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220B GLY* 2.9 26.1 + - - +
221B LEU* 4.0 21.0 - - - +
222B ALA 3.2 0.4 - - - -
223B ARG* 1.3 79.4 - - + +
225B LEU* 1.3 62.3 + - - +
226B ASN 3.4 1.2 + - - -
227B VAL* 4.7 9.7 - - - +
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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