Contacts of the helix formed by residues 141 - 151 (chain A) in PDB entry 2XZF
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PRO* 5.1 1.8 - - - +
137A TYR 5.6 0.7 - - - -
138A GLU 6.0 0.2 - - - -
139A ASP 3.2 8.5 + - - +
140A PHE* 1.3 72.3 - - - +
142A GLU* 1.3 65.1 + - - +
143A LYS* 3.0 32.1 + - - +
144A LEU* 3.0 29.7 + - + +
145A PHE* 3.2 19.1 + - - +
201A HIS* 4.4 0.4 - - - -
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Residues in contact with GLU 142 (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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140A PHE 3.4 5.1 + - - -
141A ASP* 1.3 73.9 + - - +
143A LYS* 1.3 61.7 + - + +
145A PHE* 3.4 3.6 - - + +
146A ARG* 2.8 47.5 + - - +
194A GLU* 4.6 2.6 - - - +
197A ILE* 4.6 8.2 - - + +
198A HIS* 2.7 55.5 + - - +
201A HIS* 3.4 39.7 + - + +
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Residues in contact with LYS 143 (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 ASP* 3.0 19.1 + - - +
142A GLU* 1.3 79.5 - - + +
144A LEU* 1.3 63.1 + - - +
146A ARG* 3.3 31.7 + - - +
147A GLU* 3.0 28.0 + - + +
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Residues in contact with LEU 144 (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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133A PRO* 6.4 2.5 - - + -
141A ASP* 3.0 25.1 + - + +
143A LYS* 1.3 73.1 - - - +
145A PHE* 1.3 65.8 + - - +
147A GLU* 3.2 10.6 + - + -
148A LYS* 2.9 56.7 + - + +
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Residues in contact with PHE 145 (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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140A PHE* 3.6 39.5 - + + -
141A ASP 3.2 13.3 + - - +
142A GLU* 3.4 8.5 - - - +
144A LEU* 1.3 77.9 - - - +
146A ARG* 1.3 64.6 + - - +
148A LYS* 3.2 6.1 + - - +
149A LEU* 3.0 47.2 + - + +
160A LEU* 4.2 6.1 - - + -
165A LEU* 3.9 38.6 - - + -
197A ILE* 3.8 32.1 - - + -
200A LEU* 3.8 18.8 - - + -
201A HIS* 4.1 17.7 - - + -
204A ILE* 4.1 7.6 - - + -
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Residues in contact with ARG 146 (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 GLU* 2.8 44.3 + - - +
143A LYS* 3.5 31.5 + - - +
145A PHE* 1.3 77.8 - - - +
147A GLU* 1.3 72.9 + - - +
149A LEU* 3.4 2.6 + - - +
150A ARG* 3.0 24.6 + - + +
194A GLU* 4.0 40.8 + - - +
197A ILE* 4.0 34.9 - - + +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LYS 3.0 17.4 + - - +
144A LEU* 3.2 16.8 + - + +
146A ARG* 1.3 87.4 + - + +
148A LYS* 1.3 62.8 + - - +
150A ARG* 3.3 22.0 + - - +
151A LYS* 3.4 33.7 + - - +
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Residues in contact with LYS 148 (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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144A LEU* 2.9 51.4 + - + +
145A PHE* 3.7 2.0 - - - +
147A GLU* 1.3 76.3 - - + +
149A LEU* 1.3 63.4 + - - +
151A LYS* 3.4 22.5 + - + +
152A SER* 3.6 12.8 + - - -
159A TYR* 4.1 14.2 + - - +
164A THR* 4.3 15.9 + - - -
165A LEU* 3.7 30.7 - - + -
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Residues in contact with LEU 149 (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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145A PHE* 3.0 50.5 + - + +
146A ARG 3.8 4.3 - - - +
148A LYS* 1.3 75.9 - - - +
150A ARG* 1.3 62.4 + - - +
151A LYS 3.3 0.9 + - - -
152A SER 3.4 2.3 + - - -
156A ILE* 3.8 12.8 - - + -
159A TYR* 4.4 2.0 - - + -
165A LEU* 3.9 21.8 - - + -
189A THR* 2.8 65.2 + - + +
190A ASN 3.3 1.2 + - - -
192A LEU* 4.3 7.9 - - + -
197A ILE* 3.9 28.5 - - + -
200A LEU* 4.7 2.2 - - + -
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Residues in contact with ARG 150 (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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146A ARG* 3.0 19.6 + - + +
147A GLU* 3.6 19.5 - - - +
148A LYS 3.3 0.2 - - - -
149A LEU* 1.3 77.8 - - - +
151A LYS* 1.3 59.6 + - + +
152A SER 3.4 0.2 - - - -
189A THR 4.9 0.2 - - - -
190A ASN* 3.2 26.0 + - - +
197A ILE* 5.5 2.2 - - + +
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Residues in contact with LYS 151 (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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147A GLU* 3.4 32.1 + - - +
148A LYS* 3.6 14.8 - - + +
149A LEU 3.2 0.4 - - - -
150A ARG* 1.3 80.0 - - + +
152A SER* 1.3 59.1 + - - +
153A THR* 5.7 0.9 - - - +
190A ASN* 5.0 1.8 - - - -
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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