Contacts of the helix formed by residues 178 - 182 (chain A) in PDB entry 2PBH
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 SER 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.3 25.6 - - - +
13A LEU* 4.3 9.0 - - - +
177A TYR* 1.3 71.5 - - - +
179A ASP* 1.3 61.7 + - - +
181A LEU* 3.2 23.0 + - - +
182A LEU* 3.9 1.0 - - - +
193A GLY* 2.9 28.4 - - - -
194A GLU* 3.0 20.9 + - - -
196A MET* 3.8 23.0 - - - +
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 5.0 5.3 - - + +
17A VAL* 4.4 14.4 - - + -
24A TRP* 3.4 21.0 - - + -
177A TYR* 3.4 5.7 - - - +
178A SER* 1.3 76.6 + - - +
180A PHE* 1.3 61.9 + - - -
182A LEU* 2.9 36.6 + - - +
188A TYR* 3.2 18.7 + - - -
189A GLN 3.6 2.1 - - - +
190A HIS* 3.3 13.2 + - - -
191A VAL* 2.8 26.3 + - - +
192A THR 3.3 26.0 + - - +
193A GLY* 4.8 0.2 - - - -
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE* 3.4 32.5 - + + -
176A VAL* 4.1 15.7 - - + -
177A TYR 3.1 11.9 + - - +
179A ASP* 1.3 81.7 + - - +
181A LEU* 1.3 66.7 + - - +
182A LEU 3.1 0.7 + - - -
183A TYR* 3.1 20.7 + - + +
188A TYR* 3.3 50.9 - + + +
199A HIS* 5.1 0.7 - + - -
219A ASN* 3.9 8.5 - - - -
221A TRP* 3.4 31.0 - + - -
225A TRP* 3.6 22.5 - + - -
231A PHE* 3.8 26.0 - + - -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.7 32.5 - - + -
29A ASN* 2.8 22.9 + - - +
30A PHE* 3.5 32.2 - - + -
35A MET* 5.6 0.4 - - + -
38A LEU* 4.4 25.8 - - + +
41A LEU* 5.0 1.3 - - + -
176A VAL* 4.9 4.9 - - + -
177A TYR 4.7 0.9 - - - +
178A SER* 3.2 13.1 + - - +
179A ASP 3.1 0.2 - - - -
180A PHE* 1.3 81.5 - - - +
182A LEU* 1.3 59.9 + - + +
196A MET* 3.9 31.6 - - + -
221A TRP* 4.1 19.3 - - + -
225A TRP* 3.3 8.8 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.6 32.1 - - + -
13A LEU* 3.7 37.9 - - + -
14A VAL* 4.1 15.7 - - + +
17A VAL* 4.7 3.1 - - + -
26A ALA* 3.2 17.7 - - + +
27A GLY 2.8 42.5 + - - +
28A HIS* 4.1 21.3 - - + -
29A ASN 5.3 0.9 - - - +
30A PHE* 6.3 0.2 - - + -
178A SER 3.9 4.9 - - - +
179A ASP* 2.9 20.5 + - - +
181A LEU* 1.3 78.4 - - - +
183A TYR* 1.3 62.7 + - - +
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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