Contacts of the helix formed by residues 159 - 169 (chain B) in PDB entry 4LXZ
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 ASN 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B TYR* 4.8 1.6 - - + -
73B HIS* 2.9 18.7 + - + +
144B LEU 3.7 7.8 + - - +
145B HIS 3.3 24.9 + - - -
147B ALA* 2.8 33.0 + - + +
158B VAL* 1.3 69.4 - - - +
160B ASP* 1.4 63.2 + - - +
161B ILE* 3.2 16.6 + - - +
162B VAL* 3.0 45.3 + - + +
163B LEU* 3.2 26.9 + - - +
187B GLY 3.8 5.3 - - - -
188B VAL* 3.9 1.1 - - - +
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B SER* 4.0 3.1 - - - +
119B THR* 3.6 39.0 - - - +
122B SER* 2.7 31.0 + - - +
123B VAL* 4.9 0.5 - - - +
142B GLY* 3.7 6.5 - - - -
143B GLY 2.8 20.9 + - - -
144B LEU* 2.9 34.0 + - - +
158B VAL 3.0 6.5 + - - +
159B ASN* 1.4 69.9 - - - +
161B ILE* 1.4 62.1 + - - +
163B LEU* 3.6 2.2 + - - +
164B ALA* 3.0 28.6 + - - +
303B LEU* 3.9 1.7 - - - +
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY* 3.5 41.5 - - - -
144B LEU 4.0 0.9 - - - +
145B HIS* 3.6 17.9 - - + -
159B ASN* 3.1 7.6 - - - +
160B ASP* 1.4 75.4 - - - +
162B VAL* 1.3 67.0 + - - +
164B ALA* 3.2 2.9 + - - +
165B ILE* 2.9 38.4 + - + +
177B TYR* 3.4 45.3 - - + +
188B VAL* 3.8 6.3 - - + -
263B VAL* 4.1 10.5 - - + -
265B GLN* 3.8 5.2 - - + -
303B LEU* 3.8 11.0 - - + -
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.5 40.8 - - + -
159B ASN* 3.0 39.8 + - + +
161B ILE* 1.3 74.5 - - - +
163B LEU* 1.3 56.8 + - - +
165B ILE* 3.2 3.3 + - - +
166B LEU* 2.9 32.3 + - + +
187B GLY 3.9 1.8 - - - +
188B VAL* 3.9 15.7 - - + -
191B ALA* 3.7 27.6 - - + -
192B PHE* 3.9 17.4 - - + -
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLU 3.3 23.6 - - - +
69B MET* 3.6 22.4 - - - +
71B LYS* 4.0 7.4 - - + -
72B TYR* 3.7 24.7 - - + +
73B HIS* 4.4 2.7 - - + -
119B THR* 3.6 25.8 - - + -
123B VAL* 3.9 18.8 - - + +
158B VAL* 3.7 18.2 - - + -
159B ASN 3.2 16.6 + - - +
160B ASP 3.9 2.7 - - - +
161B ILE 3.2 0.4 - - - -
162B VAL* 1.3 76.4 - - - +
164B ALA* 1.3 62.1 + - - +
166B LEU* 3.4 6.2 + - + +
167B GLU* 3.1 21.3 + - - +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B SER* 3.7 15.5 - - - +
123B VAL* 4.3 3.7 - - - +
126B ALA* 3.5 8.8 - - + +
160B ASP 3.0 19.3 + - - +
161B ILE* 3.2 7.2 + - - +
163B LEU* 1.3 76.1 - - - +
165B ILE* 1.3 59.0 + - + +
167B GLU* 3.3 6.3 + - - +
168B LEU* 3.0 32.5 + - - +
301B LEU* 3.5 31.4 - - + -
303B LEU* 5.2 0.2 - - + -
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ILE* 2.9 37.9 + - + +
162B VAL 3.7 3.1 - - - +
164B ALA* 1.3 71.5 - - - +
166B LEU* 1.3 60.3 - - - +
168B LEU* 3.1 8.2 + - - +
169B LEU* 2.8 29.7 + - + +
175B VAL* 4.1 12.1 - - + -
177B TYR* 4.1 19.5 - - + -
188B VAL* 3.8 20.2 - - + -
192B PHE* 3.5 14.6 - - + -
198B VAL* 3.5 34.3 - - + -
263B VAL* 3.8 22.2 - - + -
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS* 3.6 34.3 - - + +
72B TYR* 3.9 21.5 - - + -
162B VAL* 2.9 25.9 + - + +
163B LEU* 3.7 6.5 - - - +
164B ALA 3.4 0.2 - - - -
165B ILE* 1.3 75.7 - - - +
167B GLU* 1.4 61.2 + - - +
169B LEU* 3.3 21.8 + - + +
170B LYS* 3.5 15.3 + - - +
192B PHE* 4.0 22.2 - - + -
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 4.3 12.2 - - + +
126B ALA* 3.6 20.4 - - + -
127B VAL* 3.5 31.7 - - + +
130B ASN* 2.8 38.3 + - - +
163B LEU 3.1 12.9 + - - +
164B ALA* 3.4 10.1 - - - +
165B ILE 3.2 0.2 - - - -
166B LEU* 1.4 72.4 - - - +
168B LEU* 1.3 63.4 + - - +
170B LYS* 2.9 54.5 + - - +
171B TYR* 4.7 2.9 - - - -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA* 3.7 25.8 - - + +
129B LEU* 4.2 16.8 - - + -
130B ASN* 3.5 17.4 - - - +
164B ALA 3.0 18.3 + - - +
165B ILE* 3.1 7.4 + - - +
167B GLU* 1.3 75.0 - - - +
169B LEU* 1.4 58.1 + - - +
171B TYR 3.1 5.5 + - - -
172B HIS* 2.8 41.6 + - + +
175B VAL* 3.9 21.1 - - + -
261B ALA* 4.4 12.3 - - + -
262B VAL 5.0 2.7 - - - +
263B VAL* 3.5 32.1 - - + -
301B LEU* 5.0 6.3 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ILE* 2.8 23.9 + - + +
166B LEU* 3.6 18.2 - - + +
167B GLU 3.2 0.2 - - - -
168B LEU* 1.4 67.8 - - - +
170B LYS* 1.3 65.2 + - - +
171B TYR 3.3 0.4 + - - -
172B HIS 3.6 10.1 + - - +
173B GLN 4.3 0.2 - - - +
175B VAL* 3.7 12.3 - - + -
192B PHE* 4.0 17.5 - - + -
195B THR* 6.1 0.4 - - + -
197B ARG* 2.8 78.0 + - + +
198B VAL* 3.7 20.0 - - + -
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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