Contacts of the helix formed by residues 213 - 219 (chain B) in PDB entry 1U54
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 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLY 3.3 4.0 + - - -
212B SER* 1.3 71.2 - - - +
214B LEU* 1.3 57.5 + - - +
216B ARG* 3.1 8.1 + - - +
217B LEU* 3.1 43.2 + - + +
224B PHE* 5.1 1.6 - - + -
232B TYR* 3.9 25.6 - - + -
255B ALA* 4.9 4.0 - - + -
258B LEU* 3.0 52.2 + - + +
259B LEU* 4.5 2.2 - - - +
260B LEU* 3.8 31.6 - - + +
266B VAL* 4.3 9.9 - - + -
323B MET* 4.3 19.5 - - + -
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Residues in contact with LEU 214 (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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212B SER* 3.0 4.4 + - - +
213B LEU* 1.3 75.5 - - - +
215B ASP* 1.3 70.9 + - - +
216B ARG 3.0 2.1 + - - -
217B LEU* 3.3 8.0 + - + +
218B ARG* 3.0 50.6 + - + +
255B ALA* 3.6 25.1 + - + +
256B ARG* 4.1 23.8 - - + +
296B TRP* 6.3 0.7 - - + -
322B GLU* 3.7 22.2 - - + +
327B GLY* 3.5 34.8 - - - +
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Residues in contact with ASP 215 (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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212B SER* 3.0 32.2 + - - +
214B LEU* 1.3 80.3 - - - +
216B ARG* 1.3 54.8 + - - +
218B ARG* 3.6 14.6 + - - +
219B LYS* 3.1 51.0 + - - +
400B ACP 5.4 2.1 + - - -
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Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.4 37.3 - - + +
212B SER 3.5 4.4 + - - +
213B LEU* 3.1 14.0 + - - +
214B LEU 3.0 1.4 - - - -
215B ASP* 1.3 76.4 - - - +
217B LEU* 1.3 66.6 + - - +
218B ARG 3.1 1.1 - - - -
219B LYS* 3.1 23.9 + - + +
220B HIS 3.2 14.7 + - - +
223B HIS* 3.8 24.9 + - - -
224B PHE* 3.4 24.2 - - + -
232B TYR* 4.6 1.0 + - - -
260B LEU* 2.7 46.2 - - + +
263B ARG* 4.2 23.8 - - - +
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Residues in contact with LEU 217 (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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213B LEU* 3.1 35.7 + - + +
214B LEU* 3.9 11.7 - - + +
216B ARG* 1.3 74.3 - - - +
218B ARG* 1.3 53.2 + - - +
219B LYS 2.9 9.9 - - - +
220B HIS 3.8 0.3 - - - +
221B GLN* 2.6 33.2 + - - +
224B PHE* 3.4 37.2 - - + -
229B LEU* 4.2 16.8 - - + -
255B ALA* 5.3 2.7 - - + -
322B GLU 3.9 7.6 - - - +
323B MET* 3.7 33.2 - - + +
326B TYR* 3.8 17.9 - - + -
327B GLY* 4.1 4.0 - - - +
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Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.0 45.6 + - + +
215B ASP* 3.6 13.9 + - - +
217B LEU* 1.3 72.6 - - - +
219B LYS* 1.3 65.9 + - + +
221B GLN* 3.8 13.8 + - - +
326B TYR 4.2 0.9 - - - -
327B GLY* 2.8 31.8 + - - +
329B GLU* 5.8 8.1 - - - +
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Residues in contact with LYS 219 (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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215B ASP* 3.1 39.4 + - - +
216B ARG* 3.1 16.3 + - + +
217B LEU 2.9 4.2 - - - +
218B ARG* 1.3 83.3 - - + +
220B HIS* 1.3 80.8 + - + +
221B GLN* 2.9 8.5 + - - +
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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