Contacts of the helix formed by residues 157 - 167 (chain A) in PDB entry 1PBH
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A SER* 1.3 70.1 + - - +
158A LYS* 1.3 88.4 + - - +
160A ILE* 3.4 1.4 + - - +
161A MET* 2.9 46.2 + - + +
215A TRP* 3.7 14.4 - - + -
235A ARG* 2.5 49.6 + - + -
236A GLY* 3.4 22.6 - - - -
243A GLU* 4.8 7.6 + - - +
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Residues in contact with LYS 158 (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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1A LEU* 4.3 8.3 - - + +
58A THR* 4.9 7.4 - - + -
156A SER* 3.3 17.5 - - - +
157A GLU* 1.3 108.6 + - - +
159A ASP* 1.3 66.2 + - - +
161A MET* 3.2 15.8 + - - +
162A ALA* 3.0 23.2 + - - +
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Residues in contact with ASP 159 (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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56A MET* 3.1 38.4 + - + +
58A THR* 4.3 11.9 + - - -
153A VAL* 3.9 4.9 - - + -
154A SER* 3.1 28.0 + - - +
156A SER* 2.8 32.1 + - - +
158A LYS* 1.3 72.1 - - - +
160A ILE* 1.3 67.0 + - - +
162A ALA* 3.1 7.6 + - - +
163A GLU* 3.0 21.1 + - - +
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Residues in contact with ILE 160 (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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153A VAL* 3.7 8.1 - - + -
154A SER 3.7 13.5 - - - +
156A SER 2.9 17.0 + - - +
157A GLU 3.7 1.6 - - - +
159A ASP* 1.3 73.2 - - - +
161A MET* 1.3 64.6 + - - +
163A GLU* 3.0 13.2 + - - +
164A ILE* 3.1 22.5 + - + +
170A VAL* 4.5 5.2 - - + -
203A ILE* 4.9 3.8 - - + -
215A TRP* 3.6 25.4 - - + -
242A ILE 5.1 0.4 - - - +
243A GLU* 3.6 41.5 - - + +
246A VAL* 3.5 40.8 - - + -
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Residues in contact with MET 161 (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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1A LEU* 4.4 15.0 - - + -
2A PRO 5.4 1.3 - - - +
157A GLU* 2.9 52.6 + - + +
158A LYS* 3.3 14.1 - - - +
160A ILE* 1.3 76.4 - - - +
162A ALA* 1.3 58.7 + - - +
164A ILE* 4.7 0.2 - - - -
165A TYR* 3.0 25.3 + - - +
206A TRP* 3.4 56.2 - - + +
215A TRP* 3.9 9.0 - - + -
235A ARG* 3.4 31.0 - - - +
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Residues in contact with ALA 162 (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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1A LEU* 4.3 11.0 - - + -
56A MET* 3.4 12.5 - - + +
58A THR* 3.6 18.4 - - + -
61A LEU* 3.4 30.5 - - + -
158A LYS 3.0 9.7 + - - +
159A ASP 3.1 7.4 + - - +
161A MET* 1.3 74.3 - - - +
163A GLU* 1.3 61.2 + - - +
165A TYR* 4.0 1.8 - - - -
166A LYS* 3.2 28.9 + - - +
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Residues in contact with GLU 163 (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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41A ARG* 2.7 27.2 + - - -
54A ARG* 3.7 6.2 + - - +
56A MET* 3.6 19.7 - - + +
151A TYR* 2.7 29.8 + - + -
153A VAL* 3.4 33.2 - - + -
159A ASP 3.0 9.6 + - - +
160A ILE* 3.0 10.1 + - - +
162A ALA* 1.3 75.2 - - - +
164A ILE* 1.3 55.9 + - - +
167A ASN* 2.7 56.9 + - - +
168A GLY 3.4 1.6 + - - +
170A VAL* 3.9 11.4 - - + -
248A ALA* 3.8 0.2 - - - +
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Residues in contact with ILE 164 (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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5A PHE* 3.8 13.9 - - + -
7A ALA* 5.1 0.4 - - + -
11A TRP* 3.4 6.6 - - - -
160A ILE* 3.1 18.5 + - + +
161A MET 3.7 6.7 - - - +
163A GLU* 1.3 77.4 - - - +
165A TYR* 1.3 58.6 + - - +
168A GLY* 2.7 42.8 + - - +
169A PRO 4.6 0.4 - - - -
170A VAL* 3.8 20.2 - - + -
203A ILE* 3.5 41.5 - - + +
204A LEU 3.8 21.8 - - - +
205A GLY 4.5 2.7 - - - +
206A TRP* 4.0 10.1 - - + -
215A TRP* 4.4 8.3 - - + -
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Residues in contact with TYR 165 (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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1A LEU* 4.1 21.3 - - + -
2A PRO* 3.6 30.2 - - + +
5A PHE* 3.4 39.0 - + - -
10A GLN* 3.6 31.4 + - - -
11A TRP* 3.7 6.8 - - - -
161A MET 3.0 17.4 + - - +
162A ALA 4.4 1.6 - - - +
164A ILE* 1.3 78.0 - - - +
166A LYS* 1.3 69.1 + - + +
206A TRP* 4.2 3.6 - + + -
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Residues in contact with LYS 166 (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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11A TRP* 5.1 3.4 - - - -
44A ILE* 5.5 0.9 - - - +
45A HIS* 4.3 5.4 - - - -
56A MET* 3.6 18.6 - - + +
57A PHE* 2.9 36.0 + - - +
61A LEU* 3.2 29.4 - - + +
162A ALA* 3.2 17.7 + - - +
165A TYR* 1.3 86.4 - - + +
167A ASN* 1.3 78.1 + - - +
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Residues in contact with ASN 167 (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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11A TRP* 4.7 0.7 - - - -
41A ARG* 3.3 23.6 + - - +
44A ILE* 4.0 6.2 - - - +
45A HIS* 3.5 36.8 + - - +
54A ARG* 5.9 0.6 - - - +
56A MET* 5.0 0.6 - - - +
151A TYR* 4.5 3.8 - - - -
163A GLU* 2.7 49.8 + - - +
166A LYS* 1.3 99.0 - - - +
168A GLY* 1.3 58.1 + - - +
250A ILE* 3.8 14.2 - - - +
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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