Contacts of the strand formed by residues 186 - 190 (chain C) in PDB entry 6UWZ
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 TRP 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C LEU* 4.4 19.1 - - + +
43C LEU* 3.6 32.3 + - + +
45C GLU* 3.7 5.7 + - - -
138C ASP 4.2 2.0 - - - -
140C GLN* 3.5 23.8 - - + -
182C GLU* 5.8 0.9 - - - +
183C ASN* 3.7 36.3 + - + +
184C GLY 3.7 0.8 - - - -
185C GLN* 1.3 101.5 + - + +
187C SER* 1.3 61.6 + - - +
188C ILE* 4.0 5.0 + - - +
213C ILE* 3.6 37.0 - - + -
214C GLN 3.5 5.2 - - - -
215C ARG* 3.2 72.9 - - + +
216C LYS* 4.1 7.8 + - - +
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C TRP* 1.3 71.0 - - - +
188C ILE* 1.3 62.7 + - - +
189C GLU* 3.4 20.5 + - - +
213C ILE* 3.2 4.5 - - - -
214C GLN* 2.8 41.2 + - - -
216C LYS* 2.8 31.5 + - - +
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Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 4.1 18.8 - - + -
40C LEU* 4.8 10.8 - - + -
175C ILE* 4.2 7.0 - - + -
180C PHE* 3.7 31.2 - - + -
186C TRP 4.0 3.8 + - - +
187C SER* 1.3 69.7 - - - +
189C GLU* 1.3 64.2 + - - +
190C HIS 3.6 20.9 - - - +
191C LYS* 4.1 19.1 - - + -
211C LEU* 3.9 15.0 - - + -
212C ILE 3.8 3.8 - - - +
213C ILE* 3.8 16.8 - - + -
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C SER* 3.5 30.3 - - - +
188C ILE* 1.3 77.4 - - - +
190C HIS* 1.3 85.3 + - + +
191C LYS* 5.9 0.2 - - - -
212C ILE* 2.8 13.4 + - + +
214C GLN* 3.7 21.9 + - + +
463C PRO* 3.9 27.1 - - + -
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Residues in contact with HIS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ILE* 3.6 7.0 - - - +
189C GLU* 1.3 98.7 + - + +
191C LYS* 1.3 68.1 + - - +
192C PRO* 3.7 8.5 - - + -
211C LEU* 3.7 0.9 - - - -
212C ILE* 3.1 46.9 + - + +
463C PRO* 5.4 0.2 - - + -
464C PRO 3.5 19.0 + - - -
465C ASP* 3.1 27.8 + - - -
467C PRO* 4.3 23.1 - - + +
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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
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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