Contacts of the helix formed by residues 222 - 227 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER* 3.7 38.0 + - - +
36A TYR* 3.1 35.3 + - + -
39A TYR* 3.8 27.1 - - + -
109A THR* 3.8 3.8 + - - +
220A HIS* 2.7 32.7 + - - +
221A PRO* 1.3 96.0 - - - +
223A LYS* 1.3 68.7 + - - +
224A ALA 3.3 0.2 - - - -
225A PRO* 3.5 3.3 - - - +
226A TYR* 3.3 23.4 + - - -
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Residues in contact with LYS 223 (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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35A SER* 5.4 0.4 + - - -
36A TYR* 5.4 0.2 + - - -
168A ALA* 4.3 4.3 - - + -
170A PHE* 4.1 30.3 - - + -
220A HIS* 3.3 51.7 + - + +
221A PRO 3.2 1.2 + - - -
222A GLU* 1.3 84.8 + - + +
224A ALA* 1.3 66.5 + - - +
227A GLU* 3.0 41.7 + - + +
234A ILE* 4.0 20.6 - - + +
236A HIS* 3.5 9.5 - - - -
286A SER* 5.1 7.3 + - - -
287A PHE* 3.7 30.1 - - - -
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Residues in contact with ALA 224 (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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166A LEU 5.2 2.5 - - - +
168A ALA* 5.7 1.0 - - - +
220A HIS 4.3 2.1 + - - +
221A PRO* 3.3 8.5 + - + +
223A LYS* 1.3 78.3 - - - +
225A PRO* 1.3 66.9 - - + +
228A TRP* 4.7 1.6 - - - -
234A ILE* 4.5 0.4 - - - +
235A SER 3.3 24.0 - - - +
236A HIS* 2.7 24.2 + - - -
240A ALA* 3.5 34.1 - - + +
241A VAL* 3.6 11.5 - - + +
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Residues in contact with PRO 225 (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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221A PRO 3.5 7.4 - - - +
222A GLU* 3.5 11.2 - - - +
224A ALA* 1.3 95.7 - - + +
226A TYR* 1.3 83.8 + - + +
227A GLU 4.0 0.2 - - - -
228A TRP* 3.6 20.9 + - - -
241A VAL* 4.0 16.4 - - + +
244A ALA* 3.6 20.2 - - + -
41B GLU* 3.3 15.6 - - - +
42B SER 3.7 19.7 - - - +
44B GLY* 3.7 7.5 - - - -
45B ALA 4.5 1.0 + - - +
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Residues in contact with TYR 226 (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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35A SER* 3.8 23.6 - - - -
38A LYS* 3.4 51.9 + - + +
39A TYR* 3.6 23.8 - + + -
42A SER* 3.4 14.3 + - - -
222A GLU 3.3 22.0 - - - +
223A LYS 3.5 0.6 + - - -
225A PRO* 1.3 104.1 - - + +
227A GLU* 1.3 67.3 + - - +
228A TRP* 3.4 17.2 + - - +
288A GLN* 3.8 7.8 - - - +
38B LYS 5.2 1.1 - - - -
41B GLU* 3.4 33.9 - - + -
42B SER* 3.4 16.9 + - - -
226B TYR* 4.9 0.2 + - - -
274B TYR* 4.0 4.2 + - - -
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Residues in contact with GLU 227 (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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33A ALA* 4.6 0.2 - - - +
35A SER* 2.7 39.8 + - - +
223A LYS* 3.0 40.8 + - + +
225A PRO 4.0 0.4 - - - -
226A TYR* 1.3 77.8 - - - +
228A TRP* 1.3 63.1 + - - +
229A LYS 3.5 1.8 - - - -
234A ILE* 3.7 15.7 - - + +
236A HIS* 2.8 24.3 + - - -
286A SER 3.9 6.0 - - - +
287A PHE* 3.5 26.1 - - - +
288A GLN* 3.0 30.5 + - - +
289A GLN 4.9 2.1 + - - +
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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