Contacts of the helix formed by residues 183 - 196 (chain H) in PDB entry 5T0J
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 GLU 183 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182H LEU* 1.3 83.6 - - + +
184H LEU* 1.3 69.8 + - - +
185H GLU* 2.7 25.7 + - - +
186H ASP* 2.4 64.1 + - + +
187H ALA* 2.8 28.8 + - - +
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Residues in contact with LEU 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ALA* 3.5 20.1 - - + +
41H ALA* 3.7 26.7 - - + +
42H ASN* 5.5 1.1 - - - +
182H LEU 3.5 2.5 + - - -
183H GLU* 1.3 79.9 - - - +
185H GLU* 1.3 77.7 + - - +
187H ALA* 3.1 10.6 + - - +
188H ILE* 3.3 17.4 + - + +
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Residues in contact with GLU 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H GLU* 2.7 22.8 + - - +
184H LEU* 1.3 82.8 - - - +
186H ASP* 1.3 62.5 + - - +
188H ILE* 3.3 18.9 + - + +
189H HIS* 3.1 20.4 + - - +
229H TYR* 5.0 7.6 + - - +
234H ALA* 3.2 37.6 - - + +
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Residues in contact with ASP 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182H LEU* 3.6 24.3 - - + +
183H GLU* 2.4 45.9 + - + +
185H GLU* 1.3 71.3 - - - +
187H ALA* 1.3 62.3 + - - +
189H HIS* 3.5 19.5 + - - +
190H THR* 3.6 11.1 + - - +
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Residues in contact with ALA 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ILE* 4.5 7.6 - - + +
39H LYS 5.3 2.5 - - - +
40H ALA* 4.4 13.0 - - + -
174H LEU* 5.7 0.2 - - - +
182H LEU* 4.9 13.7 - - + +
183H GLU 2.8 19.2 + - - +
184H LEU 3.1 5.6 + - - +
186H ASP* 1.3 76.4 - - - +
188H ILE* 1.3 63.6 + - - +
190H THR* 3.4 10.3 - - + +
191H ALA* 3.2 24.3 + - - +
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Residues in contact with ILE 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ILE* 3.7 33.7 - - + -
40H ALA* 4.7 2.0 - - + -
45H VAL* 3.7 27.6 - - + -
184H LEU* 3.3 16.5 + - + +
185H GLU* 3.3 22.8 + - + +
187H ALA* 1.3 75.9 - - - +
189H HIS* 1.3 65.0 + - - +
191H ALA* 3.3 0.5 + - - +
192H ILE* 2.9 41.1 + - + +
210H VAL* 6.1 1.6 - - + -
212H ILE* 6.0 0.4 - - + -
229H TYR* 6.5 1.1 - - + -
233H ILE* 3.5 21.5 - - + +
234H ALA* 5.2 2.5 - - - -
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Residues in contact with HIS 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H GLU 3.1 12.8 + - - +
186H ASP* 3.5 13.7 - - - +
187H ALA 3.2 0.4 - - - -
188H ILE* 1.3 75.6 - - - +
190H THR* 1.3 64.4 + - - +
192H ILE* 3.0 7.1 + - - +
193H LEU* 2.9 36.8 + - + +
232H ALA* 5.2 12.6 - - + +
233H ILE 4.6 6.7 + - - -
234H ALA* 4.7 13.5 - - + -
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Residues in contact with THR 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H PHE* 3.3 22.0 - - - -
174H LEU* 4.4 9.8 - - + +
177H ARG* 4.0 13.1 - - + +
178H TYR* 5.0 12.3 - - + -
182H LEU* 6.4 0.9 - - + -
186H ASP 3.7 9.9 - - - +
187H ALA* 3.4 15.9 - - - +
189H HIS* 1.3 82.5 + - - +
191H ALA* 1.3 64.0 + - - +
193H LEU* 3.8 8.9 - - - +
194H THR* 3.2 24.6 + - - +
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Residues in contact with ALA 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H VAL* 4.9 8.9 - - + +
37H GLY 5.2 1.1 - - - +
38H ILE* 3.6 33.4 - - + -
160H ALA* 4.9 4.7 - - + -
174H LEU* 4.2 13.9 - - + -
187H ALA 3.2 19.4 + - - +
188H ILE 3.7 0.2 - - - +
189H HIS 3.1 0.8 - - - -
190H THR* 1.3 79.2 - - - +
192H ILE* 1.3 58.0 + - - +
194H THR* 3.2 11.2 - - - +
195H LEU* 3.2 23.7 + - - +
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Residues in contact with ILE 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ILE* 5.1 4.7 - - + -
47H ALA* 5.3 9.4 - - + -
188H ILE* 2.9 25.9 + - + +
189H HIS* 3.7 3.6 - - - +
191H ALA* 1.3 77.8 - - - +
193H LEU* 1.3 57.8 + - - +
194H THR 3.2 0.4 - - - -
195H LEU* 3.0 8.7 + - + -
196H LYS* 2.9 35.6 + - + +
203H MET* 5.5 3.1 - - + -
210H VAL* 5.5 9.9 - - + -
231H ALA 3.6 20.4 - - - +
232H ALA* 3.7 9.4 - - - +
233H ILE* 3.3 44.9 - - + +
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Residues in contact with LEU 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H PHE* 4.8 12.1 - - + -
189H HIS* 2.9 26.8 + - + +
190H THR* 3.8 11.0 - - - +
192H ILE* 1.3 76.9 - - - +
194H THR* 1.3 59.0 + - - +
196H LYS* 3.6 5.9 + - - +
197H GLU* 3.4 16.8 + - - +
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Residues in contact with THR 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H ALA* 6.3 2.2 - - + -
166H ASN* 3.3 12.8 - - - +
170H GLY* 3.3 25.5 - - - -
173H PHE* 3.4 30.3 - - + +
174H LEU* 4.1 17.0 - - + -
190H THR 3.2 11.5 + - - +
191H ALA* 3.2 20.6 - - - +
193H LEU* 1.3 76.8 - - - +
195H LEU* 1.3 62.9 + - - +
197H GLU* 3.3 29.1 + - - +
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Residues in contact with LEU 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H VAL* 4.5 17.5 - - + -
47H ALA* 6.0 2.9 - - + -
166H ASN* 3.7 12.5 - - - +
191H ALA 3.2 18.3 + - - +
192H ILE* 3.0 15.3 + - + +
194H THR* 1.3 79.4 - - - +
196H LYS* 1.3 56.4 + - - +
197H GLU 3.2 1.4 + - - -
199H PHE* 3.4 15.6 - - - +
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Residues in contact with LYS 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H ILE* 2.9 16.6 + - + +
193H LEU* 3.9 6.7 - - - +
194H THR 3.4 0.2 - - - -
195H LEU* 1.3 75.1 - - - +
197H GLU* 1.3 65.9 + - - +
198H SER 3.6 0.4 - - - -
199H PHE* 3.6 19.4 + - - +
200H GLU 5.5 0.2 - - - +
203H MET* 4.1 29.8 - - + -
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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