Contacts of the helix formed by residues 178 - 189 (chain T) in PDB entry 5JPQ
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 ASP 178 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176T ILE* 3.3 2.0 - - - +
177T GLU* 1.3 79.0 - - + +
179T HIS* 1.3 65.9 + - - +
180T GLU* 4.6 1.8 - - + +
181T GLU* 3.6 19.9 - - + +
182T TYR* 3.0 23.1 + - - +
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Residues in contact with HIS 179 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158T SER* 3.9 28.0 - - - -
177T GLU 3.5 5.6 + - - -
178T ASP* 1.3 71.6 - - - +
180T GLU* 1.3 63.8 + - - +
182T TYR* 3.3 7.2 + - - +
183T ALA* 2.9 24.9 + - - +
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Residues in contact with GLU 180 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178T ASP* 3.4 3.0 - - + +
179T HIS* 1.3 78.6 - - - +
181T GLU* 1.3 63.3 + - - +
183T ALA* 3.4 5.9 + - - +
184T THR* 3.0 23.0 + - - -
244T TYR* 5.3 14.1 - - + -
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Residues in contact with GLU 181 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176T ILE* 5.0 8.7 - - + -
178T ASP* 3.3 22.3 + - + +
179T HIS 3.3 0.4 - - - -
180T GLU* 1.3 74.4 - - - +
182T TYR* 1.3 68.5 + - - +
184T THR* 2.9 18.8 + - - -
185T ILE* 3.2 11.1 + - - +
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Residues in contact with TYR 182 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162T ARG* 6.6 0.2 - - + -
172T LEU 6.0 0.7 - - - +
176T ILE* 4.5 20.5 - - + +
178T ASP 3.0 14.9 + - - +
179T HIS* 3.6 10.8 - - - +
181T GLU* 1.3 76.2 - - - +
183T ALA* 1.3 63.6 + - - +
185T ILE* 3.2 14.4 + - - +
186T VAL* 3.3 12.8 + - - +
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Residues in contact with ALA 183 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179T HIS 2.9 18.2 + - - +
180T GLU* 3.6 6.7 - - - +
182T TYR* 1.3 76.5 - - - +
184T THR* 1.3 55.7 + - - +
185T ILE 3.3 0.2 + - - -
186T VAL* 3.3 2.8 + - - +
187T SER* 2.8 33.4 + - - -
237T ALA* 3.6 29.8 - - - +
240T ILE* 4.2 16.4 - - + -
241T LEU* 5.0 6.7 - - + +
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Residues in contact with THR 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180T GLU 3.0 12.6 + - - -
181T GLU* 2.9 14.1 + - - -
183T ALA* 1.3 75.0 - - - +
185T ILE* 1.3 57.3 + - - +
187T SER* 3.7 6.4 - - - -
188T ARG* 3.0 31.9 + - - +
241T LEU* 6.0 3.3 - - - +
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Residues in contact with ILE 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181T GLU 3.2 9.7 + - - +
182T TYR* 3.5 11.2 - - - +
183T ALA 3.2 0.2 - - - -
184T THR* 1.3 74.1 - - - +
186T VAL* 1.3 65.0 + - - +
188T ARG* 3.4 2.8 + - - +
189T PHE* 3.0 30.2 + - + +
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Residues in contact with VAL 186 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161T LEU* 6.6 0.2 - - + -
165T TYR* 5.2 14.8 - - + -
182T TYR 3.3 8.0 + - - +
183T ALA* 3.3 7.4 + - - +
185T ILE* 1.3 78.1 - - - +
187T SER* 1.3 62.6 + - - +
190T GLY* 3.3 27.7 + - - +
233T MET* 5.8 4.0 - - + +
234T ARG* 4.1 15.4 - - - +
237T ALA* 4.0 14.1 - - + -
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Residues in contact with SER 187 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183T ALA 2.8 19.1 + - - -
184T THR* 3.7 7.4 - - - -
186T VAL* 1.3 80.9 - - - +
188T ARG* 1.3 60.3 + - - +
189T PHE 3.7 0.3 + - - -
234T ARG* 4.9 9.4 - - - +
237T ALA* 3.9 19.9 - - - +
238T ASN* 4.7 8.1 - - - -
241T LEU* 5.7 4.3 - - - -
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Residues in contact with ARG 188 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184T THR 3.0 17.5 + - - +
185T ILE* 4.3 2.5 - - - +
187T SER* 1.3 77.4 - - - +
189T PHE* 1.3 60.7 + - + +
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Residues in contact with PHE 189 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185T ILE* 3.0 14.5 + - + +
187T SER 3.4 0.6 - - - -
188T ARG* 1.3 81.6 - - + +
190T GLY* 1.3 62.1 + - - +
191T ASP* 3.1 22.6 + - - +
194T PHE* 4.1 24.6 - - + +
195T LEU* 5.3 5.6 - - + +
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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