Contacts of the strand formed by residues 192 - 206 (chain B) in PDB entry 3C0M
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 SER 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B VAL* 3.3 19.8 - - - +
190B THR 3.9 2.5 + - - -
191B GLN* 1.3 83.9 - - - +
193B ASP* 1.3 73.0 + - - +
252B GLU* 5.8 0.3 + - - -
253B THR* 4.7 5.4 - - - +
301B ASP 3.1 9.8 + - - -
302B ILE* 4.0 12.0 - - - +
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Residues in contact with ASP 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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191B GLN* 3.9 8.4 + - - +
192B SER* 1.3 93.2 + - - +
194B ARG* 1.3 62.5 + - - +
195B GLN* 4.1 2.2 + - - +
252B GLU* 6.1 0.9 - - - -
253B THR* 5.2 2.7 - - - +
299B LYS 3.9 0.3 - - - +
300B ALA* 3.1 21.7 - - - +
301B ASP* 2.7 33.0 + - - +
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Residues in contact with ARG 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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110A ALA* 3.2 31.8 - - - +
111A ASN* 5.4 0.6 + - - -
193B ASP* 1.3 72.0 - - - +
195B GLN* 1.3 62.2 - - - +
196B LEU 3.9 1.0 + - - -
252B GLU* 2.7 45.8 + - + +
298B TYR* 3.1 61.2 + - + -
299B LYS 3.3 5.4 - - - +
300B ALA* 3.4 20.0 - - + -
410B PHE* 3.6 15.5 - - - -
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Residues in contact with GLN 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 ASP* 4.1 1.9 + - - +
194B ARG* 1.3 74.3 - - - +
196B LEU* 1.3 67.8 + - - +
197B VAL* 3.2 13.6 + - + +
298B TYR* 3.5 4.2 - - - +
299B LYS* 2.8 40.0 + - + +
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Residues in contact with LEU 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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194B ARG 3.9 2.0 + - - -
195B GLN* 1.3 76.5 - - - +
197B VAL* 1.3 59.3 - - - +
198B LYS* 3.3 27.9 - - - +
199B THR* 4.1 18.4 - - + -
296B GLU* 3.5 38.8 - - + +
297B LEU 3.5 7.6 - - - +
298B TYR* 3.8 16.4 - - + -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLN* 3.2 13.0 + - + +
196B LEU* 1.3 71.9 - - - +
198B LYS* 1.3 73.5 + - + +
297B LEU* 3.1 17.1 + - + +
299B LYS* 3.3 44.0 - - + +
409B GLN* 5.4 1.6 - - - +
455B LEU* 4.3 17.6 - - + +
457B PHE* 4.0 26.2 - - + -
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Residues in contact with LYS 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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196B LEU* 3.3 6.7 - - - +
197B VAL* 1.3 92.5 - - + +
199B THR* 1.3 69.0 + - - +
200B VAL* 4.1 18.2 - - - +
297B LEU* 2.6 41.8 + - + +
448B ASP* 6.2 1.6 - - - +
451B GLU* 3.1 32.1 + - - +
452B LEU* 3.6 31.9 - - + -
455B LEU* 4.1 14.6 - - + -
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Residues in contact with THR 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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196B LEU* 4.1 19.3 - - + -
198B LYS* 1.3 88.1 + - - +
200B VAL* 1.3 60.8 + - - +
201B VAL* 3.5 21.5 + - - +
294B LYS* 3.9 14.6 - - - +
295B ILE 3.5 4.5 - - - -
296B GLU* 4.0 19.8 + - - +
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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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198B LYS* 4.1 23.1 - - - +
199B THR* 1.3 69.2 - - - +
201B VAL* 1.3 63.6 + - - +
293B VAL 4.0 0.5 - - - +
294B LYS* 3.6 2.1 - - - -
295B ILE* 3.0 42.7 + - + +
297B LEU* 4.2 19.3 - - + -
445B ILE* 3.2 37.3 - - + +
446B PRO 4.2 8.7 - - - +
447B LEU* 4.0 20.9 - - + -
452B LEU* 4.4 5.6 - - + -
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Residues in contact with VAL 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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135A TYR* 5.0 4.9 - - + +
199B THR* 3.5 21.5 + - - +
200B VAL* 1.3 82.1 - - - +
202B GLY* 1.3 59.6 + - - +
293B VAL 3.5 6.1 - - - +
294B LYS* 4.1 14.6 - - + -
445B ILE* 4.4 5.3 - - - +
446B PRO* 3.7 19.9 - - - +
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Residues in contact with GLY 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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135A TYR* 5.1 0.2 + - - -
201B VAL* 1.3 75.9 - - - +
203B TRP* 1.3 73.1 + - - -
292B PRO* 3.3 8.1 - - - +
293B VAL* 2.9 31.6 + - - +
444B GLU 3.8 7.6 - - - -
445B ILE* 3.7 16.1 - - - +
446B PRO* 4.7 0.4 - - - -
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Residues in contact with TRP 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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134A GLN* 4.3 14.8 - - - -
202B GLY* 1.3 83.1 - - - -
204B ALA* 1.3 60.7 + - - +
205B VAL* 4.0 5.4 - - + -
290B LYS* 3.3 52.3 - - + -
291B ILE 3.0 9.4 - - - +
292B PRO* 3.5 37.9 - - + -
293B VAL* 4.4 4.9 - - - +
420B VAL* 4.8 9.6 - - + -
443B LEU* 3.7 2.9 - - - -
444B GLU* 2.8 43.9 + - + +
445B ILE* 4.1 3.9 - - - +
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Residues in contact with ALA 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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203B TRP* 1.3 73.6 - - - +
205B VAL* 1.3 62.7 + - - +
206B ASN 4.1 0.3 + - - -
217B VAL* 5.1 4.0 - - + -
283B PRO* 5.3 0.7 - - + -
285B VAL* 4.7 3.4 - - + +
290B LYS* 3.0 2.9 - - - -
291B ILE* 2.9 51.5 + - + +
293B VAL* 4.2 7.8 - - + +
441B LEU* 4.9 15.3 - - + -
442B ARG 3.7 4.5 - - - +
443B LEU* 3.6 21.1 - - + -
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Residues in contact with VAL 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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203B TRP* 4.7 4.5 - - + -
204B ALA* 1.3 75.0 - - - +
206B ASN* 1.3 63.4 + - - +
207B ASP* 3.5 28.9 + - - +
289B SER 3.6 2.5 - - - +
290B LYS* 3.6 22.9 - - + -
422B LEU* 3.7 27.4 - - + -
441B LEU* 3.5 10.7 - - - +
442B ARG* 2.8 49.0 + - + +
444B GLU* 4.1 25.8 - - + +
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Residues in contact with ASN 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 ALA 4.1 0.4 + - - -
205B VAL* 1.3 72.7 - - - +
207B ASP* 1.3 58.2 + - - +
208B SER* 2.7 38.1 + - - +
210B THR 3.2 6.3 + - - -
211B PRO* 3.7 0.2 - - - +
212B GLN* 2.9 41.0 - - - +
285B VAL* 3.1 27.4 + - + +
286B PRO 2.5 25.9 + - - +
288B ARG* 3.6 2.9 - - - -
289B SER 2.7 23.4 + - - +
422B LEU* 4.0 1.4 - - - +
441B LEU* 4.0 3.6 - - + +
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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