Contacts of the helix formed by residues 207 - 222 (chain B) in PDB entry 1WG8
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 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ARG* 2.8 35.5 + - - +
203B ILE 2.8 9.7 + - - -
204B TYR* 3.1 11.6 + - - +
205B VAL 3.5 1.1 - - - +
206B ASN* 1.3 78.0 - - - +
208B GLU* 1.3 63.8 + - - +
209B LEU 3.4 2.3 + - - -
210B ASN* 2.9 29.3 + - - +
211B ALA* 3.0 17.5 + - - +
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Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 5.2 1.6 - - - -
98B GLY* 5.6 0.9 + - - -
123B MET* 3.8 12.1 - - + +
202B ARG* 2.8 70.0 + - - +
203B ILE* 3.0 24.5 + - + +
206B ASN* 2.9 18.7 + - + +
207B ASP* 1.3 76.5 - - - +
209B LEU* 1.3 62.6 + - + +
211B ALA* 3.4 4.8 + - - +
212B LEU* 2.9 31.5 + - - +
235B HIS* 3.8 9.9 + - - +
238B GLU* 4.1 5.9 - - + +
3141B SAM 6.0 0.2 - - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 4.7 11.9 - - + -
203B ILE* 3.5 26.1 - - + +
207B ASP 3.5 0.8 - - - -
208B GLU* 1.3 77.4 - - + +
210B ASN* 1.3 60.8 - - - +
212B LEU* 3.3 8.1 + - + +
213B LYS* 2.9 51.7 + - - +
235B HIS* 4.2 22.7 - - + -
237B LEU* 3.9 27.6 - - + -
238B GLU* 4.8 4.9 - - + +
241B VAL* 4.3 19.7 - - + +
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Residues in contact with ASN 210 (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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76B ARG* 3.7 15.5 - - - +
207B ASP* 2.9 28.4 + - - +
209B LEU* 1.3 76.2 - - - +
211B ALA* 1.3 66.1 + - - +
213B LYS* 3.2 22.0 + - - +
214B GLU* 3.0 32.6 + - - +
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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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74B ASN* 4.0 15.7 - - - +
75B PHE* 3.7 16.2 - - + -
76B ARG* 3.9 27.3 - - - +
206B ASN 4.7 3.6 - - - +
207B ASP 3.0 19.0 + - - +
208B GLU* 3.8 6.1 - - - +
210B ASN* 1.3 76.1 - - - +
212B LEU* 1.3 58.9 + - - +
214B GLU* 3.2 2.3 + - - +
215B PHE* 2.9 29.3 + - - +
3141B SAM 4.3 4.5 - - - +
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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
----------------------------------------------------------
75B PHE* 3.8 11.4 - - + -
97B LEU* 4.0 30.1 - - + -
208B GLU 2.9 19.0 + - - +
209B LEU* 3.6 6.3 - - + +
211B ALA* 1.3 77.1 - - - +
213B LYS* 1.3 62.6 + - - +
215B PHE* 3.3 13.0 + - + +
216B LEU* 2.9 43.6 + - + +
231B VAL* 5.0 1.8 - - + -
238B GLU* 3.8 34.1 - - + +
241B VAL* 3.7 26.2 - - + -
242B VAL* 4.1 9.2 - - + -
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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
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209B LEU* 2.9 38.0 + - - +
210B ASN* 3.2 20.0 + - - +
212B LEU* 1.3 75.4 - - - +
214B GLU* 1.3 63.0 + - + +
216B LEU* 3.4 9.4 + - - +
217B GLU* 3.2 24.2 + - - +
241B VAL* 3.7 34.3 - - + -
245B PHE* 5.1 3.4 - - - -
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Residues in contact with GLU 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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76B ARG* 2.9 54.1 + - + +
77B HIS* 5.7 1.0 - - - -
210B ASN* 3.0 21.7 + - - +
211B ALA 3.6 3.6 - - - +
213B LYS* 1.3 75.3 - - + +
215B PHE* 1.3 67.4 + - - +
217B GLU* 3.4 6.5 + - - +
218B GLN* 3.1 42.9 + - - +
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Residues in contact with PHE 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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29B ALA* 3.5 19.1 - - + -
75B PHE* 3.5 47.6 - + + +
76B ARG* 4.3 1.2 - - - +
78B LEU* 3.9 16.4 - - + -
93B ILE* 3.7 28.7 - - + -
95B ALA* 3.8 29.2 - - + -
211B ALA 2.9 17.7 + - - +
212B LEU* 3.6 13.5 - - + +
214B GLU* 1.3 77.9 - - - +
216B LEU* 1.3 74.3 + - + +
218B GLN* 3.2 6.3 + - - +
219B ALA* 2.8 35.6 + - + +
229B LEU* 4.9 1.8 - - + -
231B VAL* 4.7 4.3 - - + -
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Residues in contact with LEU 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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212B LEU* 2.9 31.2 + - + +
213B LYS* 3.7 5.2 - - - +
214B GLU 3.2 0.4 - - - -
215B PHE* 1.3 91.8 - - + +
217B GLU* 1.3 66.5 + - - +
219B ALA* 3.2 3.4 + - - +
220B ALA 3.0 19.8 + - - -
229B LEU* 4.1 21.2 - - + +
231B VAL* 4.1 13.2 - - + -
241B VAL* 4.2 14.8 - - + -
242B VAL* 4.1 17.9 - - + -
245B PHE* 3.2 52.0 - - + -
246B LEU* 4.9 3.1 - - + -
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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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213B LYS 3.2 15.6 + - - +
214B GLU* 3.8 6.8 - - - +
215B PHE 3.4 0.2 - - - -
216B LEU* 1.3 79.3 - - - +
218B GLN* 1.3 63.6 + - + +
220B ALA* 3.6 3.9 + - - +
221B GLU* 3.2 23.3 + - - +
245B PHE* 3.7 16.1 - - + -
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Residues in contact with GLN 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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76B ARG 3.0 22.4 + - - +
77B HIS* 3.8 1.7 - - - -
78B LEU* 3.2 23.0 + - + -
79B LYS* 3.1 38.0 + - + +
80B ARG 4.7 0.2 + - - -
214B GLU* 3.1 30.2 + - - +
215B PHE 3.6 3.1 - - - +
217B GLU* 1.3 77.7 - - + +
219B ALA* 1.3 59.3 + - - +
221B GLU* 3.0 15.0 + - - +
222B VAL* 2.9 32.2 + - - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.8 9.4 - - + +
93B ILE* 3.5 31.8 - - + +
215B PHE* 2.8 26.8 + - + +
216B LEU* 3.2 6.5 + - - +
218B GLN* 1.3 72.9 - - - +
220B ALA* 1.3 63.5 + - - +
222B VAL 3.4 0.3 + - - -
223B LEU* 3.1 30.3 + - - +
229B LEU* 4.2 17.5 - - + -
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Residues in contact with ALA 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 LEU 3.0 16.5 + - - +
217B GLU* 3.8 4.9 - - - +
219B ALA* 1.3 77.8 - - - +
221B GLU* 1.3 60.4 - - - +
223B LEU* 3.8 7.5 + - - +
229B LEU* 5.0 1.2 - - - +
245B PHE* 3.9 16.4 - - + -
249B SER* 5.2 3.8 - - - +
251B LEU* 4.1 30.0 - - + +
282B LYS* 2.9 29.6 + - - +
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Residues in contact with GLU 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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79B LYS* 2.8 41.5 - - - +
89B ARG* 3.4 28.7 + - - +
217B GLU* 3.2 16.1 + - - +
218B GLN* 3.0 15.3 + - - +
219B ALA 3.0 0.8 - - - -
220B ALA* 1.3 80.1 - - - +
222B VAL* 1.3 64.1 + - + +
223B LEU 3.5 3.6 + - - +
282B LYS* 4.5 5.3 + - - +
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Residues in contact with VAL 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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78B LEU* 4.0 11.0 - - + -
79B LYS* 4.1 32.8 - - + -
82B LEU* 4.1 19.3 - - + -
88B GLU* 3.6 21.3 - - - +
89B ARG* 3.1 13.2 - - - +
90B VAL* 3.0 24.2 + - + -
93B ILE* 3.9 17.0 - - + -
218B GLN 2.9 20.6 + - - +
219B ALA* 3.6 7.0 - - - +
221B GLU* 1.3 76.8 - - + +
223B LEU* 1.3 63.1 + - - +
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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