Contacts of the strand formed by residues 198 - 208 (chain B) in PDB entry 1M6X
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 VAL 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B ASP 3.4 13.7 - - - +
195B ILE* 2.9 25.1 - - - +
196B LYS 3.2 2.4 - - - -
197B ASN* 1.3 78.1 - - - +
199B ASP* 1.3 68.6 + - - +
200B PRO* 3.0 6.8 - - - +
203B PHE* 4.3 7.6 - - + -
217B CYS* 3.5 34.8 - - + -
218B LEU 3.5 8.3 - - - +
219B VAL* 3.7 11.9 - - + +
230B ILE* 3.9 15.7 - - + -
270B GLN* 4.0 0.2 - - - -
273B GLN* 3.5 2.4 - - - -
274B LEU* 3.0 37.5 + - + -
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Residues in contact with ASP 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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197B ASN 3.4 2.0 + - - -
198B VAL* 1.3 74.1 - - - +
200B PRO* 1.3 59.1 - - - +
201B LYS* 3.0 26.4 + - - +
202B SER* 2.7 53.9 + - - +
203B PHE* 4.4 0.3 + - - -
218B LEU* 3.0 16.4 + - + +
270B GLN* 3.7 42.4 - - - +
271B GLU 5.2 0.5 + - - -
272B TYR 4.4 2.1 + - - +
142D LYS* 5.1 8.3 + - - -
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Residues in contact with PRO 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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198B VAL* 3.0 12.7 - - + +
199B ASP* 1.3 85.4 - - - +
201B LYS* 1.3 58.5 + - - +
202B SER 3.1 1.6 + - - -
203B PHE* 3.0 38.2 + - + -
272B TYR* 3.3 38.1 - - + +
273B GLN* 3.8 7.4 - - - +
274B LEU* 4.0 4.5 - - + +
403B TRP* 3.9 28.7 - - + -
406B ILE* 4.1 13.9 - - + -
407B ILE* 3.8 12.4 - - + +
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Residues in contact with LYS 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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199B ASP* 2.9 19.3 + - - +
200B PRO* 1.3 75.3 - - - +
202B SER* 1.3 58.5 + - - +
203B PHE 3.5 2.3 + - - +
271B GLU* 3.0 31.8 + - + +
272B TYR* 4.1 18.4 - - + -
405B GLY 4.6 8.9 + - - -
406B ILE* 3.6 38.5 - - + +
407B ILE* 5.8 0.4 - - - -
408B SER* 5.7 2.4 + - - -
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Residues in contact with SER 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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199B ASP* 2.7 31.5 + - - -
201B LYS* 1.3 79.1 - - - +
203B PHE* 1.3 64.0 + - - +
204B LYS* 3.5 17.3 + - - +
216B GLN* 3.3 11.1 - - - +
217B CYS* 3.7 3.5 - - - -
218B LEU* 2.8 46.7 + - - +
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Residues in contact with PHE 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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198B VAL* 4.3 2.0 - - + -
200B PRO* 3.0 39.7 - - + +
201B LYS 3.5 3.4 - - - +
202B SER* 1.3 77.7 - - - +
204B LYS* 1.3 63.4 + - - +
215B ILE* 3.4 27.8 - - + -
216B GLN 3.5 3.8 - - - -
217B CYS* 4.0 24.9 - - + +
232B PHE* 4.0 21.3 - + - -
245B LEU* 4.9 15.0 - - + -
249B LEU* 5.8 1.3 - - + -
274B LEU* 4.2 23.1 - - + -
407B ILE* 3.9 36.6 - - + -
408B SER* 3.6 21.0 - - - +
411B VAL* 3.9 12.3 - - + -
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Residues in contact with LYS 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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202B SER* 3.6 16.2 - - - +
203B PHE* 1.3 80.7 - - - +
205B LEU* 1.3 70.5 - - - +
206B VAL* 4.4 7.9 - - + -
215B ILE* 3.5 4.7 - - - +
216B GLN* 2.9 47.2 + - - +
408B SER* 5.5 0.2 - - - -
410B GLU* 5.3 2.5 - - - +
411B VAL* 3.9 7.8 - - - +
145D LYS* 3.4 30.9 - - - +
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Residues in contact with LEU 205 (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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204B LYS* 1.3 76.5 - - - +
206B VAL* 1.3 62.4 + - - +
213B VAL* 4.6 16.2 - - + -
214B ILE 3.6 3.4 - - - +
215B ILE* 4.1 15.9 - - + -
384B TRP* 6.0 1.8 - - - +
410B GLU* 3.4 53.3 + - + +
411B VAL* 4.0 16.3 - - + +
414B TYR* 3.7 40.6 - - + -
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Residues in contact with VAL 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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204B LYS* 4.2 10.1 - - + +
205B LEU* 1.3 80.6 - - - +
207B GLN* 1.3 74.5 + - - +
213B VAL* 3.3 4.1 - - - -
214B ILE* 2.9 43.4 + - + +
216B GLN* 3.9 41.5 - - + +
231B TYR* 5.9 1.1 - - + -
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Residues in contact with GLN 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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205B LEU 6.1 0.2 - - - -
206B VAL* 1.3 89.5 - - - +
208B ASN* 1.3 61.9 + - - +
212B GLY 3.4 8.0 + - - +
213B VAL* 4.1 5.4 - - + -
214B ILE* 5.3 0.9 - - - +
352B ASP* 4.8 4.2 - - - +
384B TRP* 3.3 34.8 - - - -
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Residues in contact with ASN 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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207B GLN* 1.3 76.5 + - - +
209B LYS* 1.3 59.8 + - - +
210B TYR* 2.8 41.1 + - - +
211B LEU* 3.2 14.6 + - - +
212B GLY* 2.8 38.0 + - - +
214B ILE* 4.2 29.4 - - + +
352B ASP* 3.3 40.1 + - - +
355B PHE* 3.6 20.7 - - - +
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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