Contacts of the helix formed by residues 205 - 221 (chain B) in PDB entry 4R1Z
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 ASP 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TYR* 3.8 26.3 - - + -
202B LYS* 3.1 28.2 + - + +
203B ARG 3.0 3.1 + - - -
204B GLY* 1.3 81.6 - - - +
206B ALA* 1.3 85.8 + - - +
207B GLU* 3.1 17.4 + - - +
208B PHE* 3.9 17.6 + - + +
209B GLU* 3.2 20.1 + - - +
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Residues in contact with ALA 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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204B GLY 3.7 1.5 + - - -
205B ASP* 1.3 84.0 + - - +
207B GLU* 1.3 60.1 + - + +
208B PHE 3.1 3.3 + - - -
209B GLU* 3.4 1.8 + - - +
210B SER* 3.1 23.9 + - - -
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Residues in contact with GLU 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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201B TYR* 2.9 39.3 + - + -
205B ASP* 3.1 8.9 + - - +
206B ALA* 1.3 77.9 - - + +
208B PHE* 1.3 56.4 + - - +
210B SER* 3.4 14.6 + - - +
211B MET* 3.3 19.2 - - - +
255B LEU* 4.0 19.9 - - + +
258B LYS* 3.8 23.0 + - - +
259B LYS* 3.4 23.8 + - - -
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO 4.6 4.9 - - - -
185B THR* 3.8 19.5 - - - -
186B ARG* 3.9 31.4 - - + -
189B THR* 4.0 20.0 - - - -
201B TYR* 3.8 42.0 - + + -
204B GLY 5.3 2.9 - - - -
205B ASP* 3.7 23.2 + - + -
206B ALA 3.1 1.0 + - - -
207B GLU* 1.3 77.9 - - - +
209B GLU* 1.3 78.9 + - + +
210B SER 3.2 1.1 - - - -
211B MET* 3.1 16.6 + - + +
212B LEU* 2.8 43.2 + - + +
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLY* 5.0 10.8 + - - +
205B ASP 3.2 16.4 + - - +
206B ALA* 4.1 1.6 - - - +
208B PHE* 1.3 95.9 - - - +
210B SER* 1.3 63.7 + - - +
212B LEU* 3.1 37.7 + - - +
213B GLN* 3.2 21.3 + - + +
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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
----------------------------------------------------------
206B ALA 3.1 14.9 + - - -
207B GLU* 3.4 21.0 + - - +
209B GLU* 1.3 77.5 - - - +
211B MET* 1.3 63.4 + - - +
213B GLN* 3.6 15.6 - - - +
214B TYR* 3.5 25.6 + - - +
251B ILE* 4.9 4.5 - - - +
255B LEU* 5.3 2.8 - - - +
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Residues in contact with MET 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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189B THR* 3.6 33.4 - - + +
201B TYR* 4.2 4.3 - - + -
207B GLU 3.3 18.4 - - - +
208B PHE* 3.1 26.3 + - + +
210B SER* 1.3 81.4 + - - +
212B LEU* 1.3 66.5 + - + +
213B GLN 3.2 0.4 - - - -
214B TYR* 3.3 34.8 + - + +
215B SER* 2.9 40.1 + - - -
255B LEU* 4.2 5.6 - - + -
311B PHE* 3.6 24.5 - - + -
315B VAL* 4.4 14.4 - - + -
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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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182B PRO 5.8 0.2 - - - +
185B THR* 4.0 19.5 - - + +
208B PHE* 2.8 37.9 + - + +
209B GLU* 3.1 31.4 + - - +
211B MET* 1.3 78.0 - - + +
213B GLN* 1.3 66.4 + - - +
215B SER* 4.3 4.3 - - - -
216B GLN* 3.8 18.0 + - - +
315B VAL* 5.6 7.4 - - + -
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Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLU* 3.2 19.8 + - + +
210B SER* 3.6 15.2 - - - +
212B LEU* 1.3 73.4 - - + +
214B TYR* 1.3 55.7 + - - +
215B SER 2.7 4.2 + - - -
216B GLN* 2.7 34.4 + - - +
217B GLY 3.1 7.1 + - - -
251B ILE* 5.9 2.5 - - + -
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER* 3.5 20.6 + - - -
211B MET* 3.3 36.7 - - + +
213B GLN* 1.3 78.2 - - - +
215B SER* 1.3 61.0 + - - +
217B GLY 3.7 0.9 - - - -
218B ILE* 3.0 32.8 + - + +
248B CYS* 3.4 23.3 - - + -
251B ILE* 3.5 40.2 - - + -
252B ARG* 3.1 47.5 - - + +
255B LEU* 4.0 16.9 - - + +
256B LEU* 5.6 0.2 - - - +
311B PHE* 4.3 9.7 - - - -
601B AER 3.6 16.8 + - - -
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Residues in contact with SER 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B MET* 2.9 29.1 + - - -
212B LEU* 4.3 5.8 - - - -
213B GLN 2.7 4.4 + - - -
214B TYR* 1.3 75.8 - - - +
216B GLN* 1.3 57.5 + - - -
217B GLY 3.0 0.9 - - - -
218B ILE* 2.7 24.9 + - - +
219B VAL* 2.7 17.8 + - - +
315B VAL* 6.1 1.3 - - - +
316B GLU* 3.9 18.8 - - - -
601B AER 3.2 26.9 + - - +
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Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 3.8 12.6 + - - +
213B GLN* 2.7 14.9 + - - +
215B SER* 1.3 74.8 - - - +
217B GLY* 1.3 60.5 + - - +
219B VAL* 3.6 9.8 - - + +
220B ASP* 3.1 45.3 + - - +
316B GLU* 5.9 0.4 - - - -
490B LYS* 6.1 0.8 - - - +
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Residues in contact with GLY 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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213B GLN 3.1 8.6 + - - -
214B TYR 3.5 5.8 - - - -
215B SER 3.0 1.2 - - - -
216B GLN* 1.3 78.8 - - - +
218B ILE* 1.3 57.3 + - - +
220B ASP* 3.4 4.0 + - - +
221B THR* 2.7 31.8 + - - -
244B ILE* 5.0 5.5 - - - +
245B LEU* 5.2 0.7 - - - -
248B CYS* 3.9 16.4 - - - -
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Residues in contact with ILE 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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118B LEU* 3.9 34.8 - - + -
214B TYR* 3.0 32.6 + - + +
215B SER* 2.7 13.4 + - - +
217B GLY* 1.3 68.7 - - - -
219B VAL* 1.3 67.0 + - - +
221B THR* 3.3 9.7 + - - -
222B VAL* 3.5 16.0 + - + +
245B LEU* 4.1 15.8 - - + +
248B CYS* 3.7 18.4 - - + -
249B ILE* 3.6 31.0 - - + +
252B ARG* 4.9 3.4 - - + -
601B AER 4.3 20.2 - - + +
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Residues in contact with VAL 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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215B SER 2.7 20.7 + - - +
216B GLN* 3.6 11.9 - - + +
218B ILE* 1.3 72.0 - - - +
220B ASP* 1.3 69.3 + - - +
222B VAL* 2.9 28.6 + - - +
316B GLU* 3.9 26.5 - - + +
492B GLY* 4.6 8.4 - - - -
493B VAL* 4.1 44.7 + - + +
496B GLN* 5.1 8.1 - - - +
601B AER 4.6 8.3 - - + -
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Residues in contact with ASP 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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216B GLN* 3.1 37.1 + - - +
217B GLY* 3.9 4.2 - - - +
219B VAL* 1.3 86.5 - - - +
221B THR* 1.3 57.5 + - - +
222B VAL 3.2 3.9 + - - -
223B ALA* 3.7 15.1 + - - +
241B ASP* 5.2 2.7 - - - +
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Residues in contact with THR 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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114B THR* 4.1 21.7 - - + +
217B GLY 2.7 23.2 + - - -
218B ILE 4.0 0.9 - - - -
219B VAL 3.1 1.8 + - - -
220B ASP* 1.3 74.1 - - - +
222B VAL* 1.3 61.0 + - - +
223B ALA* 3.3 7.8 + - - +
224B LYS 4.6 0.7 + - - -
241B ASP* 3.5 46.4 + - + +
242B LEU* 5.0 0.4 - - - +
244B ILE* 3.7 14.0 - - - +
245B LEU* 3.6 28.9 - - + +
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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