Contacts of the helix formed by residues 187 - 195 (chain P) in PDB entry 2JA7
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 THR 187 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LYS* 2.8 52.5 + - + +
36A ARG* 3.9 7.6 - - - +
185P CYS* 4.2 0.2 - - - +
186P ASP* 1.3 83.2 + - - +
188P ALA* 1.3 70.8 + - - +
189P ASP* 3.2 7.6 - - - +
190P GLU* 4.0 13.2 + - - +
191P ALA* 3.5 11.6 + - - +
208P GLU* 2.8 11.4 - - - +
211P LEU* 3.1 16.9 - - - +
167S TYR* 4.8 7.1 + - - -
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Residues in contact with ALA 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 5.6 3.4 - - + -
187P THR* 1.3 76.6 - - + +
189P ASP* 1.3 53.7 - - - +
191P ALA* 3.3 5.5 - - - +
192P LYS* 2.7 41.2 + - - +
204P ASP* 3.8 46.7 - - + +
207P LEU* 4.4 8.7 - - + -
208P GLU* 2.5 16.6 + - - +
211P LEU* 4.4 2.7 - - - -
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Residues in contact with ASP 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 4.2 20.8 - - + +
57A ARG* 5.1 2.3 + - - -
187P THR* 3.7 2.1 - - - +
188P ALA* 1.3 75.7 - - - +
190P GLU* 1.3 64.6 + - - +
191P ALA 2.8 6.0 + - - -
192P LYS* 4.5 2.7 - - - +
193P THR* 3.1 41.3 + - - +
167S TYR* 3.3 31.1 - - - +
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Residues in contact with GLU 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184P ALA* 3.8 18.9 - - - +
185P CYS* 3.6 4.1 - - + -
186P ASP* 3.1 36.5 + - - +
187P THR* 3.8 16.0 + - - +
188P ALA 3.6 0.2 - - - -
189P ASP* 1.3 78.3 - - - +
191P ALA* 1.3 58.3 + - - +
194P LEU* 3.1 35.0 - - + +
144S ARG* 4.0 9.2 + - - -
167S TYR* 3.2 53.6 - - + +
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Residues in contact with ALA 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P LEU* 4.8 7.0 - - + -
185P CYS* 4.2 16.4 - - + -
187P THR 3.5 12.4 + - - +
188P ALA 3.3 8.0 + - - +
189P ASP 2.8 1.2 - - - -
190P GLU* 1.3 76.7 - - - +
192P LYS* 1.3 53.6 + - - +
193P THR 2.6 17.1 + - - -
194P LEU* 2.9 13.2 + - - -
195P ILE* 3.0 19.6 + - - +
198P LEU* 4.7 0.7 - - - -
207P LEU* 3.8 20.6 - - + -
211P LEU* 4.1 10.5 - - + -
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Residues in contact with LYS 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 6.3 0.9 - - - +
188P ALA 2.7 24.8 + - - +
189P ASP* 4.0 2.2 - - - +
191P ALA* 1.3 69.5 - - - +
193P THR* 1.3 58.6 + - - +
195P ILE 4.1 12.1 - - - -
196P PRO* 3.7 12.6 - - - +
198P LEU* 4.1 9.4 - - + -
199P ASN* 3.1 67.5 + - - +
202P ILE* 3.8 18.8 - - + +
204P ASP* 3.3 23.8 + - - +
207P LEU* 3.2 24.7 - - + -
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Residues in contact with THR 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189P ASP* 3.1 26.3 + - - +
191P ALA 2.6 7.9 + - - -
192P LYS* 1.3 76.8 + - - +
194P LEU* 1.3 66.6 + - + +
195P ILE 3.1 4.5 - - - -
196P PRO* 3.4 15.9 - - - +
165S GLU* 6.1 2.2 - - + -
166S ASP* 4.9 6.5 - - + +
167S TYR* 4.2 20.2 - - + -
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Residues in contact with LEU 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179P GLN* 5.1 0.9 - - - +
183P LEU* 4.8 6.1 - - + -
184P ALA 5.3 0.2 - - - +
185P CYS* 5.6 2.7 - - - -
190P GLU* 3.1 24.0 + - + +
191P ALA 2.9 2.7 + - - +
193P THR* 1.3 84.9 - - + +
195P ILE* 1.3 67.4 + - + +
196P PRO* 3.3 5.5 - - - +
84S GLY 4.9 1.4 - - - +
86S VAL* 2.9 48.2 + - + +
144S ARG* 2.9 38.8 - - - +
146S LYS* 6.1 0.7 - - + -
165S GLU* 6.2 0.7 - - + -
166S ASP 4.0 12.3 - - - +
167S TYR* 3.7 28.9 - - + +
168S LEU* 4.2 9.9 - - + -
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Residues in contact with ILE 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P ALA* 6.0 0.9 - - - -
175P PHE* 6.0 2.7 - - + -
176P GLU* 4.2 14.8 - - + -
179P GLN* 3.6 33.2 - - + +
180P LEU* 3.4 34.3 - - + +
183P LEU* 5.0 5.8 - - + -
185P CYS* 5.3 3.8 - - - -
191P ALA* 3.0 13.6 + - - +
192P LYS 4.0 5.5 - - - +
194P LEU* 1.3 90.0 - - + +
196P PRO* 1.3 53.7 - - - +
197P SER* 2.8 27.7 + - - +
198P LEU* 3.0 34.7 + - + +
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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