Contacts of the strand formed by residues 190 - 196 (chain B) in PDB entry 3C9G
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 190 (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* 1.3 75.8 - - - +
191B ILE* 1.3 68.8 + - - +
192B GLU* 4.0 13.7 - - + +
230B ARG* 2.8 45.1 + - + +
232B TYR* 3.8 26.7 + - + -
292B THR 3.5 1.6 - - - +
293B PHE* 3.5 3.8 - - - -
294B ARG* 2.8 44.9 + - + +
296B ASN* 4.3 8.0 - - - +
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Residues in contact with ILE 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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189B VAL* 4.5 3.4 - - + -
190B GLU* 1.3 76.0 - - - +
192B GLU* 1.3 62.2 + - - +
193B ILE* 4.0 13.2 + - + -
214B PHE* 4.0 12.1 - - + -
230B ARG* 3.2 10.4 - - - +
231B ALA* 2.8 47.3 + - + +
232B TYR* 3.5 31.0 - - - +
233B SER 3.9 6.7 - - - +
234B LEU* 3.4 27.4 - - + -
291B VAL* 3.9 26.7 - - + -
292B THR 3.8 1.8 - - - +
293B PHE* 3.8 17.0 - - + -
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Residues in contact with GLU 192 (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 GLU* 4.0 21.2 - - + +
191B ILE* 1.3 75.5 - - - +
193B ILE* 1.3 62.4 - - - +
194B ARG* 5.8 3.1 - - + -
229B GLY 3.5 5.6 - - - +
230B ARG* 4.5 11.6 + - - +
262B GLU* 3.8 12.2 - - - +
290B LYS 3.8 0.2 - - - +
291B VAL* 3.4 2.8 - - - +
292B THR* 2.7 61.0 + - - +
294B ARG* 3.7 22.9 - - - +
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Residues in contact with ILE 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 ILE* 4.0 10.1 - - + +
192B GLU* 1.3 79.1 - - - +
194B ARG* 1.3 73.3 + - - +
210B ILE* 4.2 31.2 - - + -
214B PHE* 3.7 33.4 - - + -
217B ALA* 4.4 7.2 - - + -
227B VAL* 3.6 3.4 - - + +
228B TYR* 3.6 0.5 - - - -
229B GLY* 2.7 49.5 + - - +
231B ALA* 4.1 17.0 - - + -
289B ILE* 3.6 28.5 - - + -
290B LYS 3.4 2.5 - - - +
291B VAL* 4.7 4.5 - - + -
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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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192B GLU* 5.4 2.2 - - + -
193B ILE* 1.3 81.8 - - - +
195B THR* 1.3 72.4 + - - +
226B GLU* 2.9 31.9 + - - -
227B VAL 3.1 22.9 + - - +
228B TYR* 3.5 39.1 + - - +
289B ILE* 3.7 0.5 - - - -
290B LYS* 2.8 62.0 + - + +
292B THR* 5.3 5.4 - - - +
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Residues in contact with THR 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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194B ARG* 1.3 86.1 + - - +
196B LYS* 1.3 73.9 + - - +
206B VAL* 4.3 10.3 - - + -
210B ILE* 3.9 18.6 - - + -
226B GLU* 3.8 0.3 - - - +
227B VAL* 3.0 47.9 + - + -
269B LYS* 3.8 12.7 - - + +
287B SER* 3.6 6.7 + - - -
288B PRO 2.7 25.9 + - - -
289B ILE* 4.1 6.5 - - + -
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Residues in contact with LYS 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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195B THR* 1.3 87.0 + - - +
197B ILE* 1.3 70.5 + - - +
198B HIS* 3.8 23.7 + - + +
201B GLU* 3.4 1.1 - - - +
206B VAL* 4.5 0.2 - - - +
224B GLU 6.1 0.9 - - - +
225B GLY 3.4 9.4 - - - +
226B GLU* 3.5 27.4 - - - +
227B VAL* 4.1 0.9 - - - -
269B LYS* 3.0 25.1 + - - -
287B SER* 3.6 24.6 + - - +
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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