Contacts of the helix formed by residues 184 - 188 (chain B) in PDB entry 6UPQ
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 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PRO 4.5 3.6 + - - -
156A PHE* 2.9 36.2 + - + +
157A GLY 4.9 1.8 + - - -
186A THR* 6.0 0.2 - - - -
187A LEU* 6.2 0.6 - - - +
51B GLY 2.8 28.7 + - - -
52B ILE* 3.5 23.1 + - + +
156B PRO* 3.6 6.2 - - + +
183B ALA* 1.3 72.3 - - + +
185B ALA* 1.3 54.8 + - - +
186B ASP* 3.1 7.2 - - - -
187B THR* 2.7 40.9 + - - +
236B VAL* 3.7 5.3 + - - +
500B GTP 3.0 75.2 + - + +
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Residues in contact with ALA 185 (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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260A TRP* 5.0 1.4 - - - -
182B ILE* 3.7 13.2 - - + +
183B ALA 3.1 3.6 + - - -
184B LYS* 1.3 71.5 - - - +
186B ASP* 1.3 57.1 + - - +
187B THR 2.9 9.8 + - - -
188B ILE* 3.1 25.1 + - + +
193B LEU* 5.3 2.4 - - + +
235B ALA* 3.6 21.8 - - + +
236B VAL 3.0 35.5 + - - +
237B VAL* 4.4 3.4 - - + -
267B HIS 6.0 1.3 - - - +
268B CYS* 5.3 1.3 - - + -
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Residues in contact with ASP 186 (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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185A ASP 4.9 5.2 - - - +
186A THR* 5.5 0.2 - - - -
258A TYR* 3.1 25.7 + - - -
260A TRP* 3.6 30.6 + - + -
184B LYS 3.2 7.8 - - - +
185B ALA* 1.3 71.5 + - - +
187B THR* 1.3 55.3 + - - -
188B ILE 3.3 0.4 - - - -
237B VAL* 3.7 17.8 - - + +
253B ARG* 2.9 17.8 + - - -
255B TYR* 2.6 30.0 + - + +
260B VAL* 4.2 7.6 - - + +
500B GTP 2.8 30.0 + - - +
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Residues in contact with THR 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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156A PHE* 3.6 19.8 - - + -
183A LYS* 3.9 7.6 - - + +
185A ASP 5.8 0.2 - - - -
186A THR* 3.2 37.3 - - + +
256A ARG* 3.1 8.1 + - - -
258A TYR* 3.2 1.7 + - - -
1401A GDP 2.8 33.7 + - - +
156B PRO* 3.7 28.5 - - + +
184B LYS* 2.7 23.5 + - - +
185B ALA 2.9 0.6 - - - -
186B ASP* 1.3 78.9 + - - +
188B ILE* 1.3 58.3 + - + +
192B GLU* 4.5 0.2 - - - +
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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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258A TYR* 3.5 10.8 - - - -
259A PRO* 5.9 0.3 - - - +
260A TRP* 5.2 2.4 - - - -
156B PRO* 3.7 17.5 - - + +
158B GLY* 5.3 5.4 - - - +
182B ILE* 3.5 24.0 - - + -
185B ALA* 3.1 16.9 + - - +
186B ASP* 5.0 0.2 - - - -
187B THR* 1.3 81.9 - - + +
189B ALA* 1.3 65.9 + - - +
192B GLU* 3.6 17.0 - - + +
193B LEU* 3.5 48.2 - - + +
196B PHE* 3.4 34.8 - - + -
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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