Contacts of the helix formed by residues 184 - 191 (chain H) in PDB entry 1PQB
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 PRO 184 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22H TYR* 3.8 26.5 - - + -
24H PHE* 6.1 0.4 - - + -
32H PRO* 4.3 14.4 - - + -
35H VAL* 4.3 6.3 - - + -
176H PRO* 3.2 21.8 - - + +
177H ASP* 5.0 0.9 - - + -
182H GLY 3.6 7.2 - - - +
183H ILE* 1.3 93.7 - - + +
185H ASP* 1.3 66.2 + - - +
186H SER* 3.9 15.9 - - - +
187H LEU* 3.2 31.0 + - + +
188H GLU* 3.2 10.2 + - - +
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Residues in contact with ASP 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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176H PRO* 3.0 29.0 + - + +
177H ASP* 3.2 4.0 - - - -
178H ARG* 2.9 62.5 + - - +
183H ILE 4.4 0.4 - - - -
184H PRO* 1.3 72.3 - - - +
186H SER* 1.3 63.5 + - - +
188H GLU* 3.4 3.3 + - - +
189H VAL* 3.1 28.9 + - - +
223H PRO* 3.8 21.0 - - + +
800I CA 4.3 2.3 - - - -
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Residues in contact with SER 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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30H GLN 5.1 2.9 + - - -
32H PRO* 4.3 16.0 - - - +
176H PRO* 5.9 0.9 - - - +
184H PRO* 3.9 12.8 - - - +
185H ASP* 1.3 78.8 - - - +
187H LEU* 1.3 61.5 + - - +
189H VAL* 3.8 2.8 - - - +
190H GLU* 2.8 59.1 + - - +
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Residues in contact with LEU 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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32H PRO* 4.1 27.4 - - + +
33H MET 6.2 0.2 - - - -
35H VAL* 4.5 5.4 - - + -
183H ILE* 4.0 8.5 - - + -
184H PRO* 3.2 25.6 + - + +
186H SER* 1.3 80.5 + - - +
188H GLU* 1.3 60.0 + - - +
190H GLU* 4.6 8.1 - - + +
191H GLY 2.7 30.8 + - - +
192H TYR* 3.2 16.6 - - + -
203H LEU* 4.0 22.9 - - + -
204H SER* 4.6 0.9 - - - -
205H PRO* 3.4 44.9 - - + -
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Residues in contact with GLU 188 (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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181H ASP* 3.4 3.9 - - - +
183H ILE* 3.5 23.8 - - + +
184H PRO 3.2 5.4 + - - +
185H ASP 3.8 6.5 - - - +
187H LEU* 1.3 78.1 - - - +
189H VAL* 1.3 62.4 + - - +
191H GLY 4.1 0.2 + - - -
192H TYR* 3.8 7.6 - - + -
220H LYS* 3.4 10.7 + - - +
221H SER* 2.7 54.2 + - - +
222H SER 2.8 6.6 - - - +
223H PRO* 3.3 15.4 - - + +
235H ASP* 3.0 3.8 - - - +
800I CA 2.4 30.5 - - - -
801I CA 2.3 28.5 - - - -
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Residues in contact with VAL 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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178H ARG* 4.7 4.9 - - - +
185H ASP 3.1 18.2 + - - +
186H SER* 3.8 4.7 - - - +
188H GLU* 1.3 77.5 - - - +
190H GLU* 1.3 66.7 + - + +
220H LYS* 3.1 22.3 + - - +
221H SER 4.5 1.8 - - - -
223H PRO* 3.7 27.1 - - + -
517H THR* 5.0 5.6 - - - +
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Residues in contact with GLU 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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186H SER* 2.8 48.3 + - - +
187H LEU* 4.4 8.7 - - + +
189H VAL* 1.3 81.8 - - + +
191H GLY* 1.3 61.9 + - - +
205H PRO* 6.5 0.2 - - + -
206H TRP* 5.2 1.4 - - - +
218H LYS* 3.9 15.2 + - - -
220H LYS* 3.9 7.5 - - - -
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Residues in contact with GLY 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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187H LEU* 2.7 19.7 + - - +
188H GLU 4.1 0.6 + - - -
189H VAL 3.6 1.0 - - - -
190H GLU* 1.3 79.0 - - - +
192H TYR* 1.3 61.7 + - - +
205H PRO* 3.6 6.9 - - - +
206H TRP* 3.0 21.8 + - - +
218H LYS* 4.1 8.5 - - - -
219H TYR 3.1 14.8 - - - -
220H LYS* 3.7 8.1 - - - -
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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