Contacts of the strand formed by residues 186 - 191 (chain A) in PDB entry 6E8Z
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 PHE 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 4.0 17.0 - + - -
18A ILE* 4.7 7.9 - - + -
21A ILE* 3.7 22.9 - - + -
147A LEU* 4.3 15.9 - - + -
151A ASN* 3.9 22.2 - - + -
156A VAL* 4.2 12.3 - - + -
162A CYS* 3.5 26.9 - - - -
163A GLU 4.4 0.9 - - - -
164A THR* 3.8 28.9 - - + -
181A MET* 3.4 24.0 - - + -
182A GLN* 3.5 9.2 - - - -
183A THR* 3.2 36.2 + - - +
184A PRO 3.5 0.2 - - - -
185A ASN* 1.3 78.9 - - - +
187A ARG* 1.3 61.4 + - - +
188A ILE* 4.1 3.8 - - + +
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 3.7 26.2 - - + -
162A CYS 3.1 8.3 + - - +
163A GLU* 3.0 8.4 - - + +
164A THR 2.7 32.1 + - - +
182A GLN* 3.3 36.6 + - - +
183A THR 2.7 36.1 + - - -
184A PRO* 3.5 20.3 - - - +
186A PHE* 1.3 74.0 - - - +
188A ILE* 1.3 55.8 - - - +
342B LEU 4.7 0.9 - - - +
343B GLN 3.2 24.3 + - - -
344B ASN* 4.4 12.9 + - - +
345B HIS 5.6 0.2 + - - -
348B HIS* 3.4 47.6 + - + +
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.8 0.4 - - + -
164A THR* 3.4 21.8 - - + +
166A ILE* 3.6 32.5 - - + -
178A LYS* 2.8 45.8 + - + +
181A MET* 3.6 32.3 - - + +
182A GLN* 3.2 24.0 + - + +
186A PHE* 4.1 11.7 - - + +
187A ARG* 1.3 79.0 - - - +
189A THR* 1.3 75.3 + - - +
190A VAL* 4.0 2.9 - - + -
348B HIS* 3.7 8.9 - - - +
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Residues in contact with THR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A THR 3.1 10.3 + - - -
165A THR* 3.4 7.4 - - - +
166A ILE 2.8 28.9 + - - +
178A LYS* 4.7 1.1 - - - +
188A ILE* 1.3 72.5 - - - +
190A VAL* 1.3 68.2 + - - +
191A VAL* 4.3 3.4 - - + -
254A GLU* 3.5 33.5 + - - +
229B ARG* 4.2 5.7 + - - -
347B GLU* 3.6 19.5 + - - +
348B HIS* 3.2 23.9 + - - -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 3.3 17.7 - - + +
168A CYS* 4.5 5.2 - - + +
171A PRO* 6.5 0.7 - - + -
174A GLY* 3.9 40.6 - - - +
175A GLN* 5.3 2.0 - - - +
178A LYS* 3.9 25.5 - - + +
188A ILE* 4.0 8.9 + - + -
189A THR* 1.3 78.0 - - - +
191A VAL* 1.3 76.0 + - - +
192A GLN* 6.3 0.4 - - + -
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A THR* 4.0 6.5 - - + -
166A ILE 2.8 10.6 + - - +
167A GLY* 3.3 3.3 - - - -
168A CYS 2.9 26.4 + - - +
189A THR* 4.3 6.3 - - + -
190A VAL* 1.3 83.6 - - - +
192A GLN* 1.3 64.3 + - - +
193A GLU* 4.1 7.6 - - + +
197A VAL* 3.6 31.2 - - + -
251A THR* 4.5 13.7 - - + +
254A GLU* 4.2 29.8 - - + +
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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