Contacts of the helix formed by residues 222 - 232 (chain B) in PDB entry 4Y2H
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 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A THR* 4.0 18.2 - - + -
119A GLN* 3.8 36.8 - - + +
122A GLU* 4.4 7.0 - - - +
123A VAL* 3.8 29.2 - - + -
208B TRP* 4.2 22.4 - - + -
219B MET* 3.5 28.3 - - + +
220B SER 3.1 2.0 - - - -
221B CYS* 1.3 83.3 - - - +
223B GLU* 1.3 64.5 + - - +
224B GLY 3.3 2.9 - - - -
225B PHE* 3.0 17.0 + - + +
226B ALA* 2.8 23.6 + - - +
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Residues in contact with GLU 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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205B LEU* 3.6 28.7 - - + +
206B GLY* 5.3 3.3 - - - -
208B TRP* 4.5 5.8 - - + +
209B SER* 4.0 16.7 + - - +
220B SER 3.2 15.2 + - - +
221B CYS 3.3 0.6 - - - -
222B LEU* 1.3 76.0 - - - +
224B GLY* 1.3 65.2 - - - +
226B ALA* 3.1 8.3 + - - +
227B THR* 2.9 34.3 + - - +
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Residues in contact with GLY 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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221B CYS 4.4 4.7 + - - -
222B LEU 3.3 0.6 - - - -
223B GLU* 1.3 77.7 - - - +
225B PHE* 1.3 56.4 + - - +
227B THR* 3.2 9.0 + - - -
228B ARG* 3.0 44.0 + - - +
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Residues in contact with PHE 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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52A SER 3.3 26.2 - - - -
54A VAL* 3.6 37.2 - - + -
57A HIS* 6.2 0.4 - - + -
93A THR* 5.9 0.9 - - + -
116A ILE* 3.5 25.1 - - + -
119A GLN* 3.6 39.9 - - + +
122A GLU* 5.8 1.3 - - - +
221B CYS 5.1 1.2 + - - +
222B LEU* 3.0 24.6 + - + +
224B GLY* 1.3 71.7 - - - +
226B ALA* 1.3 67.5 + - - +
228B ARG* 3.4 25.9 + - + +
229B CYS* 3.1 35.4 + - - -
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Residues in contact with ALA 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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54A VAL* 4.0 15.3 - - + -
204B ARG 4.8 0.2 - - - +
205B LEU* 3.9 17.0 - - + -
208B TRP* 3.7 29.4 - - + +
222B LEU 2.8 15.7 + - - +
223B GLU* 3.4 9.0 - - - +
225B PHE* 1.3 73.6 - - - +
227B THR* 1.3 57.8 + - - +
229B CYS* 3.4 0.5 + - - +
230B LEU* 2.9 39.8 + - + +
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Residues in contact with THR 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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205B LEU* 3.7 20.4 - - - +
223B GLU* 2.9 20.1 + - - +
224B GLY* 3.2 11.3 + - - -
226B ALA* 1.3 74.9 - - - +
228B ARG* 1.3 58.6 + - + +
231B MET* 2.8 35.1 + - - +
232B GLY 3.3 4.3 + - - -
326B ASN 3.7 17.8 - - - +
327B GLU* 3.8 21.1 - - + -
328B PRO* 4.0 11.4 - - + +
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Residues in contact with ARG 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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119A GLN* 4.4 8.9 - - - +
224B GLY* 3.0 30.5 + - - +
225B PHE* 3.7 37.2 - - + +
227B THR* 1.3 74.4 - - + +
229B CYS* 1.3 60.4 + - - +
232B GLY* 2.9 32.9 + - - +
233B HIS 3.9 0.3 + - - -
326B ASN 5.1 1.6 - - - -
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Residues in contact with CYS 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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52A SER 4.8 0.2 - - - -
53A ASP* 3.5 23.8 - - - +
54A VAL* 3.6 34.1 - - + -
225B PHE* 3.1 41.2 + - - +
226B ALA 3.7 3.4 - - - +
228B ARG* 1.3 80.0 - - - +
230B LEU* 1.3 60.6 + - + +
233B HIS* 3.4 21.3 - - - +
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Residues in contact with LEU 230 (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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53A ASP* 5.5 1.3 - - - +
54A VAL* 3.8 18.4 - - + -
55A SER* 3.8 9.4 - - - +
58A GLU* 4.3 2.2 - - - +
201B LEU* 4.0 16.6 - - + +
204B ARG* 3.5 62.6 - - + +
205B LEU* 4.1 13.9 - - + -
208B TRP* 6.3 0.2 - - - +
226B ALA* 2.9 23.8 + - + +
229B CYS* 1.3 77.7 - - + +
231B MET* 1.3 62.2 + - - +
233B HIS* 2.9 23.2 + - - -
324B TYR* 3.9 10.2 - - - -
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Residues in contact with MET 231 (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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201B LEU* 3.8 26.9 - - + -
205B LEU* 3.9 11.0 - - + -
227B THR* 2.8 14.4 + - + +
230B LEU* 1.3 78.7 - - + +
232B GLY* 1.3 61.5 + - - +
233B HIS* 3.2 6.2 + - - +
286B HIS* 3.4 34.5 - - + +
324B TYR* 4.1 8.7 - - + +
325B LEU 3.2 30.5 - - - +
326B ASN* 3.3 16.6 - - - +
327B GLU* 3.5 19.7 - - - +
328B PRO* 3.7 26.9 - - + -
369B LYS* 2.8 25.8 + - - -
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Residues in contact with GLY 232 (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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227B THR 3.3 4.2 + - - -
228B ARG* 2.9 23.3 + - - -
231B MET* 1.3 73.8 - - - +
233B HIS* 1.3 63.8 + - - +
234B SER* 4.7 2.4 + - - -
326B ASN* 3.8 22.7 + - - +
369B LYS* 4.2 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