Contacts of the helix formed by residues 183 - 198 (chain B) in PDB entry 6S6A
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 ASN 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B ASN* 4.7 8.4 - - - +
181B ILE* 3.7 3.5 - - - +
182B PRO* 1.3 88.1 - - - +
184B VAL* 1.3 65.6 + - - +
185B GLN 3.2 2.7 - - - -
186B GLN* 3.2 25.8 + - + +
187B LEU* 3.0 20.5 + - - +
300B LEU* 6.2 0.2 - - + -
347C GLU* 5.8 1.9 - - - +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 3.4 39.3 - - + +
181B ILE* 3.8 33.9 - - + +
182B PRO 3.4 3.8 + - - -
183B ASN* 1.3 77.2 - - - +
185B GLN* 1.3 67.4 + - - +
187B LEU* 3.1 10.3 + - + +
188B GLU* 2.9 22.7 + - - +
214B ILE 4.2 6.1 - - - +
215B SER* 4.7 2.9 - - - +
347C GLU* 3.5 22.8 + - + +
348C ARG* 4.0 20.9 - - + +
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Residues in contact with GLN 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASN 3.2 0.6 - - - -
184B VAL* 1.3 82.1 - - - +
186B GLN* 1.3 53.9 + - - +
188B GLU* 3.0 6.7 + - - +
189B MET* 2.8 58.1 + - + +
319C LYS* 5.8 3.4 - - - +
343C GLU 5.7 0.2 + - - -
346C PHE* 4.1 13.9 + - - -
347C GLU* 3.6 55.1 + - + +
349C LYS* 5.9 1.0 - - - +
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Residues in contact with GLN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASN* 3.2 26.7 + - + +
185B GLN* 1.3 76.4 - - - +
187B LEU* 1.3 65.4 + - - +
189B MET* 3.4 9.6 + - + +
190B ASN* 3.1 32.2 + - - +
300B LEU* 3.1 29.4 - - + +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 5.4 2.5 - - + -
181B ILE* 4.9 15.5 - - + -
183B ASN 3.0 12.2 + - - +
184B VAL* 3.3 12.1 - - + +
186B GLN* 1.3 77.1 - - - +
188B GLU* 1.3 57.0 + - - +
190B ASN* 3.5 1.9 + - - +
191B LEU* 3.1 24.7 + - + +
205B LEU* 3.8 28.9 - - + -
214B ILE* 4.3 17.9 - - + +
215B SER* 3.5 20.0 - - - +
297B PHE* 4.0 20.2 - - + +
300B LEU* 4.1 18.2 - - + +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 2.5 30.5 + - - -
184B VAL 2.9 13.2 + - - +
185B GLN* 3.7 5.6 - - - +
187B LEU* 1.3 71.7 - - - +
189B MET* 1.4 70.0 + - + +
191B LEU* 3.3 3.9 + - + +
192B ARG* 3.0 24.9 + - - +
215B SER* 3.2 26.1 + - - +
216B HIS 4.0 13.0 + - - +
217B TYR* 5.8 0.2 - - - +
403B 9JE 2.5 33.3 + - - -
347C GLU 4.2 7.8 - - - +
349C LYS* 4.3 1.0 + - - +
350C GLY* 3.2 18.6 + - - -
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Residues in contact with MET 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 6.3 3.4 - - - -
185B GLN* 2.8 49.7 + - + +
186B GLN* 3.8 9.4 - - + +
188B GLU* 1.4 74.2 - - + +
190B ASN* 1.3 66.2 - - - +
192B ARG* 3.3 21.9 - - - +
193B ASN* 3.2 22.5 + - - +
349C LYS* 6.1 4.9 - - + -
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Residues in contact with ASN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLN* 3.1 21.9 + - - +
187B LEU 3.8 1.1 - - - +
189B MET* 1.3 81.3 - - - +
191B LEU* 1.3 61.7 + - - +
193B ASN* 3.1 19.5 + - - +
194B PHE* 3.1 11.1 + - - +
296B HIS* 5.4 7.6 + - - +
297B PHE* 3.5 26.7 - - + -
300B LEU* 3.4 33.2 - - + +
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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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187B LEU 3.1 17.4 + - - +
188B GLU* 3.8 6.7 - - - +
189B MET 3.3 0.2 - - - -
190B ASN* 1.3 75.8 - - - +
192B ARG* 1.3 51.2 + - - +
194B PHE* 3.2 11.2 - - + +
195B ALA* 2.9 34.2 + - - +
203B VAL* 3.9 28.5 - - + +
205B LEU* 4.2 27.1 - - + -
215B SER* 3.7 13.7 - - - +
216B HIS* 3.5 40.4 - - - +
217B TYR* 4.2 1.1 - - - +
266B PHE* 5.0 1.3 - - + -
272B VAL* 5.0 1.6 - - + -
297B PHE* 3.6 22.9 - - + -
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG* 4.3 11.1 - - - +
283A SER* 2.5 36.6 + - - -
284A ALA* 5.5 2.8 - - - +
188B GLU 3.0 13.7 + - - +
189B MET* 3.3 29.4 - - - +
191B LEU* 1.3 74.8 - - - +
193B ASN* 1.3 55.8 + - - +
195B ALA* 3.5 2.9 + - - +
196B GLN* 3.0 48.6 + - - +
217B TYR* 3.1 52.0 + - + +
349C LYS* 5.8 4.4 - - - +
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Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO* 4.5 8.7 - - - +
284A ALA* 4.0 25.9 - - + +
285A ALA 5.5 0.2 + - - -
189B MET 3.2 8.9 + - - +
190B ASN* 3.1 17.8 + - - +
192B ARG* 1.3 74.2 - - - +
194B PHE* 1.3 61.6 + - - +
196B GLN* 3.4 9.3 + - - +
197B ILE* 3.0 61.1 + - - +
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Residues in contact with PHE 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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190B ASN 3.1 11.1 + - - +
191B LEU* 3.2 17.0 - - + +
193B ASN* 1.3 73.7 - - - +
195B ALA* 1.3 61.6 + - - +
196B GLN 3.1 0.7 + - - -
197B ILE* 3.2 6.3 + - + -
198B ILE* 2.9 63.9 + - + +
203B VAL* 3.8 31.2 - - + -
266B PHE* 4.0 17.7 - + - -
272B VAL* 4.1 8.5 - - + -
274B VAL* 4.0 8.7 - - + -
289B ASN 3.9 8.5 - - - -
290B ILE* 4.1 10.5 - - + -
293B ALA* 3.3 31.2 - - + -
297B PHE* 4.1 11.2 - + + -
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Residues in contact with ALA 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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191B LEU 2.9 18.4 + - - +
192B ARG 3.5 1.3 - - - +
194B PHE* 1.3 72.9 - - - +
196B GLN* 1.3 56.5 + - - +
198B ILE* 3.7 4.0 - - - +
199B GLU* 3.1 4.9 + - - -
200B ALA* 3.0 33.3 + - + +
202B GLU 5.5 0.2 - - - -
203B VAL* 3.4 31.9 - - + -
217B TYR* 3.3 34.3 - - + -
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Residues in contact with GLN 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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282A PRO* 3.1 43.8 - - + +
283A SER* 3.7 6.0 + - - +
284A ALA* 4.8 2.4 + - - +
192B ARG* 3.0 46.5 + - - +
193B ASN* 3.7 7.9 - - - +
194B PHE 3.2 0.2 - - - -
195B ALA* 1.3 73.0 - - - +
197B ILE* 1.3 67.0 + - - +
199B GLU* 3.3 15.9 + - - +
217B TYR* 3.0 34.5 + - + +
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO* 4.8 11.7 - - + -
193B ASN* 3.0 49.5 + - - +
194B PHE* 3.8 5.2 - - + +
196B GLN* 1.3 73.6 - - - +
198B ILE* 1.3 56.6 + - - +
199B GLU* 2.4 26.5 + - - +
289B ASN* 5.6 4.9 - - - +
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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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194B PHE* 2.9 54.7 + - + +
195B ALA* 3.7 11.4 - - - +
197B ILE* 1.3 72.7 - - - +
199B GLU* 1.3 67.6 + - - +
200B ALA* 3.8 15.7 - - + -
203B VAL* 5.0 0.2 - - + -
274B VAL* 4.3 15.5 - - + -
276B MET* 3.4 15.2 - - - +
281B ILE* 5.2 3.1 - - - +
286B THR* 3.5 24.1 - - + +
289B ASN* 3.2 48.3 + - + +
290B ILE* 4.0 5.2 - - + -
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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