Contacts of the helix formed by residues 156 - 164 (chain A) in PDB entry 3C51
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 GLN 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ALA* 3.3 21.4 + - - +
153A HIS* 2.8 37.2 + - + +
154A LEU 3.3 0.2 - - - -
155A GLY* 1.3 75.2 - - - +
157A ALA* 1.3 81.2 + - + +
158A PRO* 4.5 0.4 - - + -
159A PHE* 4.8 0.2 - - - -
160A GLN* 3.4 22.0 + - - +
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Residues in contact with ALA 157 (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 HIS* 6.2 0.7 - - + -
156A GLN* 1.3 84.9 - - + +
158A PRO* 1.3 66.6 - - + +
159A PHE 3.1 1.3 - - - -
160A GLN* 2.6 30.6 + - - +
161A GLU* 2.9 19.4 + - + +
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Residues in contact with PRO 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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72A PHE* 4.4 2.0 - - + -
75A PHE* 3.6 4.0 - - - -
76A LEU* 4.1 13.7 - - + -
82A HIS* 3.4 41.5 - - + +
153A HIS* 3.4 35.0 - - + +
154A LEU* 3.6 14.8 - - + +
156A GLN* 4.5 0.9 - - + -
157A ALA* 1.3 95.6 - - + +
159A PHE* 1.3 55.9 + - - +
161A GLU* 3.3 7.4 + - + +
162A PHE* 2.8 28.4 + - - +
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Residues in contact with PHE 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 LEU 5.6 0.2 - - - -
57A GLY* 4.2 5.6 - - - -
58A PHE* 3.4 43.7 - + + -
61A MET* 3.7 15.9 - - - -
62A CYS* 3.3 27.6 - - - -
72A PHE* 3.9 6.7 - + - -
154A LEU 3.0 13.8 + - - +
155A GLY 3.3 27.4 - - - +
156A GLN 4.8 0.7 - - - -
157A ALA 3.1 0.4 - - - -
158A PRO* 1.3 76.0 - - - +
160A GLN* 1.3 65.2 + - - +
162A PHE* 3.1 8.6 + + - +
163A LEU* 2.9 65.6 + - + +
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Residues in contact with GLN 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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156A GLN 3.4 16.4 - - - +
157A ALA* 2.6 19.4 + - - +
159A PHE* 1.3 75.5 - - + +
161A GLU* 1.3 61.9 + - + +
163A LEU* 3.2 35.2 + - - +
164A ASP* 3.3 14.4 + - - +
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Residues in contact with GLU 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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75A PHE* 3.7 15.1 - - + -
79A HIS* 5.2 1.0 - - - -
81A GLN* 3.9 18.9 + - - +
82A HIS* 2.9 32.4 + - - -
157A ALA* 2.9 17.6 + - + +
158A PRO* 3.5 9.3 - - - +
160A GLN* 1.3 76.0 - - + +
162A PHE* 1.3 61.2 + - - +
164A ASP* 3.2 27.1 + - - +
165A SER* 3.7 3.8 - - - -
43B PRO* 5.6 1.4 - - - +
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Residues in contact with PHE 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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61A MET* 3.8 28.3 - - + -
62A CYS* 4.0 5.8 - - - -
68A GLY 4.8 2.2 - - - -
71A LEU* 3.9 2.2 - - + -
72A PHE* 3.6 42.6 - + + -
75A PHE* 3.8 34.9 - - + -
158A PRO 2.8 16.6 + - - +
159A PHE* 3.3 18.8 - + - +
161A GLU* 1.3 71.3 - - - +
163A LEU* 1.3 65.1 + - - +
165A SER* 2.4 27.4 + - - -
167A TYR* 3.7 22.0 - - + -
168A PHE* 3.2 31.9 - + - +
171A PHE* 4.6 9.2 - + + -
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Residues in contact with LEU 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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51A ARG* 5.6 2.6 + - - -
56A LEU 6.1 0.7 - - - +
61A MET* 4.3 1.8 - - + -
159A PHE* 2.9 59.8 + - + +
160A GLN* 3.2 31.1 + - - +
162A PHE* 1.3 75.0 - - + +
164A ASP* 1.3 57.8 + - + +
165A SER 3.3 5.1 + - - +
168A PHE* 3.3 54.1 - - + +
169A LEU* 5.8 0.7 - - - +
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Residues in contact with ASP 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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160A GLN 3.3 8.2 + - - +
161A GLU* 3.2 15.0 + - - +
162A PHE 3.2 0.4 - - - -
163A LEU* 1.3 75.9 - - + +
165A SER* 1.3 60.1 + - - +
43B PRO* 3.2 20.5 - - + +
44B LEU* 3.0 24.9 + - - +
45B SER* 2.7 48.6 + - - -
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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