Contacts of the helix formed by residues 157 - 164 (chain A) in PDB entry 2IHD
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 ASP 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.0 34.1 + - - +
156A LYS* 1.3 90.9 - - - +
158A SER* 1.3 65.1 + - - +
159A TYR 3.5 0.4 - - - -
160A PRO* 3.4 10.0 - - - +
161A ARG* 3.5 43.8 + - - +
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Residues in contact with SER 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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70A PHE* 3.8 9.4 - - - -
73A PHE* 3.6 2.8 - - - -
74A LEU* 3.4 31.6 - - - +
77A GLU* 4.0 4.9 + - - -
79A SER* 4.0 7.4 + - - -
82A ASN* 5.3 2.9 + - - -
153A LEU 3.8 1.1 + - - -
154A MET* 3.3 14.7 + - - +
157A ASP* 1.3 76.7 - - - +
159A TYR* 1.3 60.3 + - - +
161A ARG* 3.2 22.2 + - - +
162A PHE* 2.8 29.6 + - - +
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Residues in contact with TYR 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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53A TRP 2.7 27.7 + - - -
54A ALA* 3.4 17.9 + - - -
56A SER* 3.1 12.3 + - - -
57A PHE* 3.5 50.9 - + + -
60A LEU* 3.8 21.8 - - + -
70A PHE* 3.9 7.8 - + - -
154A MET 2.8 21.7 + - - +
155A GLU* 3.8 13.2 - - + +
158A SER* 1.3 73.4 - - - +
160A PRO* 1.4 69.1 - - + +
162A PHE* 3.1 14.1 + + - +
163A LEU* 3.1 38.0 + - + +
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Residues in contact with PRO 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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155A GLU 3.2 20.9 - - - +
156A LYS* 3.6 17.3 - - - +
157A ASP 3.4 12.6 - - - +
159A TYR* 1.4 93.7 - - + +
161A ARG* 1.3 59.7 + - - +
163A LEU* 3.4 17.8 + - + +
164A ARG* 3.5 41.7 + - - +
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Residues in contact with ARG 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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73A PHE* 3.7 12.0 - - + -
77A GLU* 3.1 37.0 + - - +
79A SER* 5.7 0.4 + - - -
157A ASP* 3.5 34.2 + - - +
158A SER* 3.2 25.0 + - - +
159A TYR 3.2 0.8 - - - -
160A PRO* 1.3 73.5 - - + +
162A PHE* 1.3 66.3 + - - +
164A ARG* 3.1 31.4 + - - +
165A SER* 3.3 11.8 + - - -
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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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53A TRP* 4.2 6.1 - + + -
60A LEU* 3.7 30.5 - - + -
69A ALA* 3.7 38.6 - - + -
70A PHE* 3.8 13.9 - + + -
73A PHE* 3.5 38.3 - + + -
158A SER 2.8 16.9 + - - +
159A TYR* 3.1 9.6 + + - +
161A ARG* 1.3 72.0 - - - +
163A LEU* 1.3 70.0 + - + +
165A SER* 2.7 30.1 + - - -
167A MET* 4.3 9.4 - - + -
168A TYR* 3.2 43.6 - + + +
171A LEU* 5.5 0.2 - - + -
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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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53A TRP 4.5 0.9 - - - +
54A ALA* 4.1 23.3 - - + +
159A TYR* 3.1 49.6 + - + +
160A PRO* 3.7 11.7 - - + +
161A ARG 3.2 0.4 - - - -
162A PHE* 1.3 94.0 - - + +
164A ARG* 1.3 58.2 + - + +
165A SER 3.5 0.2 - - - -
168A TYR* 3.5 44.9 - - + -
169A LEU* 3.6 12.5 - - - +
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Residues in contact with ARG 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 PRO* 3.5 41.6 + - - +
161A ARG* 3.1 25.1 + - - +
163A LEU* 1.3 79.4 - - + +
165A SER* 1.3 62.9 + - - +
166A LYS 3.9 0.5 + - - -
169A LEU* 3.6 15.4 - - - +
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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