Contacts of the strand formed by residues 186 - 191 (chain B) in PDB entry 6E8Y
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B TRP* 4.5 8.7 - + - -
18B ILE* 4.6 8.3 - - + -
21B ILE* 3.8 22.0 - - + -
147B LEU* 4.2 20.6 - - + -
151B ASN* 4.0 19.7 - - - -
156B VAL* 3.7 25.6 - - + -
162B CYS* 3.5 20.2 - - - -
163B GLU 4.6 0.4 - - - -
164B THR* 3.7 29.2 - - + -
181B MET* 3.3 24.7 - - + +
182B GLN* 3.4 10.2 - - - +
183B THR* 3.1 33.3 + - - +
185B ASN* 1.3 78.8 - - - +
187B ARG* 1.3 59.8 + - - +
188B ILE* 3.9 4.8 + - + +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LEU 4.6 1.1 - - - +
343A GLN 3.2 25.6 + - - -
344A ASN* 4.3 13.3 + - - +
345A HIS 5.5 0.2 + - - -
348A HIS* 3.5 45.5 + - + +
161B PHE* 3.6 30.3 - - + -
162B CYS 3.1 9.1 + - - +
163B GLU* 3.3 5.3 - - + +
164B THR 2.8 27.2 + - - +
182B GLN* 3.4 34.5 - - - +
183B THR 2.9 30.7 + - - -
184B PRO* 3.5 15.8 - - - +
186B PHE* 1.3 72.9 - - - +
188B ILE* 1.3 60.3 + - - +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A HIS* 3.7 8.4 - - - +
147B LEU* 4.9 0.4 - - + -
164B THR* 3.4 21.8 - - + +
166B ILE* 3.7 35.0 - - + -
178B LYS* 3.0 41.7 + - + +
181B MET* 3.2 44.9 - - + +
182B GLN* 2.9 20.5 + - + +
186B PHE* 4.0 10.1 - - + +
187B ARG* 1.3 76.9 - - - +
189B THR* 1.3 73.5 + - - +
190B VAL* 4.1 3.4 - - + -
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ARG* 4.3 6.2 + - - -
347A GLU* 3.5 20.1 + - - +
348A HIS* 3.3 22.2 + - - -
164B THR 3.1 9.8 + - - -
165B THR* 3.4 9.2 - - - +
166B ILE 2.9 22.9 + - - -
178B LYS* 4.8 1.6 - - - +
188B ILE* 1.3 75.2 - - - +
190B VAL* 1.3 71.0 + - - +
191B VAL* 4.3 2.5 - - + -
254B GLU* 3.4 35.2 + - - +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 3.3 17.9 - - + +
168B CYS* 4.6 6.1 - - + +
171B PRO* 5.8 2.2 - - + +
174B GLY* 3.7 39.5 - - - +
175B GLN* 4.9 1.3 - - - +
178B LYS* 3.9 26.7 - - + +
188B ILE* 4.1 7.6 + - + -
189B THR* 1.3 79.2 - - - +
191B VAL* 1.3 74.9 + - - +
192B GLN* 5.8 2.2 - - + -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B THR* 4.0 6.3 - - + -
166B ILE 2.9 11.8 + - - +
167B GLY* 3.3 1.9 - - - -
168B CYS 2.8 26.6 + - - +
189B THR* 4.3 5.4 - - + -
190B VAL* 1.3 80.4 - - - +
192B GLN* 1.3 65.1 + - - +
193B GLU* 4.1 8.1 - - + +
197B VAL* 3.5 32.3 - - + -
251B THR* 4.3 15.7 - - + +
254B GLU* 4.1 30.5 - - + +
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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