Contacts of the helix formed by residues 186 - 195 (chain B) in PDB entry 4L5L
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 LEU 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B TYR* 3.9 26.5 - - + -
142B TYR* 3.9 16.8 - - - +
148B PRO* 4.0 14.8 - - + -
153B PHE* 4.3 9.2 - - + -
182B ARG* 3.2 14.2 + - + +
183B ILE* 3.3 24.6 + - + +
185B ALA* 1.3 73.1 - - - +
187B PRO* 1.3 75.4 - - + +
188B ASN 3.3 0.9 - - - -
189B ILE* 2.8 27.3 + - + +
190B LYS 2.8 12.0 + - - -
303B MES 3.9 21.3 - - - +
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Residues in contact with PRO 187 (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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185B ALA 3.4 9.4 - - - +
186B LEU* 1.3 83.7 - - + +
188B ASN* 1.3 63.6 + - - +
190B LYS* 3.7 5.1 - - + +
191B ALA* 2.9 26.6 + - - +
303B MES 3.4 26.0 - - - +
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Residues in contact with ASN 188 (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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22B GLU* 3.2 32.0 + - - +
23B TYR* 3.3 17.2 + - - -
25B GLY* 4.0 12.3 - - - +
187B PRO* 1.3 75.7 - - - +
189B ILE* 1.3 57.6 + - - +
191B ALA* 3.8 5.8 - - - +
192B PHE* 3.0 27.4 + - - +
303B MES 2.8 39.5 + - - +
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Residues in contact with ILE 189 (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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19B LEU* 3.2 45.8 - - + +
22B GLU* 4.5 2.9 - - + -
23B TYR* 3.9 14.4 - - + +
153B PHE* 3.8 21.3 - - + -
156B TYR* 6.0 0.7 - - + -
183B ILE* 3.3 22.9 - - + +
186B LEU* 2.8 25.5 + - + +
188B ASN* 1.3 76.5 - - - +
190B LYS* 1.3 52.7 + - - +
192B PHE* 3.2 3.8 + - + +
193B MET* 2.8 66.7 + - + +
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Residues in contact with LYS 190 (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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184B GLU 3.6 20.5 + - - +
185B ALA* 4.2 14.1 - - - +
186B LEU 2.8 9.6 + - - +
187B PRO* 3.7 8.7 - - + +
189B ILE* 1.3 72.8 - - - +
191B ALA* 1.3 67.7 + - - +
193B MET* 3.0 7.7 + - + +
194B GLU* 2.9 57.2 + - + +
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Residues in contact with ALA 191 (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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187B PRO 2.9 17.0 + - - +
188B ASN* 3.8 7.4 - - - +
190B LYS* 1.3 75.5 - - - +
192B PHE* 1.3 63.2 + - - +
194B GLU* 3.2 13.7 + - - +
195B SER* 3.1 22.0 + - - -
197B ARG* 5.6 0.9 - - - -
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Residues in contact with PHE 192 (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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15B GLN* 5.2 2.9 - - - -
18B ARG* 4.2 26.0 - - + -
19B LEU* 3.9 27.1 - - + -
22B GLU* 3.3 51.4 - - + +
28B TYR* 4.5 2.5 - - - -
30B GLU* 5.4 1.8 - - - -
188B ASN 3.0 20.6 + - - +
189B ILE* 3.5 7.2 - - + +
190B LYS 3.2 0.2 - - - -
191B ALA* 1.3 75.2 - - - +
193B MET* 1.3 58.4 + - - +
195B SER* 2.7 31.3 + - - -
197B ARG* 3.7 30.9 - - + +
198B PHE* 3.4 39.2 - + - +
199B ILE 5.1 1.6 - - - -
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Residues in contact with MET 193 (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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19B LEU* 5.2 1.6 - - + -
156B TYR* 3.9 20.0 - - + +
184B GLU* 3.4 42.4 - - + +
189B ILE* 2.8 47.8 + - + +
190B LYS* 3.7 5.4 - - + +
192B PHE* 1.3 75.7 - - + +
194B GLU* 1.3 61.5 + - + +
195B SER 3.4 1.6 - - - +
198B PHE* 3.6 50.8 - - + +
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Residues in contact with GLU 194 (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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190B LYS* 2.9 55.0 + - + +
191B ALA* 3.6 10.7 - - - +
193B MET* 1.3 76.0 - - + +
195B SER* 1.3 64.1 + - - +
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Residues in contact with SER 195 (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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191B ALA 3.1 8.7 + - - -
192B PHE* 2.7 21.8 + - - -
193B MET 4.1 1.4 - - - +
194B GLU* 1.3 83.1 - - - +
196B ASP* 1.3 62.6 + - - +
197B ARG* 3.1 48.1 + - - +
198B PHE* 3.6 14.6 + - - +
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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