Contacts of the helix formed by residues 149 - 158 (chain B) in PDB entry 2L1R
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 SER 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A CYS* 4.4 11.3 + - - -
86A LYS* 5.5 2.6 + - - -
91A SXK 6.3 0.2 - - - -
147B ARG* 6.4 0.2 - - - -
148B ILE* 1.3 77.4 - - - +
150B ALA* 1.3 61.4 + - - +
151B ASP* 3.5 12.3 + - - +
152B ALA* 3.5 22.6 + - - +
153B MET* 2.8 30.5 + - - +
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Residues in contact with ALA 150 (chain B).
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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20A PHE* 5.7 0.2 - - + -
81A MET* 3.7 49.8 - - + +
84A CYS* 4.4 8.3 + - - +
85A MET* 4.2 23.3 - - + -
149B SER* 1.3 75.6 + - - +
151B ASP* 1.3 62.7 + - - +
153B MET* 4.0 1.4 - - - +
154B MET* 3.0 28.8 + - - +
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Residues in contact with ASP 151 (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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149B SER* 3.5 5.9 + - - +
150B ALA* 1.3 79.8 - - - +
152B ALA* 1.3 59.7 + - - +
154B MET* 3.6 6.3 - - - +
155B GLN* 2.8 54.7 + - - +
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Residues in contact with ALA 152 (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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48A LEU* 5.8 6.7 - - + +
148B ILE* 5.4 1.1 - - + -
149B SER* 3.5 29.8 + - - +
151B ASP* 1.3 81.6 + - - +
153B MET* 1.3 63.3 + - - +
155B GLN* 3.3 6.5 + - - +
156B ALA* 3.1 23.0 + - - +
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Residues in contact with MET 153 (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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27A PHE* 3.6 34.3 - - + -
41A LEU* 3.8 20.2 - - + -
44A VAL* 3.6 23.3 - - + +
45A MET* 4.8 2.9 - - + +
48A LEU* 5.4 9.0 - - - -
81A MET* 4.8 7.0 - - + -
91A SXK 3.7 22.2 - - + -
148B ILE* 3.3 35.2 - - + +
149B SER 2.8 22.1 + - - +
150B ALA 4.0 2.0 - - - +
152B ALA* 1.3 73.5 - - - +
154B MET* 1.3 57.6 + - - +
156B ALA* 3.3 5.7 + - - +
157B LEU* 2.8 30.6 + - - +
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Residues in contact with MET 154 (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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19A GLU* 3.4 39.5 - - - +
20A PHE* 5.5 9.4 - - + -
23A ALA* 4.3 26.0 - - + -
27A PHE* 6.2 0.2 - - - -
81A MET* 4.9 13.7 - - + +
150B ALA 3.0 20.9 + - - +
151B ASP* 3.6 8.1 - - - +
153B MET* 1.3 78.4 - - - +
155B GLN* 1.3 62.3 + - - +
157B LEU* 3.1 15.9 + - - +
158B LEU* 3.1 32.3 + - + +
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Residues in contact with GLN 155 (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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151B ASP* 2.8 42.4 + - - +
152B ALA* 3.5 7.4 - - - +
154B MET* 1.3 73.0 - - - +
156B ALA* 1.3 59.4 + - - +
158B LEU 5.3 0.4 - - - -
159B GLY* 3.1 30.9 + - - -
160B ALA 3.4 1.2 + - - -
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Residues in contact with ALA 156 (chain B).
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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44A VAL* 5.2 10.3 - - + -
47A MET* 3.6 21.5 - - + +
48A LEU* 5.1 14.6 - - + +
152B ALA 3.1 16.2 + - - +
153B MET* 3.7 6.7 - - - +
155B GLN* 1.3 76.0 - - - +
157B LEU* 1.3 66.4 + - - +
160B ALA* 3.5 31.9 + - + +
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Residues in contact with LEU 157 (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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23A ALA* 4.6 8.7 - - + +
26A ILE* 3.2 51.2 - - + +
27A PHE* 3.3 37.7 - - + -
44A VAL* 3.6 26.2 - - + -
47A MET* 5.1 4.1 - - + +
153B MET 2.8 16.4 + - - +
154B MET* 3.1 11.6 + - + +
156B ALA* 1.3 77.9 - - - +
158B LEU* 1.3 65.4 + - + +
162B ALA* 3.0 18.4 - - - +
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Residues in contact with LEU 158 (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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19A GLU* 5.8 1.6 - - - +
22A ALA* 4.8 3.8 - - + +
23A ALA* 4.8 8.3 - - - -
26A ILE* 3.8 32.5 - - + -
154B MET* 3.1 29.6 + - + +
155B GLN* 3.8 2.9 - - - -
157B LEU* 1.3 88.4 - - + +
159B GLY* 1.3 56.0 + - - +
162B ALA* 3.9 5.6 - - + -
163B LYS* 3.5 39.8 + - + +
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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