Contacts of the helix formed by residues 221 - 228 (chain B) in PDB entry 4G1U
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 GLY 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B ARG* 3.9 13.5 - - - -
218B LEU 3.2 9.5 + - - +
219B GLN 3.2 4.6 - - - -
220B LEU* 1.3 80.7 - - - +
222B ASP* 1.3 63.0 + - - -
223B GLU 3.4 2.7 - - - -
224B GLU* 3.7 8.3 - - - -
225B ALA* 3.0 29.6 + - - +
95C GLU* 4.4 9.0 - - - -
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Residues in contact with ASP 222 (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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81B ARG* 3.0 16.0 + - - +
139B ARG* 2.5 35.5 + - - +
218B LEU* 4.3 2.6 - - - +
221B GLY* 1.3 73.5 - - - +
223B GLU* 1.3 58.2 + - - +
224B GLU* 4.1 0.2 + - - -
225B ALA* 4.8 0.4 - - - -
226B HIS* 2.9 24.8 + - - +
232B VAL* 3.3 23.7 - - + +
236B LYS* 2.8 33.0 + - - +
60C TYR* 4.5 9.6 - - - +
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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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222B ASP* 1.3 75.2 - - - +
224B GLU* 1.3 76.5 + - - +
226B HIS* 2.8 14.0 + - - +
227B TYR* 2.6 52.7 + - + +
54C LEU* 6.1 0.3 - - - +
55C ARG* 3.0 41.9 + - - +
60C TYR* 3.5 40.7 + - + +
89C VAL* 5.3 1.2 - - - +
91C ARG* 3.8 18.3 + - - +
172C ASP* 5.4 0.5 - - - +
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Residues in contact with GLU 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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220B LEU* 3.4 37.5 - - + +
221B GLY* 3.7 8.3 - - - +
222B ASP 4.1 0.3 + - - -
223B GLU* 1.3 84.6 + - - +
225B ALA* 1.3 61.8 + - - +
227B TYR* 3.3 22.4 + - + +
228B LEU* 3.5 18.5 + - - +
89C VAL 5.8 1.3 - - - +
91C ARG* 3.0 46.1 + - + +
93C TYR 4.5 7.4 - - - +
95C GLU* 5.5 2.8 - - - +
154C ARG* 3.8 25.5 + - - +
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Residues in contact with ALA 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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217B LEU 3.3 28.0 + - - +
218B LEU* 4.1 7.6 - - + -
221B GLY 3.0 19.2 + - - +
222B ASP 3.8 2.7 - - - +
224B GLU* 1.3 73.4 - - - +
226B HIS* 1.3 66.2 + - - +
228B LEU* 3.1 15.9 + - - +
230B VAL* 3.2 34.0 + - + +
232B VAL* 4.0 10.3 - - + -
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Residues in contact with HIS 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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222B ASP 2.9 14.0 + - - +
223B GLU 2.8 10.4 + - - +
225B ALA* 1.3 75.7 - - - +
227B TYR* 1.3 69.5 + - - +
229B GLY* 3.3 12.6 + - - -
230B VAL 3.7 15.9 - - - +
231B ASN* 6.0 0.9 - - - -
232B VAL* 3.5 9.8 - - + +
59C GLY 4.3 8.4 + - - -
60C TYR* 3.4 45.9 - + + -
80C PRO* 6.0 0.2 - - - +
83C LEU* 6.0 1.8 - - + -
87C ARG* 4.2 14.8 + - - -
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Residues in contact with TYR 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 GLU* 2.6 60.2 + - + +
224B GLU* 3.5 12.8 - - + +
225B ALA 3.1 0.6 - - - -
226B HIS* 1.3 84.5 - - - +
228B LEU* 1.3 58.2 + - + +
229B GLY 3.2 0.7 - - - -
55C ARG* 4.4 1.4 - - - +
58C THR* 3.0 44.2 + - + +
60C TYR* 3.6 9.9 - - + +
84C ALA* 3.3 13.2 - - - +
87C ARG* 2.7 38.6 + - - +
89C VAL* 3.5 45.7 - - + +
91C ARG* 5.2 3.6 - - - -
158C GLN* 3.5 13.5 + - - +
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Residues in contact with LEU 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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217B LEU* 3.9 10.3 - - + -
220B LEU* 3.7 29.8 - - + -
224B GLU 3.6 12.6 - - - +
225B ALA* 3.1 12.0 + - - +
227B TYR* 1.3 75.8 - - - +
229B GLY* 1.3 56.4 + - - +
230B VAL* 3.4 8.7 + - + +
81C LYS* 5.8 0.7 - - - +
84C ALA* 3.6 13.3 - - - +
108C MET 3.7 16.6 - - - +
109C GLY* 3.9 19.1 - - - +
111C ALA* 4.0 17.4 - - + +
112C PRO* 3.9 12.7 - - + +
154C ARG* 3.9 8.3 - - - +
158C GLN* 3.3 33.0 - - + +
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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