Contacts of the helix formed by residues 222 - 229 (chain b) in PDB entry 4IL6
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 PRO 222 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220b ARG 3.5 4.7 - - - +
221b PRO* 1.3 83.4 - - + +
223b GLN* 1.3 66.5 + - - +
224b ARG* 5.2 0.2 - - + -
225b LEU* 2.9 16.6 + - + +
226b TYR* 2.8 21.3 + - - +
612b CLA 3.4 33.0 - - - +
22h ALA* 3.7 11.0 - - + +
24h GLY 3.6 8.5 - - - +
25h TRP* 3.3 28.5 - - - +
26h GLY* 4.3 0.9 - - - -
27h THR* 3.9 11.2 - - - +
28h THR* 3.6 12.3 - - - +
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Residues in contact with GLN 223 (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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221b PRO 3.4 1.2 + - - -
222b PRO* 1.3 70.7 - - - +
224b ARG* 1.3 63.8 + - + +
226b TYR* 3.5 3.6 + - - +
227b LYS* 3.0 45.1 + - + +
21h VAL* 3.7 31.6 - - + +
22h ALA 2.8 21.0 + - - +
23h PRO* 4.7 1.1 - - + +
24h GLY* 3.3 15.5 + - - +
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Residues in contact with ARG 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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222b PRO* 3.0 1.4 - - + -
223b GLN* 1.3 82.2 - - + +
225b LEU* 1.3 60.7 + - - +
227b LYS* 4.1 4.4 - - - +
228b ALA* 3.2 28.1 + - - +
625b LMT 3.1 51.4 + - + +
15d PHE* 4.4 0.6 - - - -
16d ASP* 2.7 39.8 + - - -
410d HTG 4.7 0.4 + - - -
24h GLY* 3.2 22.4 + - - +
25h TRP* 3.2 65.7 - - + +
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Residues in contact with LEU 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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222b PRO* 2.9 17.4 + - + +
224b ARG* 1.3 75.8 - - - +
226b TYR* 1.3 60.7 + - - +
227b LYS 3.2 0.4 - - - -
228b ALA* 4.5 1.8 - - + +
229b LEU* 2.9 38.6 + - + +
231b MET* 3.5 13.5 - - + +
612b CLA 3.8 46.0 - - + +
625b LMT 3.8 37.0 - - + -
25h TRP* 5.2 0.7 - - + -
28h THR* 3.5 27.6 - - + +
31h MET* 3.8 16.8 - - + -
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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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136b PRO* 4.4 11.6 - - + +
220b ARG* 5.1 0.4 - - - -
221b PRO* 3.7 16.2 - - + -
222b PRO 2.8 15.3 + - - +
223b GLN* 3.7 5.2 - - - +
225b LEU* 1.3 76.9 - - - +
227b LYS* 1.3 63.1 + - + +
230b ARG* 3.2 2.8 + - - -
231b MET* 2.9 57.8 + - + +
232b GLY* 3.4 33.0 - - - -
18h TYR* 4.1 7.8 - - - -
19h GLY* 3.4 36.8 + - - -
20h LYS 4.8 1.1 - - - -
21h VAL* 3.5 27.4 - - + -
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Residues in contact with LYS 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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223b GLN* 3.0 31.0 + - + +
224b ARG* 4.1 4.7 - - - +
226b TYR* 1.3 78.4 - - - +
228b ALA* 1.3 65.4 + - - +
230b ARG* 3.3 27.9 + - - +
625b LMT 3.2 39.1 + - - +
411d UNL 3.8 18.2 - - - +
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Residues in contact with ALA 228 (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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224b ARG 3.2 18.6 + - - +
225b LEU* 4.1 2.7 - - - +
227b LYS* 1.3 78.6 - - - +
229b LEU* 1.3 60.7 + - + +
230b ARG* 2.8 18.2 + - - -
474b LEU* 3.5 10.9 - - - +
625b LMT 3.9 30.5 - - + -
411d UNL 3.6 36.5 - - + +
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Residues in contact with LEU 229 (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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225b LEU* 2.9 17.7 + - + +
228b ALA* 1.3 76.2 - - + +
230b ARG* 1.3 67.5 + - - +
231b MET* 3.4 16.8 + - + -
236b THR* 2.7 30.7 + - - +
473b THR* 5.0 0.4 - - - -
611b CLA 3.8 28.0 - - + +
612b CLA 3.3 58.1 - - + +
613b CLA 3.9 25.1 - - + -
625b LMT 6.2 1.1 - - + -
411d UNL 4.1 15.9 - - + -
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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