Contacts of the helix formed by residues 193 - 203 (chain B) in PDB entry 6MJL
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 GLY 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ALA 3.4 1.2 + - - +
191B GLY 3.2 3.4 - - - -
192B ASP* 1.3 81.7 - - - +
194B SER* 1.3 56.9 + - - -
195B ALA 3.2 2.8 + - - -
196B PHE* 3.3 3.2 + - - +
197B ARG* 2.8 35.5 + - - +
239B ASN* 3.7 22.4 - - - -
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Residues in contact with SER 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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193B GLY* 1.3 71.6 - - - -
195B ALA* 1.3 58.4 + - - +
197B ARG* 3.4 16.9 - - - +
198B ASP* 2.8 36.5 + - - -
239B ASN* 3.7 9.5 - - - +
240B LYS 3.0 25.1 + - - -
241B ASN 3.4 4.6 + - - -
242B PRO* 3.7 27.9 + - - -
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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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193B GLY 3.3 1.0 - - - -
194B SER* 1.3 80.8 - - - +
196B PHE* 1.3 64.9 + - + +
198B ASP* 3.8 5.6 - - - +
199B LEU* 2.8 30.4 + - - +
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Residues in contact with PHE 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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152B SER 4.8 0.4 - - - -
155B THR* 4.2 3.6 - - + -
156B LYS* 3.8 46.9 - - + -
159B VAL* 3.9 33.9 - - + -
160B ASP* 5.4 1.1 - - - -
164B ILE* 5.6 0.7 - - + -
189B ILE* 3.3 24.2 - - + +
190B ALA* 4.4 1.6 - - - -
192B ASP* 3.6 33.9 - - + -
193B GLY 3.3 5.9 + - - +
195B ALA* 1.3 81.5 - - + +
197B ARG* 1.3 66.2 + - - +
199B LEU* 3.7 13.4 - - + +
200B VAL* 2.9 30.7 + - - +
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Residues in contact with ARG 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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190B ALA* 3.8 19.2 + - - +
193B GLY 2.8 19.3 + - - +
194B SER* 3.4 12.2 + - - +
196B PHE* 1.3 75.1 - - - +
198B ASP* 1.3 98.8 + - - +
200B VAL* 3.0 15.1 + - - +
201B ILE* 3.2 16.9 + - + +
235B ASN 3.8 15.0 - - - +
236B LEU* 3.6 29.4 - - + +
238B ARG 2.7 37.5 + - - -
239B ASN* 2.8 23.8 + - - +
242B PRO* 2.9 22.0 + - - +
243B ALA 3.1 12.7 + - - -
244B PRO* 3.5 14.5 - - - +
245B PRO* 4.6 0.2 - - - +
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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
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194B SER 2.8 23.1 + - - +
195B ALA* 3.9 5.4 - - - +
197B ARG* 1.3 108.6 + - - +
199B LEU* 1.3 56.9 + - - +
201B ILE* 3.0 10.2 + - - +
202B LYS* 2.9 37.9 + - + +
242B PRO* 3.9 15.2 - - - +
245B PRO* 3.3 23.8 - - + +
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Residues in contact with LEU 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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159B VAL* 4.3 24.2 - - + -
164B ILE* 4.3 4.9 - - + -
195B ALA 2.8 22.6 + - - +
196B PHE* 3.7 15.3 - - + +
197B ARG 3.2 0.2 - - - -
198B ASP* 1.3 73.3 - - - +
200B VAL* 1.3 62.1 + - - +
202B LYS* 3.3 17.6 + - + -
203B HIS* 2.9 56.8 + - + +
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Residues in contact with VAL 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 ILE* 3.9 18.2 - - + -
168B ILE* 4.1 0.8 - - + +
186B LEU* 4.2 24.7 - - + +
189B ILE* 3.8 27.6 - - + -
190B ALA 4.5 5.6 - - - +
196B PHE 2.9 18.7 + - - +
197B ARG 3.4 8.1 - - - +
199B LEU* 1.3 75.5 - - - +
201B ILE* 1.3 62.8 + - - +
203B HIS* 3.4 9.4 + - - +
204B GLY 3.5 0.5 + - - -
205B ALA* 3.4 36.8 + - + +
209B LEU* 5.7 0.2 - - + -
236B LEU* 4.2 18.8 - - + -
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Residues in contact with ILE 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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197B ARG* 3.2 16.8 + - + +
198B ASP* 3.0 11.5 + - - +
200B VAL* 1.3 77.7 - - - +
202B LYS* 1.3 58.3 + - + +
204B GLY* 2.8 22.9 + - - +
205B ALA* 4.0 4.0 + - - +
206B ILE* 3.9 30.0 + - + -
236B LEU* 4.3 28.5 - - + +
245B PRO* 4.0 24.5 - - + -
248B ALA* 3.9 25.8 - - + -
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Residues in contact with LYS 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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198B ASP* 2.9 22.1 + - + +
199B LEU* 3.7 21.8 - - + +
200B VAL 3.3 0.2 - - - -
201B ILE* 1.3 78.0 - - + +
203B HIS* 1.3 62.0 + - - +
204B GLY* 3.2 1.9 + - - -
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Residues in contact with HIS 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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164B ILE* 3.5 15.6 - - + +
165B PRO* 3.7 35.0 - - + +
168B ILE* 3.4 29.5 - - + +
199B LEU* 2.9 53.8 + - + +
200B VAL 3.7 2.5 - - - +
201B ILE 3.2 0.4 - - - -
202B LYS* 1.3 75.4 - - + +
204B GLY* 1.3 58.7 + - - +
205B ALA 3.7 0.7 - - - -
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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