Contacts of the strand formed by residues 186 - 194 (chain I) in PDB entry 1MWA
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184I SER* 4.6 5.8 + - - +
185I PRO* 1.3 78.2 - - - +
187I ALA* 1.3 58.9 + - - +
188I HIS* 5.2 1.6 - - - -
204I TRP 3.7 0.9 - - - +
205I ALA* 3.5 1.6 - - - -
206I LEU* 2.9 51.7 + - + +
207I GLY* 4.5 10.3 + - - -
270I LEU* 5.0 0.9 - - - -
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Residues in contact with ALA 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I PRO 4.1 1.2 + - - -
186I LYS* 1.3 75.1 - - - +
188I HIS* 1.3 63.1 + - - +
203I CYS* 4.9 0.7 - - - -
204I TRP 2.8 17.7 - - - +
205I ALA* 4.5 3.4 - - + -
261I VAL* 4.2 11.7 - - + -
270I LEU* 4.1 17.2 - - + +
272I LEU* 3.5 30.4 - - + +
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Residues in contact with HIS 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I LYS 5.2 1.1 - - - -
187I ALA* 1.3 79.2 - - - +
189I VAL* 1.3 64.9 + - - +
190I THR* 3.5 21.7 - - + +
202I ARG 3.8 0.2 - - - +
204I TRP* 2.9 66.5 + + + +
206I LEU* 4.3 19.3 - - + +
272I LEU* 3.4 10.0 - - - +
14M PRO* 6.3 0.4 - - - +
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Residues in contact with VAL 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I HIS* 1.3 83.5 + - - +
190I THR* 1.3 64.2 + - - +
201I LEU* 5.5 1.6 - - + -
202I ARG 3.1 8.5 - - - +
203I CYS* 4.1 17.7 - - + -
217I TRP* 4.4 15.7 - - + -
259I CYS* 4.5 1.1 - - + -
272I LEU* 3.5 28.9 - - + +
273I ARG 4.2 6.3 - - - +
274I TRP* 2.9 56.5 + - + +
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Residues in contact with THR 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I HIS* 3.5 28.9 - - + +
189I VAL* 1.3 75.0 - - - +
191I HIS* 1.3 60.4 + - - +
192I HIS* 2.8 33.4 + - + +
201I LEU* 3.6 5.1 - - - +
202I ARG* 2.9 31.2 + - - +
204I TRP* 3.1 18.9 + - + +
274I TRP* 4.3 3.8 - - - +
98M ASP* 6.1 0.2 - - - +
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Residues in contact with HIS 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I THR* 1.3 75.1 - - - +
192I HIS* 1.3 88.8 + - - +
193I SER* 4.2 8.7 + - - -
199I VAL* 3.3 35.5 - - + +
200I THR 4.2 1.8 - - - -
201I LEU* 4.4 4.5 - - + -
251I LEU* 5.1 4.6 - - + +
254I GLU* 3.1 25.5 + - + -
274I TRP* 3.2 58.6 - + + +
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Residues in contact with HIS 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I THR* 2.8 40.5 + - + +
191I HIS* 1.3 84.4 + - - +
193I SER* 1.3 67.1 + - - +
199I VAL* 3.1 4.7 - - - -
200I THR* 2.9 59.7 + - + +
202I ARG* 3.6 29.3 + - - +
98M ASP* 3.6 36.1 + - + +
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Residues in contact with SER 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I HIS* 4.2 10.1 + - - -
192I HIS* 1.3 76.2 - - - +
194I ARG* 1.3 61.0 + - - +
198I LYS 4.3 2.2 - - - -
199I VAL* 4.7 2.7 - - - +
200I THR* 5.5 0.7 - - - +
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Residues in contact with ARG 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I HIS 4.3 0.9 - - - +
193I SER* 1.3 78.6 - - - +
195I PRO* 1.3 92.2 - - + +
196I GLU* 6.4 0.2 - - - +
197I ASP* 4.0 2.8 + - - -
198I LYS* 2.9 44.2 + - - +
199I VAL* 4.1 3.6 - - - +
200I THR* 4.2 15.7 - - + -
248I VAL* 2.7 54.0 - - - +
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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
------------------------------------------------------------
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