Contacts of the helix formed by residues 153 - 160 (chain A) in PDB entry 1XD0
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A LYS* 5.2 6.9 - - - +
150A ASN* 3.3 8.8 + - - +
151A TYR 3.1 0.8 - - - -
152A ASN* 1.3 78.6 - - - +
154A ALA* 1.3 62.1 + - - +
155A THR* 3.1 22.0 + - - -
156A GLN* 3.0 48.5 + - + +
157A VAL* 3.3 18.9 + - - +
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Residues in contact with ALA 154 (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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152A ASN 3.8 4.2 + - - -
153A ASP* 1.3 72.9 + - - +
155A THR* 1.3 61.4 + - - +
157A VAL* 3.7 1.9 + - - +
158A ARG* 3.2 38.4 + - - +
203A TRP* 4.7 2.9 - - + -
241A PRO* 4.1 15.3 - - + +
242A ILE* 3.9 29.4 - - + -
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Residues in contact with THR 155 (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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142A LYS* 3.2 33.4 - - + +
153A ASP* 3.1 12.3 + - - -
154A ALA* 1.3 76.0 - - - +
156A GLN* 1.3 61.4 + - - +
158A ARG* 3.2 3.6 + - - +
159A ASP* 2.9 34.7 + - - +
203A TRP* 4.1 19.0 - - + -
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Residues in contact with GLN 156 (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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142A LYS* 4.7 6.0 - - + +
143A THR* 3.5 17.7 - - + +
148A ILE* 3.5 6.2 - - + +
149A GLU* 2.6 36.3 + - - +
150A ASN* 2.9 25.4 + - - +
153A ASP* 3.0 40.3 + - - +
155A THR* 1.3 76.0 - - - +
157A VAL* 1.3 64.7 + - + +
158A ARG 3.1 2.0 - - - -
159A ASP* 4.9 0.2 - - - -
160A CYS* 2.9 53.8 + - + +
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Residues in contact with VAL 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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148A ILE* 3.5 15.3 - - + +
150A ASN 4.0 2.9 - - - +
151A TYR* 3.8 37.2 - - + +
153A ASP 3.3 16.6 - - - +
154A ALA 3.7 8.7 - - - +
155A THR 3.2 0.4 - - - -
156A GLN* 1.3 77.8 - - - +
158A ARG* 1.3 59.0 + - - +
160A CYS 4.5 1.4 - - - +
200A LYS* 3.9 16.6 - - + +
201A HIS* 3.0 50.6 + - + +
242A ILE* 3.7 22.9 - - + -
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Residues in contact with ARG 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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137A ASN* 4.2 1.4 + - - -
154A ALA* 3.2 25.6 + - - +
155A THR 3.2 4.8 + - - +
156A GLN 3.1 0.2 - - - -
157A VAL* 1.3 81.2 - - - +
159A ASP* 1.3 61.5 + - - +
160A CYS 3.6 0.4 - - - -
167A ASP* 3.0 2.4 - - - +
200A LYS 2.8 23.9 + - - -
201A HIS 3.2 5.6 - - - +
202A MET 3.7 23.3 - - - -
203A TRP* 3.2 60.7 - - + +
204A PRO* 3.7 11.5 - - - +
242A ILE* 3.5 31.6 - - - +
246A ASP* 5.0 4.9 + - - +
247A TYR* 2.9 25.6 + - - -
498A CA 2.4 28.1 - - - -
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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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137A ASN* 3.2 28.9 + - - +
140A LYS* 2.9 39.3 + - + +
141A CYS* 3.5 12.0 - - - +
142A LYS* 2.9 28.6 + - - +
155A THR* 2.9 24.1 + - - +
158A ARG* 1.3 77.1 - - - +
160A CYS* 1.3 63.0 + - - +
167A ASP* 3.6 5.0 - - - +
203A TRP* 3.0 26.4 + - - -
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Residues in contact with CYS 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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141A CYS* 2.0 51.8 - - - -
142A LYS* 3.9 3.1 - - - -
143A THR* 3.7 8.1 - - - -
147A ASP 3.8 16.6 - - - -
148A ILE* 3.9 10.4 - - - +
156A GLN* 2.9 37.7 + - - +
157A VAL 4.5 1.4 - - - +
158A ARG 4.4 1.9 - - - +
159A ASP* 1.3 79.5 - - - +
161A ARG* 1.3 66.1 + - - +
162A LEU* 3.6 1.6 + - - +
167A ASP* 3.5 17.9 - - - +
201A HIS* 5.9 0.9 - - - +
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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