Contacts of the helix formed by residues 222 - 227 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D SER* 3.7 36.1 + - - +
36D TYR* 3.2 36.1 + - + -
39D TYR* 3.8 25.9 - - + -
109D THR* 3.8 3.5 + - - +
220D HIS* 2.8 31.7 + - - +
221D PRO* 1.3 88.9 - - - +
223D LYS* 1.3 68.1 + - + +
224D ALA 3.3 0.4 - - - -
225D PRO* 3.4 3.1 - - - +
226D TYR* 3.3 26.7 + - - +
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Residues in contact with LYS 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D SER* 5.4 0.8 + - - -
36D TYR* 5.5 0.2 + - - -
168D ALA* 4.4 4.3 - - + -
170D PHE* 4.0 28.9 - - + -
220D HIS* 3.3 49.0 + - + +
221D PRO 3.2 1.4 + - - -
222D GLU* 1.3 86.2 + - + +
224D ALA* 1.3 66.5 + - - +
227D GLU* 3.1 43.1 + - + +
234D ILE* 4.1 21.0 - - + +
236D HIS* 3.5 9.2 - - - -
286D SER* 5.0 7.5 + - - -
287D PHE* 3.8 30.3 - - - -
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Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D LEU 5.3 2.0 - - - +
168D ALA* 5.8 1.0 - - - +
220D HIS 4.4 2.1 + - - +
221D PRO* 3.3 9.0 + - + +
222D GLU 3.3 0.2 - - - -
223D LYS* 1.3 77.9 - - - +
225D PRO* 1.3 66.1 - - + +
228D TRP* 4.7 1.4 - - - -
234D ILE* 4.5 0.8 - - - +
235D SER 3.3 23.6 - - - +
236D HIS* 2.7 24.7 + - - +
240D ALA* 3.4 35.0 - - + +
241D VAL* 3.7 11.9 - - - +
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Residues in contact with PRO 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLU* 3.3 17.2 - - - +
42C SER 3.7 20.0 - - - +
44C GLY* 3.7 7.7 - - - -
45C ALA 4.5 1.6 + - - +
221D PRO 3.6 7.2 - - - +
222D GLU 3.4 11.7 - - - +
224D ALA* 1.3 94.8 - - + +
226D TYR* 1.3 81.4 + - + +
228D TRP* 3.6 20.7 + - - -
241D VAL* 4.0 15.5 - - + +
244D ALA* 3.7 20.2 - - + -
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Residues in contact with TYR 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LYS 5.2 1.3 - - - -
41C GLU* 3.5 33.2 - - + -
42C SER* 3.3 16.7 + - - -
226C TYR* 4.9 0.2 + - - -
274C TYR* 4.0 4.1 + - - -
35D SER* 3.8 23.6 - - - -
38D LYS* 3.4 51.0 + - + +
39D TYR* 3.7 24.2 - + + -
42D SER* 3.4 13.9 + - - -
222D GLU 3.3 21.3 - - - +
223D LYS 3.5 0.8 + - - -
225D PRO* 1.3 102.6 - - + +
227D GLU* 1.3 67.4 + - - +
228D TRP* 3.4 17.5 + - - +
288D GLN* 3.7 8.3 - - - +
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA* 4.6 0.3 - - - +
35D SER* 2.7 38.1 + - - +
223D LYS* 3.1 39.7 + - + +
225D PRO 4.1 0.2 - - - -
226D TYR* 1.3 78.8 - - - +
228D TRP* 1.3 61.3 + - - +
229D LYS 3.6 2.0 - - - +
234D ILE* 3.7 15.9 - - + +
236D HIS* 2.8 25.0 + - - -
286D SER 3.9 6.2 - - - +
287D PHE* 3.5 25.0 - - - +
288D GLN* 2.9 32.2 + - - +
289D GLN 4.9 1.6 + - - +
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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