Contacts of the helix formed by residues 195 - 215 (chain B) in PDB entry 6J7Z
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 ARG 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU* 3.3 4.0 - - - -
62B GLU* 2.7 35.7 + - - +
80B ASN* 4.6 12.9 - - - +
82B ILE* 4.4 14.5 - - - +
104B SER* 4.4 28.6 + - - +
106B LEU* 4.6 11.5 - - - +
193B SER* 2.9 19.0 + - - +
194B HIS* 1.3 79.0 - - - +
196B ALA* 1.3 65.2 + - - +
197B LEU* 3.4 2.0 - - + +
198B ASP* 3.4 25.2 + - - +
199B ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 3.3 44.6 - - - +
49B GLU* 3.4 7.3 + - + -
62B GLU* 3.1 23.8 + - + +
63B MET* 3.9 5.8 - - - -
64B ALA* 3.6 17.7 - - + +
80B ASN* 4.6 0.4 - - - +
195B ARG* 1.3 72.2 - - - +
197B LEU* 1.3 63.2 + - - +
199B ALA 3.3 0.7 + - - -
200B ILE* 2.9 21.7 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 3.5 13.1 - - + +
65B CYS 5.5 0.9 - - - +
66B LEU* 4.1 28.0 - - + -
77B GLU* 3.8 23.3 - - + +
78B GLY 6.1 0.2 - - - +
80B ASN* 3.9 36.6 + - + +
195B ARG* 3.4 1.6 - - + +
196B ALA* 1.3 77.8 - - - +
198B ASP* 1.3 68.2 + - - +
200B ILE* 3.2 10.9 - - + +
201B SER* 3.0 27.4 + - - -
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Residues in contact with ASP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B SER* 3.7 23.4 + - - +
195B ARG* 3.4 30.8 + - - +
197B LEU* 1.3 81.1 - - - +
199B ALA* 1.3 63.1 + - - +
201B SER* 3.4 6.2 + - - -
202B GLU* 2.9 36.9 + - + +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 3.2 29.4 - - - +
193B SER 5.2 2.9 + - - +
195B ARG 3.0 14.0 + - - +
196B ALA 3.6 0.2 - - - +
198B ASP* 1.3 78.4 - - - +
200B ILE* 1.3 57.4 + - - +
202B GLU* 3.3 12.5 + - - +
203B SER* 2.8 31.7 + - - -
301B MG 3.8 12.6 - - - -
302B MG 4.2 7.9 - - - -
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Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 3.6 45.1 - - + +
46B VAL 3.5 33.9 - - - +
47B ASP* 3.9 9.6 - - + +
64B ALA* 4.5 8.1 - - + +
66B LEU* 3.9 22.4 - - + -
140B ALA 3.8 2.7 - - - +
141B GLY* 4.0 7.2 - - - -
196B ALA 2.9 16.2 + - - +
197B LEU* 3.2 19.3 - - + +
199B ALA* 1.3 74.3 - - - +
201B SER* 1.3 68.3 + - - +
203B SER* 3.2 5.9 + - - +
204B ILE* 3.0 24.9 + - - +
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Residues in contact with SER 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.7 11.0 - - - -
197B LEU* 3.0 20.8 + - - -
198B ASP* 3.7 6.3 - - - -
200B ILE* 1.3 79.1 - - - +
202B GLU* 1.3 59.7 + - - +
204B ILE* 3.3 7.9 + - - +
205B LYS* 3.0 27.9 + - - +
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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
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142B ASN* 5.0 0.7 - - - -
188B PRO* 5.5 1.2 - - - +
193B SER 5.2 3.6 - - - +
198B ASP* 2.9 32.0 + - - +
199B ALA* 3.7 8.8 - - - +
201B SER* 1.3 78.2 - - - +
203B SER* 1.3 56.2 + - - +
205B LYS* 3.4 7.8 + - - +
206B GLU* 2.9 30.9 + - - +
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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
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45B TRP* 3.9 16.9 - - - -
47B ASP* 5.8 0.5 + - - -
141B GLY 4.6 0.2 - - - -
142B ASN* 2.7 43.7 + - - +
169B VAL* 4.0 4.5 - - - +
199B ALA* 2.8 20.9 + - - +
200B ILE* 3.2 14.1 + - - +
202B GLU* 1.3 73.5 - - - +
204B ILE* 1.3 66.8 + - - +
206B GLU* 3.2 3.5 + - - +
207B LEU* 3.0 23.9 + - - +
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Residues in contact with ILE 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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45B TRP* 3.5 36.8 - - + -
66B LEU* 3.7 30.5 - - + -
68B THR* 3.7 22.9 - - + -
72B LEU* 4.0 29.4 - - + +
74B ILE* 4.0 14.6 - - + -
200B ILE 3.0 14.2 + - - +
201B SER* 3.6 7.9 - - - +
203B SER* 1.3 75.6 - - - +
205B LYS* 1.3 64.2 + - - +
207B LEU* 3.3 2.8 + - - +
208B GLN* 3.0 22.2 + - + +
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Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO* 3.8 32.6 - - + +
201B SER* 3.0 16.5 + - - +
202B GLU* 3.8 7.6 - - - +
203B SER 3.3 0.2 - - - -
204B ILE* 1.3 78.7 - - - +
206B GLU* 1.3 57.4 + - - +
208B GLN* 3.2 11.8 + - + +
209B PHE* 2.9 34.7 + - - +
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Residues in contact with GLU 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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142B ASN* 3.2 27.3 + - - +
169B VAL* 3.9 5.8 - - + -
173B LYS* 2.8 29.1 + - - +
187B ALA* 5.3 0.2 - - + -
188B PRO* 4.0 32.3 - - + +
202B GLU 2.9 17.2 + - - +
203B SER 3.6 3.8 - - - +
205B LYS* 1.3 76.1 - - - +
207B LEU* 1.3 62.6 + - - +
209B PHE* 3.2 4.2 + - - +
210B TYR* 2.6 67.6 + - + +
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Residues in contact with LEU 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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175A LEU* 4.2 8.5 - - + -
179A TRP* 4.1 19.1 - - + -
43B MET* 5.2 0.2 - - - -
45B TRP* 3.7 23.3 - - + -
72B LEU* 3.8 24.9 - - + -
167B ILE* 4.4 15.7 - - + -
169B VAL* 4.0 17.1 - - + +
172B VAL* 4.2 32.8 - - + -
203B SER 3.0 14.5 + - - +
204B ILE 3.8 4.0 - - - +
206B GLU* 1.3 76.4 - - - +
208B GLN* 1.3 58.2 + - - +
210B TYR* 3.2 6.9 + - + -
211B ARG* 2.9 26.7 + - - +
215B PHE* 5.4 0.2 - - + -
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Residues in contact with GLN 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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71B ASP 3.7 7.9 + - - +
72B LEU* 3.6 31.2 - - + +
73B ASN* 5.6 0.5 - - - +
204B ILE* 3.0 15.6 + - + +
205B LYS* 3.2 16.4 + - + +
207B LEU* 1.3 77.7 - - - +
209B PHE* 1.3 56.6 + - - +
211B ARG* 3.3 17.5 + - - +
212B ASN* 2.9 68.3 + - - +
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Residues in contact with PHE 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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176B CYS* 5.4 0.4 - - - -
183B GLU* 3.3 32.5 - - + -
186B PHE* 3.7 19.1 - - + -
187B ALA* 3.5 25.1 - - + -
188B PRO* 3.5 19.5 - - + -
205B LYS* 2.9 21.1 + - - +
206B GLU 3.2 6.9 + - - +
208B GLN* 1.3 76.8 - - - +
210B TYR* 1.3 75.3 + + - +
212B ASN* 3.2 3.9 + - - +
213B ASN* 2.8 68.3 + - + +
214B ILE* 5.6 0.2 - - + -
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Residues in contact with TYR 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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169B VAL* 4.2 4.3 - - + -
172B VAL* 3.6 30.7 - - + -
173B LYS* 3.3 34.7 - - + +
176B CYS* 3.7 32.1 - - + -
184B TYR* 3.7 9.3 - + - -
187B ALA* 4.1 19.4 - - + +
206B GLU* 2.6 59.6 + - + +
207B LEU* 3.2 10.7 + - + +
209B PHE* 1.3 83.8 - + - +
211B ARG* 1.3 57.3 + - - +
214B ILE* 2.9 41.5 + - + +
215B PHE* 3.4 4.1 - - + -
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Residues in contact with ARG 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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179A TRP* 3.4 76.8 + - + +
180A TYR* 5.4 5.1 + - - +
71B ASP* 3.0 39.8 + - - +
72B LEU* 5.2 1.3 - - + -
207B LEU 2.9 14.8 + - - +
208B GLN* 3.3 20.5 + - - +
210B TYR* 1.3 76.1 - - - +
212B ASN* 1.3 64.5 + - - +
213B ASN 3.4 0.5 + - - -
215B PHE* 3.6 31.3 + - + +
217B LYS* 5.4 1.6 + - - +
218B LYS* 5.4 7.3 - - - +
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Residues in contact with ASN 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 GLN* 2.9 51.0 + - - +
209B PHE* 3.2 2.2 + - - +
211B ARG* 1.3 80.2 - - - +
213B ASN* 1.3 72.4 + - - +
215B PHE 5.1 0.7 - - - +
217B LYS* 3.3 33.1 + - - +
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Residues in contact with ASN 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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216A LYS* 2.8 33.7 + - - +
183B GLU* 4.3 9.6 - - + +
209B PHE* 2.8 66.8 + - + +
212B ASN* 1.3 91.1 - - - +
214B ILE* 1.3 66.3 + - + +
215B PHE 3.7 1.3 - - - -
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Residues in contact with ILE 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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215A PHE* 3.5 29.9 - - + -
216A LYS* 2.7 34.4 + - - +
172B VAL* 4.3 16.8 - - + +
176B CYS* 3.7 38.8 - - + +
180B TYR* 3.8 34.4 + - + -
183B GLU* 3.9 10.8 - - + -
209B PHE* 5.6 0.2 - - + -
210B TYR* 2.9 23.2 + - + +
213B ASN* 1.3 86.3 - - + +
215B PHE* 1.3 63.6 + - + +
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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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172A VAL* 5.4 2.2 - - + -
175A LEU* 4.2 18.2 - - + -
179A TRP* 4.2 23.3 - + - -
180A TYR* 3.4 21.8 - + + +
214A ILE* 3.5 32.5 - - + -
215A PHE* 3.7 26.5 - + - -
216A LYS* 3.8 7.7 - - - +
172B VAL* 4.0 22.7 - - + -
207B LEU* 5.4 0.7 - - + -
210B TYR* 3.4 22.6 + - + -
211B ARG* 3.6 28.5 + - + +
213B ASN 4.9 1.7 - - - -
214B ILE* 1.3 91.6 + - + +
216B LYS* 1.3 65.6 - - - +
217B LYS* 3.4 11.4 + - - +
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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