Contacts of the helix formed by residues 184 - 196 (chain T) in PDB entry 5A0Q
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 LEU 184 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42T THR* 3.8 2.8 - - + +
43T HIS* 3.0 49.1 - - + +
45T VAL* 3.7 11.0 - - + -
183T ASN* 1.3 77.2 + - - +
185T ASN* 1.3 66.2 + - - +
187T LEU* 3.6 8.2 - - - +
188T VAL* 3.1 30.8 + - + +
214T ILE* 2.6 61.2 - - + -
219T LEU* 4.7 5.4 - - + -
224T TYR* 4.8 5.2 - - + +
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Residues in contact with ASN 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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183T ASN* 3.1 10.3 + - - +
184T LEU* 1.3 83.9 - - - +
186T GLU* 1.4 56.7 + - - +
188T VAL* 3.3 5.0 + - - +
189T LYS* 3.0 35.5 + - + +
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Residues in contact with GLU 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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182T CYS* 3.3 38.5 - - + -
183T ASN* 3.0 5.0 + - - +
185T ASN* 1.4 75.0 - - - +
187T LEU* 1.4 65.1 + - - +
189T LYS* 3.3 33.5 + - - +
190T HIS* 3.1 59.3 + - + +
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Residues in contact with LEU 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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38T LEU* 3.6 27.3 - - + +
39T LYS 4.3 1.6 - - - +
40T SER* 3.5 23.8 - - - +
43T HIS 3.6 8.1 - - - +
45T VAL* 3.4 30.3 - - + -
179T PHE* 3.1 36.1 - - + +
182T CYS* 3.2 17.3 - - + +
183T ASN 3.1 9.2 + - - +
184T LEU* 3.6 19.3 - - - +
185T ASN 3.3 0.2 - - - -
186T GLU* 1.4 75.2 - - - +
188T VAL* 1.4 53.2 + - - +
190T HIS* 3.2 8.5 + - - +
191T GLY* 2.8 29.5 + - - -
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Residues in contact with VAL 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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45T VAL* 3.7 25.8 - - + -
47T VAL* 5.5 0.9 - - + -
184T LEU* 3.1 20.6 + - + +
185T ASN* 3.6 4.7 - - - +
187T LEU* 1.4 71.4 - - - +
189T LYS* 1.4 66.0 + - - +
190T HIS 3.2 0.4 - - - -
191T GLY* 3.8 3.8 - - - +
192T LEU* 3.0 30.6 + - + +
212T ILE* 3.2 35.2 - - + -
214T ILE* 3.8 17.7 - - + -
224T TYR* 6.3 0.9 - - + -
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Residues in contact with LYS 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 ASN* 3.0 24.3 + - + +
186T GLU* 3.3 38.1 - - - +
187T LEU 3.3 0.4 - - - -
188T VAL* 1.4 76.3 - - + +
190T HIS* 1.3 63.5 + - + +
192T LEU* 3.8 13.6 - - + +
193T ARG* 3.7 20.1 + - - +
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Residues in contact with HIS 190 (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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171T TYR* 3.0 29.5 + - - +
175T HIS* 6.3 1.8 - + - -
179T PHE* 3.5 32.5 - + + -
182T CYS* 6.1 0.7 - - + -
186T GLU* 3.1 46.3 + - + +
187T LEU 3.4 7.4 - - - +
189T LYS* 1.3 77.5 - - + +
191T GLY* 1.3 61.9 + - - +
192T LEU 3.3 1.8 - - - -
193T ARG* 3.7 28.7 + - - -
194T ALA* 3.1 15.6 + - - +
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Residues in contact with GLY 191 (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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36T VAL* 4.9 2.2 - - - +
38T LEU* 4.3 12.1 - - - -
47T VAL* 4.2 25.1 - - - +
179T PHE* 6.1 0.2 - - - -
187T LEU 2.8 18.1 + - - -
188T VAL* 3.0 4.6 + - - -
190T HIS* 1.3 74.6 - - - +
192T LEU* 1.3 57.0 + - - +
194T ALA* 3.5 7.6 + - - +
195T LEU* 3.0 27.2 + - - +
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Residues in contact with LEU 192 (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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47T VAL* 4.4 3.6 - - + -
188T VAL* 3.0 24.6 + - + +
189T LYS* 3.8 13.7 - - + +
191T GLY* 1.3 77.1 - - - +
193T ARG* 1.4 55.5 + - - +
195T LEU* 3.4 7.1 + - - +
196T ARG* 3.2 34.4 + - - +
210T VAL* 3.6 43.9 - - + +
212T ILE* 4.1 12.6 - - + -
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Residues in contact with ARG 193 (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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171T TYR* 3.6 26.4 - - + +
189T LYS* 3.7 12.6 + - - +
190T HIS* 3.3 32.7 + - - +
191T GLY 3.3 0.2 - - - -
192T LEU* 1.4 73.9 - - - +
194T ALA* 1.4 63.3 + - - +
196T ARG* 3.6 20.3 + - - +
197T GLU* 3.5 22.9 - - - +
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Residues in contact with ALA 194 (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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36T VAL* 4.3 20.9 - - + -
168T ALA* 3.9 17.3 - - + +
171T TYR* 3.5 33.4 - - + -
172T LEU* 5.3 2.7 - - + -
179T PHE* 6.0 0.7 - - + -
190T HIS 3.1 7.8 + - - +
191T GLY* 3.5 10.5 - - - +
193T ARG* 1.4 72.4 - - - +
195T LEU* 1.3 64.9 + - - +
196T ARG 3.3 0.4 - - - -
197T GLU* 3.3 21.9 + - - +
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Residues in contact with LEU 195 (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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34T ALA* 4.5 13.2 - - + +
35T THR* 5.4 0.4 - - - -
36T VAL* 4.4 20.2 - - + -
47T VAL* 4.3 10.3 - - + -
48T ALA* 4.9 0.4 - - - -
49T LEU* 3.5 54.4 - - + +
191T GLY 3.0 17.9 + - - +
192T LEU* 3.6 7.9 - - - +
193T ARG 3.4 0.2 - - - -
194T ALA* 1.3 75.0 - - - +
196T ARG* 1.3 61.3 + - - +
197T GLU 3.2 5.1 + - - -
210T VAL* 3.0 37.2 - - + -
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Residues in contact with ARG 196 (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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164T ARG* 5.8 0.3 + - - -
192T LEU* 3.2 20.8 + - - +
193T ARG* 3.8 22.1 - - - +
194T ALA 3.3 0.8 - - - -
195T LEU* 1.3 75.5 - - - +
197T GLU* 1.3 68.1 + - - +
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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