Contacts of the strand formed by residues 186 - 193 (chain J) in PDB entry 3MGO
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 LYS 186 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J ALA 4.1 12.3 - - - +
185J PRO* 1.3 73.2 - - - +
187J THR* 1.3 61.7 + - - +
188J HIS* 4.3 1.1 + - - -
204J TRP 3.7 0.9 - - - +
205J ALA* 3.6 1.2 - - - -
206J LEU* 2.8 52.6 + - + +
207J SER* 4.2 18.1 + - - +
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Residues in contact with THR 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J PRO* 3.6 26.1 + - + +
186J LYS* 1.3 78.1 - - - +
188J HIS* 1.3 64.2 + - - +
204J TRP 3.1 14.6 - - - +
205J ALA* 4.4 2.0 - - - -
261J VAL* 4.3 21.3 - - + -
270J LEU* 4.1 17.0 - - + +
272J LEU* 3.6 25.7 - - - +
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Residues in contact with HIS 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J LYS 5.2 1.6 + - - -
187J THR* 1.3 78.2 - - - +
189J MET* 1.3 77.0 + - - +
190J THR* 3.7 21.2 - - + +
203J CYS* 3.8 3.6 - - - -
204J TRP* 2.8 67.1 + + + +
206J LEU* 4.2 18.9 - - + +
272J LEU* 5.3 5.4 - - - -
14K PRO* 5.8 4.7 - - + -
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Residues in contact with MET 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J HIS* 1.3 80.9 - - - +
190J THR* 1.3 65.6 + - - +
201J LEU* 4.3 6.3 - - + -
202J ARG 3.3 17.3 - - - +
203J CYS* 4.5 2.2 - - - -
217J TRP* 3.7 25.6 - - + -
259J CYS* 4.5 3.4 - - + -
272J LEU* 3.4 49.8 - - + +
273J ARG 3.8 4.0 - - - +
274J TRP* 3.3 54.1 - - + +
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Residues in contact with THR 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J HIS* 3.7 26.2 - - + +
189J MET* 1.3 74.9 - - - +
191J HIS* 1.3 62.4 + - - +
192J HIS* 4.1 19.4 + - + -
200J THR 3.4 3.1 + - - +
201J LEU* 3.5 7.6 - - - +
202J ARG* 3.0 55.4 + - - +
204J TRP* 3.6 12.3 + - + +
274J TRP* 4.0 1.6 - - - -
98K ASP* 5.0 4.8 + - + +
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Residues in contact with HIS 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J THR* 1.3 77.3 - - - +
192J HIS* 1.3 77.5 + - - +
193J ALA* 4.7 3.8 + - + -
199J ALA* 3.3 26.8 - - + +
200J THR 3.4 3.6 - - - -
201J LEU* 3.5 24.0 - - + -
254J GLU* 2.8 36.3 + - + -
274J TRP* 3.4 37.9 + + + -
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Residues in contact with HIS 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J THR* 4.1 25.5 + - + -
191J HIS* 1.3 88.8 + - - +
193J ALA* 1.3 63.4 + - - +
194J VAL* 3.5 0.8 + - + +
199J ALA* 3.2 4.2 - - - -
200J THR* 2.6 47.2 + - - +
202J ARG* 5.0 5.3 + - - -
98K ASP* 3.1 43.2 + - + +
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Residues in contact with ALA 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191J HIS* 4.7 5.1 + - + -
192J HIS* 1.3 73.1 - - - +
194J VAL* 1.3 61.9 + - - +
195J SER 3.7 16.8 - - - +
198J GLU 3.8 8.5 - - - +
199J ALA* 4.1 5.4 - - + -
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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