Contacts of the helix formed by residues 159 - 169 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A TYR* 4.3 3.1 - - + -
73A HIS* 2.9 18.9 + - + +
144A LEU 3.8 6.2 - - - +
145A HIS 3.2 25.7 + - - -
147A ALA* 2.8 33.5 + - + +
158A VAL* 1.3 68.3 - - - +
160A ASP* 1.4 61.5 + - - +
161A ILE* 3.2 16.3 + - - +
162A VAL* 3.0 37.9 + - + +
163A LEU* 3.3 25.2 + - - +
187A GLY 3.8 5.1 - - - -
188A VAL* 3.9 1.3 - - - +
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Residues in contact with ASP 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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118A SER* 3.9 3.7 + - - +
119A THR* 3.7 33.0 - - - +
122A SER* 2.6 30.0 + - - +
123A VAL* 4.8 0.3 - - - +
142A GLY* 3.6 7.1 - - - -
143A GLY 2.8 20.9 + - - -
144A LEU* 2.9 33.8 + - - +
158A VAL 3.0 6.2 + - - +
159A ASN* 1.4 71.0 - - - +
161A ILE* 1.3 58.7 + - - +
163A LEU* 3.8 7.0 - - - +
164A ALA* 2.9 29.5 + - - +
303A LEU* 3.8 4.0 - - - +
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Residues in contact with ILE 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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143A GLY* 3.5 35.2 - - - +
144A LEU 4.0 1.1 - - - +
145A HIS* 3.5 25.1 - - + -
159A ASN* 3.1 7.3 - - - +
160A ASP* 1.3 75.8 - - - +
162A VAL* 1.3 60.5 + - - +
164A ALA* 3.2 3.2 + - - +
165A ILE* 2.8 37.6 + - + +
177A TYR* 3.3 50.7 - - + +
188A VAL* 3.8 6.5 - - + -
263A VAL* 3.9 11.4 - - + -
265A GLN* 3.8 4.7 - - + -
303A LEU* 3.8 10.8 - - + -
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Residues in contact with VAL 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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72A TYR* 3.6 40.2 - - + -
159A ASN* 3.0 37.7 + - + +
161A ILE* 1.3 74.4 - - - +
163A LEU* 1.3 57.7 + - - +
165A ILE* 3.2 3.2 + - - +
166A LEU* 2.9 33.2 + - + +
187A GLY 4.1 0.9 - - - +
188A VAL* 3.9 16.6 - - + -
191A ALA* 3.7 20.6 - - + -
192A PHE* 3.8 26.0 - - + -
404A PG4 5.3 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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68A GLU 3.4 22.4 - - - +
69A MET* 3.7 24.9 - - - +
71A LYS* 4.0 7.6 - - + -
72A TYR* 3.7 24.5 - - + +
73A HIS* 4.4 1.8 - - + -
119A THR* 3.6 25.1 - - + -
123A VAL* 3.8 17.9 - - + +
158A VAL* 3.8 18.6 - - + -
159A ASN 3.3 15.4 + - - +
160A ASP* 3.8 6.7 - - - +
161A ILE 3.2 0.4 - - - -
162A VAL* 1.3 75.1 - - - +
164A ALA* 1.3 63.8 + - - +
166A LEU* 3.3 7.3 + - + +
167A GLU* 3.1 22.3 + - - +
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Residues in contact with ALA 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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122A SER* 3.6 17.3 - - - +
123A VAL* 4.1 4.9 - - - +
126A ALA* 3.5 7.6 - - + +
160A ASP 2.9 18.6 + - - +
161A ILE* 3.2 6.5 + - - +
163A LEU* 1.3 76.8 - - - +
165A ILE* 1.4 57.9 + - + +
167A GLU* 3.2 6.4 + - - +
168A LEU* 3.0 31.5 + - - +
263A VAL* 5.5 0.2 - - + -
301A LEU* 3.6 30.1 - - + -
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Residues in contact with ILE 165 (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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161A ILE* 2.8 28.1 + - + +
162A VAL 3.8 3.6 - - - +
164A ALA* 1.4 72.2 - - - +
166A LEU* 1.3 59.7 + - - +
168A LEU* 3.1 7.2 + - - +
169A LEU* 2.8 30.8 + - + +
175A VAL* 3.9 13.7 - - + -
177A TYR* 4.0 19.3 - - + -
188A VAL* 3.8 29.4 - - + -
192A PHE* 3.7 14.6 - - + -
198A VAL* 3.5 34.3 - - + -
263A VAL* 3.8 21.5 - - + -
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Residues in contact with LEU 166 (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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71A LYS* 3.5 40.2 - - + +
72A TYR* 4.0 13.9 - - + -
162A VAL* 2.9 24.3 + - + +
163A LEU* 3.3 7.4 + - - +
165A ILE* 1.3 75.4 - - - +
167A GLU* 1.3 62.2 + - - +
169A LEU* 3.4 14.6 + - + +
170A LYS* 3.7 14.3 + - - +
192A PHE* 3.9 19.5 - - + -
404A PG4 3.7 46.1 + - - +
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Residues in contact with GLU 167 (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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123A VAL* 4.1 16.4 - - + +
126A ALA* 3.7 15.5 - - + -
127A VAL* 3.7 32.3 - - + +
130A ASN* 2.9 23.0 + - - +
163A LEU 3.1 13.5 + - - +
164A ALA* 3.3 11.0 - - - +
165A ILE 3.1 0.2 - - - -
166A LEU* 1.3 73.6 - - - +
168A LEU* 1.3 63.5 + - - +
170A LYS* 2.9 56.0 + - - +
171A TYR* 5.7 0.7 - - - -
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Residues in contact with LEU 168 (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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126A ALA* 3.9 24.7 - - + +
129A LEU* 4.3 16.2 - - + -
130A ASN* 3.6 17.4 - - - +
164A ALA 3.0 17.9 + - - +
165A ILE* 3.1 8.0 + - - +
167A GLU* 1.3 76.4 - - - +
169A LEU* 1.3 56.4 + - - +
171A TYR 3.0 7.3 + - - -
172A HIS* 2.9 40.2 + - + -
175A VAL* 3.9 22.4 - - + -
261A ALA* 4.3 13.7 - - + -
262A VAL 4.9 2.2 - - - +
263A VAL* 3.5 32.3 - - + -
301A LEU* 5.1 5.2 - - + -
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Residues in contact with LEU 169 (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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165A ILE* 2.8 28.0 + - + +
166A LEU* 3.7 13.5 - - + +
167A GLU 3.3 0.6 - - - -
168A LEU* 1.3 71.3 - - - +
170A LYS* 1.4 60.3 + - - +
171A TYR 3.2 0.8 + - - -
172A HIS 3.5 12.1 + - - +
173A GLN 4.1 0.2 - - - +
175A VAL* 3.9 9.6 - - + -
192A PHE* 4.0 8.5 - - + -
197A ARG* 2.8 76.1 + - + +
198A VAL* 3.7 18.6 - - + -
404A PG4 3.7 30.7 - - - +
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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