Contacts of the strand formed by residues 186 - 193 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H SER 3.7 4.5 + - - +
185H PRO* 1.3 75.2 - - - +
187H ALA* 1.3 61.8 + - - +
188H HIS* 4.8 1.9 - - - -
204H TRP 3.8 1.4 - - - +
206H LEU* 3.1 36.3 + - + +
207H GLY* 6.4 0.7 - - - -
270H LEU* 5.3 0.4 - - - -
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Residues in contact with ALA 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H PRO 3.7 3.2 + - - +
186H LYS* 1.3 77.2 - - - +
188H HIS* 1.3 69.9 + - - +
203H CYS* 5.1 0.4 - - - -
204H TRP 3.0 13.5 - - - +
205H ALA* 4.9 1.8 - - - -
261H VAL* 4.1 14.1 - - + -
270H LEU* 3.8 17.3 - - + +
272H LEU* 3.4 30.6 - - + +
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Residues in contact with HIS 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H LYS 4.8 2.0 - - - -
187H ALA* 1.3 82.1 - - - +
189H VAL* 1.3 65.3 + - - +
190H THR* 3.7 19.2 - - + +
203H CYS* 3.4 1.7 - - - -
204H TRP* 2.7 81.5 + + + +
206H LEU* 4.2 18.6 - - + +
272H LEU* 3.1 8.4 - - - +
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Residues in contact with VAL 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H HIS* 1.3 83.1 + - - +
190H THR* 1.3 78.2 + - - +
201H LEU* 4.3 4.5 - - + -
202H ARG 3.1 14.4 - - - +
203H CYS* 4.0 15.0 - - + -
217H TRP* 4.1 20.6 - - + -
272H LEU* 3.8 30.5 - - + +
273H ARG 4.9 0.9 - - - +
274H TRP* 3.8 35.8 + - + +
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Residues in contact with THR 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H HIS* 3.7 19.3 - - + +
189H VAL* 1.3 78.7 - - - +
191H HIS* 1.3 62.6 + - - +
192H HIS* 3.0 25.0 + - + +
200H THR 3.7 0.3 - - - +
201H LEU* 3.5 5.9 - - - -
202H ARG* 2.7 34.6 + - - +
204H TRP* 3.0 31.2 + - + +
274H TRP* 4.1 3.8 - - - +
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Residues in contact with HIS 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H THR* 1.3 74.2 - - - +
192H HIS* 1.3 73.9 + - - +
193H SER* 4.3 9.7 + - - -
199H VAL* 3.1 42.6 - - + +
200H THR 3.7 1.8 - - - -
201H LEU* 3.9 7.4 - - + -
251H LEU* 4.3 7.3 - - + +
254H GLU* 3.9 11.2 + - - -
274H TRP* 3.1 57.3 - + + +
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Residues in contact with HIS 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H THR* 3.0 32.5 + - + -
191H HIS* 1.3 84.2 + - - +
193H SER* 1.3 66.4 + - - +
199H VAL* 3.7 1.7 - - - +
200H THR* 2.9 55.3 + - + -
202H ARG* 3.8 31.1 + - + +
204H TRP* 5.2 0.8 + + - -
98L ASP* 3.2 44.6 + - + +
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Residues in contact with SER 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H HIS* 4.2 10.7 + - - -
192H HIS* 1.3 76.1 - - - +
194H ARG* 1.3 62.1 + - - +
195H PRO* 5.0 0.2 - - - +
198H LYS 4.5 2.9 - - - -
199H VAL* 4.6 6.1 - - - -
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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