Contacts of the helix formed by residues 200 - 212 (chain B) in PDB entry 3DGR
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 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLN* 3.8 12.1 - - - -
200A SER* 3.3 6.6 + - - -
202A GLU* 3.6 11.6 - - - +
203A THR* 2.9 22.2 + - - -
206A ILE* 3.8 19.1 - - - -
198B VAL* 3.3 11.5 + - - +
199B SER* 1.3 83.1 + - - +
201B GLN* 1.3 59.3 + - - +
202B GLU 3.6 2.3 + - - -
203B THR* 3.3 16.6 + - - -
204B ALA* 3.0 22.5 + - - +
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Residues in contact with GLN 201 (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 PHE* 3.7 14.7 - - + -
14A ALA* 4.0 1.2 + - - +
69A TYR* 3.5 35.0 - - + +
151A ILE* 3.5 29.1 - - - +
154A GLN* 2.9 25.4 + - - +
202A GLU* 3.4 10.1 + - - +
195B TYR* 2.6 39.9 + - - -
200B SER* 1.3 71.5 - - - +
202B GLU* 1.3 66.6 + - - +
204B ALA* 3.1 15.2 + - - +
205B GLY* 3.2 10.7 + - - -
222B ALA* 4.9 5.7 - - - +
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A SER* 3.8 12.8 - - - +
201A GLN* 3.5 3.7 + - - +
202A GLU* 3.0 48.9 + - + +
64B TYR* 2.8 29.3 + - - +
68B LYS* 4.5 5.8 - - - -
69B TYR* 2.5 34.2 + - - -
200B SER 3.3 0.2 - - - -
201B GLN* 1.3 76.7 - - - +
203B THR* 1.3 63.4 + - - +
205B GLY* 3.5 1.8 + - - -
206B ILE* 3.2 27.3 + - + +
226B LEU* 5.4 0.3 - - - +
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Residues in contact with THR 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 SER* 2.6 36.6 + - - +
200A SER* 2.8 22.6 + - - -
203A THR* 3.0 6.1 + - - -
157B TYR* 3.4 22.0 + - + +
198B VAL* 3.9 17.0 - - + +
199B SER* 4.2 2.0 - - - +
200B SER* 3.3 16.2 + - - -
202B GLU* 1.3 79.0 - - - +
204B ALA* 1.3 55.9 + - - +
206B ILE* 4.6 3.6 - - - -
207B GLY* 2.9 29.3 + - - -
387B LEU 4.7 0.7 - - - +
388B GLN* 4.8 1.3 - - - +
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Residues in contact with ALA 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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195B TYR* 3.5 37.2 - - + -
198B VAL* 3.7 15.7 - - + +
200B SER 3.0 13.8 + - - +
201B GLN 3.1 10.3 + - - +
203B THR* 1.3 76.5 - - - +
205B GLY* 1.4 57.3 + - - +
208B ALA* 3.0 33.4 + - - +
220B THR* 3.8 10.0 - - + +
222B ALA* 5.2 0.7 - - + -
387B LEU* 4.6 4.4 - - - +
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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 GLN 3.2 8.8 + - - -
202B GLU 3.5 2.7 + - - -
204B ALA* 1.4 73.8 - - - +
206B ILE* 1.3 65.0 + - - +
209B SER* 3.1 21.7 + - - -
222B ALA* 3.8 14.3 - - - +
223B GLY* 3.5 25.8 - - - -
226B LEU* 3.6 10.6 - - - +
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Residues in contact with ILE 206 (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 SER 4.0 5.6 - - - +
200A SER* 3.8 26.2 - - - -
60B TYR* 4.6 0.6 - - + -
64B TYR* 3.6 45.1 - - + +
157B TYR* 3.8 19.5 - - + -
158B PRO* 3.9 25.6 - - + -
202B GLU* 3.2 21.2 + - + +
203B THR* 3.9 2.7 - - - +
205B GLY* 1.3 75.7 - - - +
207B GLY* 1.3 63.7 + - - +
209B SER* 2.8 18.7 + - - +
210B ALA* 3.1 9.5 + - - +
226B LEU* 3.6 10.7 - - + +
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Residues in contact with GLY 207 (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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157B TYR* 3.6 26.9 - - - -
161B VAL* 3.5 3.9 - - - +
203B THR 2.9 12.5 + - - -
206B ILE* 1.3 76.0 - - - +
208B ALA* 1.3 59.5 + - - +
210B ALA* 3.1 6.1 + - - -
211B HIS 3.0 23.9 + - - -
387B LEU* 3.4 21.4 - - - +
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Residues in contact with ALA 208 (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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192B ASP* 3.1 28.4 - - - +
204B ALA 3.0 19.9 + - - +
207B GLY* 1.3 73.0 - - - +
209B SER* 1.3 65.9 + - - +
211B HIS* 3.3 4.0 + - - +
212B LEU* 3.1 28.7 + - - +
218B THR* 3.9 6.5 + - + +
220B THR* 3.8 15.7 - - - -
223B GLY* 3.9 16.2 - - - -
387B LEU* 4.1 2.4 - - + +
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Residues in contact with SER 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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60B TYR* 2.8 26.2 + - - -
205B GLY 3.1 16.3 + - - -
206B ILE* 2.8 19.4 + - - +
207B GLY 3.2 0.2 - - - -
208B ALA* 1.3 76.9 - - - +
210B ALA* 1.3 60.7 + - - +
212B LEU 3.2 8.5 + - - -
213B VAL 3.4 0.3 + - - -
223B GLY* 3.9 7.5 - - - -
226B LEU* 3.7 12.7 - - - +
227B ILE* 3.7 26.7 - - - -
473B PHE* 3.3 21.5 - - - -
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 3.5 18.8 - - + -
158B PRO* 3.6 28.3 - - + +
161B VAL* 3.7 16.8 - - + -
162B ALA* 3.8 11.5 - - - +
206B ILE 3.1 9.3 + - - +
207B GLY* 3.1 8.7 + - - +
209B SER* 1.3 81.6 + - - +
211B HIS* 1.3 61.6 + - - +
213B VAL* 3.2 20.9 + - - +
214B ASN* 3.8 1.4 + - - -
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Residues in contact with HIS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL* 3.9 6.6 - - + +
165B SER* 2.8 27.3 + - - -
190B LEU* 2.8 40.3 + - + -
192B ASP* 3.6 15.6 + - + -
207B GLY 3.0 12.7 + - - +
208B ALA* 3.8 9.9 - - - +
209B SER 3.3 0.2 - - - -
210B ALA* 1.3 76.6 - - - +
212B LEU* 1.3 61.8 + - + +
213B VAL 3.1 0.2 - - - -
214B ASN* 3.0 21.0 + - - +
215B PHE* 3.1 42.9 + + + +
217B GLY 3.5 19.3 + - - -
386B LEU* 3.6 21.4 - - + +
387B LEU* 4.7 0.7 - - + -
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Residues in contact with LEU 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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208B ALA 3.1 22.2 + - - +
209B SER 3.6 5.6 - - - +
210B ALA 3.2 0.8 - - - -
211B HIS* 1.3 75.0 - - + +
213B VAL* 1.3 62.7 + - - +
214B ASN 3.0 1.6 - - - -
215B PHE 3.2 20.2 + - - +
216B LYS* 3.6 24.5 - - - +
217B GLY 4.1 4.7 - - - +
218B THR* 3.9 21.8 - - + -
223B GLY 4.9 0.2 - - - -
224B LEU* 3.9 27.8 - - + +
227B ILE* 3.6 20.9 - - + -
238B PRO* 4.1 3.4 - - + +
239B GLY* 4.2 3.6 - - - +
473B PHE* 3.7 8.1 - - + -
477B ARG* 2.7 35.7 + - - +
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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