Contacts of the helix formed by residues 187 - 201 (chain B) in PDB entry 3SAJ
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 GLU 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B PHE* 4.0 8.8 - - - +
108B ARG* 2.6 44.5 + - - -
132B ASP* 3.5 13.2 + - - +
134B ASP* 5.3 4.7 - - - +
135B ARG* 3.0 19.1 + - - +
186B CYS* 1.3 79.9 - - - +
188B SER* 1.3 61.0 + - - +
189B GLU* 3.5 6.9 + - + +
190B ARG* 3.6 7.9 + - + +
191B LEU* 3.0 25.8 + - - +
214B ASN* 4.1 1.6 - - - +
270B TYR* 3.4 8.1 + - - -
271B THR* 4.9 3.1 - - - +
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Residues in contact with SER 188 (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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187B GLU* 1.3 75.0 + - - +
189B GLU* 1.3 73.3 + - - +
191B LEU* 3.6 5.8 - - - +
192B ASN* 2.8 30.8 + - - +
214B ASN* 3.4 22.7 + - - +
219B ASP* 4.7 6.3 + - - +
220B ILE* 4.7 16.4 - - - -
269B LYS* 6.1 2.7 - - - -
270B TYR* 3.7 19.0 - - - -
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 3.5 4.7 - - + +
188B SER* 1.3 86.0 + - - +
190B ARG* 1.3 61.7 + - + +
192B ASN* 3.1 27.7 + - - +
193B ALA* 3.4 6.3 + - - +
220B ILE* 6.1 0.2 - - - -
269B LYS* 5.8 4.2 + - - -
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Residues in contact with ARG 190 (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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132B ASP* 4.4 16.5 - - - +
159B ILE* 4.1 28.2 - - + +
186B CYS* 4.5 10.3 - - + -
187B GLU* 3.6 11.2 + - + +
189B GLU* 1.3 74.8 - - + +
191B LEU* 1.3 59.6 + - - +
192B ASN 3.2 1.8 - - - -
193B ALA* 3.0 10.1 + - + +
194B ILE* 2.8 34.8 + - + +
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Residues in contact with LEU 191 (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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184B VAL* 3.1 43.5 - - + +
186B CYS* 3.9 15.5 - - - +
187B GLU 3.0 20.2 + - - +
188B SER* 3.6 10.1 - - - +
190B ARG* 1.3 74.3 - - - +
192B ASN* 1.3 63.9 + - - +
194B ILE* 3.3 3.9 + - - +
195B LEU* 2.9 59.3 + - + +
212B LEU* 4.3 23.1 - - + -
214B ASN* 4.9 14.4 - - + +
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Residues in contact with ASN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER 2.8 19.5 + - - +
189B GLU* 3.1 12.3 + - - +
191B LEU* 1.3 83.6 - - - +
193B ALA* 1.3 61.7 + - - +
195B LEU* 3.3 8.3 + - - +
196B GLY* 3.0 19.1 + - - -
220B ILE* 3.4 50.3 - - - +
221B ASP* 4.9 6.8 - - - +
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Residues in contact with ALA 193 (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 GLU 3.4 3.6 + - - +
190B ARG* 3.0 16.0 + - + +
192B ASN* 1.3 77.5 - - - +
194B ILE* 1.3 64.7 + - + +
196B GLY* 3.0 4.0 + - - +
197B GLN* 2.9 31.5 + - + +
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Residues in contact with ILE 194 (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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130B ILE* 5.1 8.3 - - + -
159B ILE* 3.8 23.8 - - + -
167B TYR* 3.5 40.8 - - + +
184B VAL* 4.2 22.7 - - + -
186B CYS* 4.9 4.0 - - - -
190B ARG* 2.8 24.4 + - + +
191B LEU* 3.6 8.1 - - - +
193B ALA* 1.3 75.3 - - + +
195B LEU* 1.3 58.5 + - + +
197B GLN* 3.4 9.7 + - + +
198B ILE* 3.1 41.7 + - + +
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Residues in contact with LEU 195 (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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184B VAL* 5.8 0.9 - - + -
191B LEU* 2.9 44.6 + - + +
192B ASN* 3.7 9.2 - - - +
193B ALA 3.2 0.2 - - - -
194B ILE* 1.3 77.0 - - + +
196B GLY* 1.3 61.1 + - - +
198B ILE* 3.5 21.9 + - + +
199B VAL* 3.3 28.4 + - - +
210B TYR* 5.9 3.1 - - + -
212B LEU* 4.5 25.6 - - + -
221B ASP* 3.6 32.5 - - + +
225B PHE* 3.9 20.6 - - + -
232B VAL* 6.2 1.3 - - + -
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Residues in contact with GLY 196 (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 ASN 3.0 10.6 + - - -
193B ALA* 3.0 7.6 + - - -
195B LEU* 1.3 75.8 - - - +
197B GLN* 1.3 62.8 + - - +
198B ILE 3.1 0.2 - - - -
199B VAL* 3.1 24.4 - - - +
200B LYS* 3.1 11.5 + - - +
224B LYS* 6.4 0.7 - - - -
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Residues in contact with GLN 197 (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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164B GLU* 3.4 52.6 + - - +
167B TYR* 4.6 16.9 - - + -
193B ALA* 2.9 17.4 + - + +
194B ILE* 3.7 15.3 - - + +
196B GLY* 1.3 75.4 - - - +
198B ILE* 1.3 51.1 + - - +
200B LYS* 3.6 9.5 + - - +
201B LEU* 2.4 60.4 + - + +
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Residues in contact with ILE 198 (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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130B ILE* 6.1 1.3 - - + -
171B PHE* 4.0 20.4 - - + -
184B VAL* 4.9 5.6 - - + -
194B ILE* 3.1 33.2 + - + +
195B LEU* 3.7 25.4 - - + +
196B GLY 3.1 0.4 - - - -
197B GLN* 1.3 75.1 - - + +
199B VAL* 1.3 60.6 + - - +
201B LEU* 3.0 13.7 + - + +
202B GLU 2.9 19.9 + - - -
203B LYS* 3.0 18.2 + - + -
210B TYR* 3.6 45.5 - - + +
225B PHE* 4.0 15.7 - - + -
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Residues in contact with VAL 199 (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 LEU 3.3 6.5 + - - +
196B GLY* 3.1 17.9 - - - +
198B ILE* 1.3 73.6 - - - +
200B LYS* 1.3 62.0 + - + +
202B GLU* 2.5 33.2 + - - +
203B LYS 4.4 0.4 - - - +
204B ASN* 3.2 30.4 + - - +
224B LYS* 4.6 27.8 - - + +
225B PHE* 3.2 36.8 - - + -
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Residues in contact with LYS 200 (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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164B GLU* 3.1 31.8 + - - +
196B GLY 3.1 13.2 + - - +
197B GLN* 3.7 11.4 - - - +
199B VAL* 1.3 77.8 - - + +
201B LEU* 1.3 58.6 + - + +
202B GLU* 2.6 20.9 + - - +
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Residues in contact with LEU 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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164B GLU* 5.1 2.0 - - + +
167B TYR* 4.1 14.8 - - + -
168B ARG* 4.1 32.1 - - + +
171B PHE* 3.2 40.1 - - + +
197B GLN* 2.4 52.0 + - + +
198B ILE* 3.0 11.6 + - + +
200B LYS* 1.3 74.8 - - + +
202B GLU* 1.3 67.0 + - - +
203B LYS* 2.9 25.2 + - + +
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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