Contacts of the helix formed by residues 201 - 214 (chain B) in PDB entry 1D8D
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 VAL 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ASP* 1.3 71.9 - - - +
202B ARG* 1.3 63.7 + - - +
203B SER 3.2 0.7 + - - -
204B ALA* 3.2 11.2 + - + +
205B TYR 3.4 7.3 + - - -
228B TRP* 3.6 20.3 - - + -
229B ILE* 4.2 16.8 - - + -
232B CYS* 4.7 1.6 - - - -
239B ILE* 4.7 4.5 - - + -
240B GLY 3.9 9.6 - - - +
241B GLY 2.8 12.4 + - - +
251B TYR* 3.4 50.5 - - + +
254B CYS* 3.9 5.9 - - + +
255B GLY* 3.8 26.9 - - - -
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Residues in contact with ARG 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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166A TYR* 3.2 26.5 + - - -
149B HIS* 4.7 1.0 - - - -
151B ALA* 5.0 0.4 - - - +
193B MET* 3.5 34.2 - - + +
198B GLU* 3.0 25.9 + - - +
200B ASP* 2.7 37.0 + - - +
201B VAL* 1.3 78.2 - - - +
203B SER* 1.3 58.0 + - - +
205B TYR* 3.3 3.6 + - - +
206B CYS* 2.8 33.0 + - - -
251B TYR* 3.8 11.9 - - + -
254B CYS* 3.8 14.1 - - - -
1000B FII 3.7 32.1 - - + -
10P ILE 3.0 28.5 + - - -
11P MET* 3.4 18.6 + - - +
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 3.6 8.2 - - - +
190B SER* 5.3 0.3 - - - -
191B PHE* 2.8 45.6 + - - +
192B LEU 3.7 6.5 - - - -
193B MET* 3.4 24.0 - - - -
199B VAL* 4.9 0.3 - - - +
200B ASP 2.9 16.8 + - - -
202B ARG* 1.3 77.1 - - - +
204B ALA* 1.3 57.0 + - - +
206B CYS* 4.4 1.1 - - - +
207B ALA* 2.8 36.9 + - - +
228B TRP* 5.6 0.7 - - - -
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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
----------------------------------------------------------
190B SER* 6.2 0.9 - - - -
191B PHE* 4.5 12.3 - - + +
201B VAL* 3.2 13.3 + - + +
203B SER* 1.3 81.4 + - - +
205B TYR* 1.3 59.5 + - - +
207B ALA* 3.9 1.0 - - - +
208B ALA* 2.9 31.7 + - - +
222B PHE* 4.5 2.4 - - - -
225B THR* 3.9 15.8 - - + +
228B TRP* 5.0 5.6 - - + -
229B ILE* 3.9 32.3 - - + -
258B ALA* 4.1 3.3 - - + +
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Residues in contact with TYR 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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154B TYR* 2.9 46.2 + + - -
201B VAL 3.4 1.6 + - - -
202B ARG 3.3 5.8 + - - +
203B SER 3.3 0.4 - - - -
204B ALA* 1.3 77.5 - - - +
206B CYS* 1.3 62.7 + - - +
209B SER* 2.8 40.9 + - - -
253B PHE* 3.7 14.7 - + - -
254B CYS* 3.4 31.6 - - + +
257B ALA* 3.5 25.1 - - + -
258B ALA* 3.8 14.7 - - - +
261B ILE* 4.5 7.4 - - + -
303B TRP* 5.4 0.7 - + - -
400B VAL 2.6 30.0 + - - -
401B TYR* 3.8 3.5 - - - -
1000B FII 3.8 25.6 - - + -
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Residues in contact with CYS 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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150B LEU* 3.4 39.5 - - + +
151B ALA* 4.0 12.6 - - - -
154B TYR* 3.8 25.4 - - + -
193B MET* 4.4 5.4 - - - -
202B ARG* 2.8 32.3 + - - +
203B SER 3.9 1.3 - - - +
205B TYR* 1.3 72.3 - - - +
207B ALA* 1.3 62.2 + - - +
209B SER* 3.8 0.9 - - - -
210B VAL* 3.2 30.6 + - - +
1000B FII 4.5 16.2 - - - -
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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
----------------------------------------------------------
150B LEU* 4.3 11.4 - - + +
181B LEU* 4.1 16.3 - - + +
191B PHE* 4.3 14.1 - - + -
203B SER 2.8 19.8 + - - +
204B ALA 3.9 2.7 - - - +
206B CYS* 1.3 74.0 - - - +
208B ALA* 1.3 60.3 + - - +
210B VAL* 3.4 8.2 - - - +
211B ALA* 2.9 34.0 + - - +
222B PHE* 3.7 17.3 - - + -
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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
----------------------------------------------------------
204B ALA 2.9 23.0 + - - +
205B TYR 3.9 2.0 - - - +
207B ALA* 1.3 73.3 - - - +
209B SER* 1.3 56.8 + - - +
212B SER* 2.8 35.0 + - - -
217B ILE* 4.8 0.3 - - - +
222B PHE* 3.5 21.5 - - + -
258B ALA* 4.4 11.9 - - + +
261B ILE* 3.8 27.1 - - + +
262B LEU* 4.7 6.1 - - + -
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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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154B TYR* 3.3 34.9 - - - -
158B ASN* 4.3 1.4 + - - -
205B TYR* 2.8 29.9 + - - -
206B CYS 3.8 0.4 - - - -
208B ALA* 1.3 72.7 - - - +
210B VAL* 1.3 62.3 + - - +
212B SER* 3.0 16.1 + - - -
213B LEU* 3.1 22.0 + - - +
261B ILE* 3.8 9.6 - - - +
401B TYR* 3.3 22.1 - - - -
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 5.1 0.4 - - + -
153B THR* 3.7 7.0 - - + +
154B TYR* 3.6 26.0 - - + +
157B VAL* 3.6 40.2 - - + -
177B LEU* 4.4 15.0 - - + -
181B LEU* 4.3 17.5 - - + -
206B CYS 3.2 19.2 + - - +
207B ALA* 3.4 10.3 - - - +
209B SER* 1.3 77.1 - - - +
211B ALA* 1.3 63.2 + - - +
213B LEU* 4.0 0.6 - - + +
214B THR* 2.8 33.8 + - - +
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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
----------------------------------------------------------
181B LEU* 3.8 13.7 - - + -
207B ALA 2.9 20.4 + - - +
208B ALA 4.1 0.2 - - - +
210B VAL* 1.3 77.3 - - - +
212B SER* 1.3 62.4 + - - +
215B ASN* 3.1 3.3 + - - -
216B ILE* 3.1 45.4 + - + -
217B ILE* 3.5 22.2 - - + +
221B LEU* 4.1 2.2 - - + -
222B PHE* 4.0 10.8 - - + -
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ALA 2.8 22.6 + - - -
209B SER 3.0 4.3 + - - -
211B ALA* 1.3 75.4 - - - +
213B LEU* 1.3 67.9 + - - +
215B ASN* 3.2 13.2 + - - +
217B ILE* 3.7 13.6 - - - +
261B ILE* 3.6 17.5 - - - +
401B TYR* 2.8 28.8 + - - -
412B THR* 4.7 7.2 - - - +
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Residues in contact with LEU 213 (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 VAL* 4.0 22.7 - - + -
158B ASN* 3.6 23.8 - - - +
161B CYS* 4.3 13.7 - - - -
209B SER* 3.1 20.8 + - - +
210B VAL* 4.0 2.9 - - + +
212B SER* 1.3 83.0 + - - +
214B THR* 1.3 59.0 + - + +
215B ASN* 3.3 0.4 - - - +
401B TYR* 3.5 33.9 - - + -
403B ILE* 4.9 3.8 - - + -
408B VAL* 4.4 9.9 - - + -
411B ALA* 4.0 12.6 - - + +
412B THR* 3.9 30.2 - - + -
415B PHE* 3.2 22.4 - - - +
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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
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157B VAL* 4.4 9.6 - - + -
172B ILE* 3.9 37.7 - - + -
174B ARG* 2.8 39.5 + - - -
177B LEU* 3.9 5.9 - - + +
210B VAL 2.8 21.1 + - - +
213B LEU* 1.3 76.4 - - - +
215B ASN* 1.3 65.0 + - - +
216B ILE* 3.5 23.6 - - - +
415B PHE* 3.6 19.0 - - + +
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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