Contacts of the helix formed by residues 222 - 227 (chain B) in PDB entry 1L9X
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 GLU 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER* 3.7 34.2 + - - +
36B TYR* 3.1 36.5 + - + -
39B TYR* 3.8 26.4 - - + -
109B THR* 3.7 3.8 + - - +
220B HIS* 2.8 32.5 + - - +
221B PRO* 1.3 92.0 - - - +
223B LYS* 1.3 68.9 + - - +
224B ALA 3.3 0.2 - - - -
225B PRO* 3.7 3.1 - - - -
226B TYR* 3.3 26.8 + - - +
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 5.3 0.8 + - - -
36B TYR* 5.3 0.6 + - - -
168B ALA* 4.4 4.5 - - + -
170B PHE* 4.1 30.3 - - + -
220B HIS* 3.3 51.5 + - + +
221B PRO 3.2 1.4 + - - -
222B GLU* 1.3 84.4 + - + +
224B ALA* 1.3 65.7 + - - +
227B GLU* 3.0 41.5 + - + +
234B ILE* 3.7 22.1 - - + +
236B HIS* 3.5 9.4 - - - -
286B SER* 5.1 7.3 + - - -
287B PHE* 3.7 30.9 - - - -
1002B BME 5.6 1.3 + - - -
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Residues in contact with ALA 224 (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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166B LEU 5.3 2.9 - - - +
168B ALA* 5.8 0.8 - - - +
220B HIS 4.4 2.3 + - - +
221B PRO* 3.3 8.3 + - + +
223B LYS* 1.3 77.9 - - - +
225B PRO* 1.3 65.7 - - + +
228B TRP* 4.7 1.2 - - - -
234B ILE* 4.5 0.6 - - - +
235B SER 3.3 23.0 - - - +
236B HIS* 2.7 23.3 + - - +
240B ALA* 3.4 34.5 - - + +
241B VAL* 3.6 11.3 - - + +
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Residues in contact with PRO 225 (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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41A GLU* 3.3 17.6 - - - +
42A SER 3.7 20.9 - - - +
44A GLY* 3.7 2.9 - - - -
45A ALA 4.6 1.2 + - - +
221B PRO 3.6 7.9 - - - +
222B GLU 3.4 10.8 - - - +
224B ALA* 1.3 93.7 - - + +
226B TYR* 1.3 84.0 + - + +
227B GLU 4.1 0.2 - - - -
228B TRP* 3.6 21.0 + - - -
241B VAL* 4.0 18.8 - - + +
244B ALA* 3.7 20.2 - - + -
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Residues in contact with TYR 226 (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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38A LYS 5.2 0.9 - - - -
41A GLU* 3.4 35.2 - - + -
42A SER* 3.3 17.0 + - - -
226A TYR* 4.9 0.2 + - - -
274A TYR* 4.0 4.2 + - - -
35B SER* 3.8 25.6 - - - -
38B LYS* 3.4 39.2 + - + +
39B TYR* 3.6 24.5 - + + -
42B SER* 3.4 23.8 + - - -
222B GLU 3.3 22.4 + - - +
223B LYS 3.5 0.8 + - - -
225B PRO* 1.3 102.0 - - + +
227B GLU* 1.3 66.3 + - - +
228B TRP* 3.4 17.3 - - - +
288B GLN* 3.8 7.8 - - - +
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Residues in contact with GLU 227 (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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33B ALA* 4.6 0.5 - - - +
35B SER* 2.6 40.6 + - - +
223B LYS* 3.0 38.9 + - + +
225B PRO 4.1 0.2 - - - -
226B TYR* 1.3 77.9 - - - +
228B TRP* 1.3 61.8 + - - +
229B LYS 3.5 1.3 - - - -
234B ILE* 3.7 16.2 - - + +
236B HIS* 2.8 25.2 + - - -
286B SER 3.8 6.8 - - - +
287B PHE* 3.4 24.3 - - - +
288B GLN* 2.9 31.7 + - - +
289B GLN 4.9 1.7 + - - +
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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