Contacts of the helix formed by residues 142 - 150 (chain D) in PDB entry 2R2N
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 TYR 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293C LEU* 4.8 5.2 - - - +
427C KYN 3.9 22.5 + - + +
118D GLN* 3.3 33.9 + - - -
141D ALA* 1.3 73.0 - - - +
143D SER* 1.3 67.9 + - - +
144D GLY* 3.6 18.8 - - - -
145D THR* 3.2 41.0 + - + -
146D LEU* 3.3 10.4 + - - +
195D TYR* 4.2 4.2 + - - +
197D VAL* 5.1 1.1 - - + -
201D ASN* 4.7 2.6 - - - +
202D ASN* 3.1 31.7 + - - +
387D PHE* 4.5 1.6 - + - -
426D PMP 3.4 68.2 - + + -
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Residues in contact with SER 143 (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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18C PRO* 4.2 14.2 - - - +
19C ILE* 3.3 30.9 - - - +
427C KYN 5.0 1.7 + - - +
141D ALA 3.3 3.6 + - - -
142D TYR* 1.3 79.7 - - - +
144D GLY* 1.3 59.2 + - - +
146D LEU* 3.3 6.8 + - - +
147D GLN* 2.8 35.5 + - - +
386D ALA 3.4 28.0 - - - -
387D PHE* 3.8 8.8 - - - -
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Residues in contact with GLY 144 (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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290C VAL* 4.0 7.1 - - - +
118D GLN* 4.0 12.7 + - - -
142D TYR* 3.2 26.1 - - - -
143D SER* 1.3 82.3 + - - +
145D THR* 1.3 55.7 + - - +
147D GLN* 3.5 5.9 + - - +
148D SER* 3.0 27.5 + - - -
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Residues in contact with THR 145 (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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118D GLN* 4.8 4.7 - - - +
121D LEU* 4.9 3.1 - - + -
125D PHE* 4.2 16.6 - - + -
137D LEU* 5.0 0.7 - - - +
141D ALA* 4.6 0.9 - - - +
142D TYR* 3.2 29.5 + - + -
144D GLY* 1.3 71.3 - - - +
146D LEU* 1.4 64.2 + - - +
148D SER* 3.0 7.6 + - - -
149D LEU* 2.8 43.6 + - - +
195D TYR* 2.7 51.1 - - + +
230D ASP* 4.2 2.7 - - - +
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Residues in contact with LEU 146 (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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137D LEU* 4.6 14.1 - - + -
139D GLU* 5.1 0.7 - - + -
141D ALA* 3.9 20.9 - - + +
142D TYR 3.3 9.6 + - - +
143D SER* 3.3 7.7 + - - +
145D THR* 1.4 81.5 + - - +
147D GLN* 1.3 71.9 + - - +
149D LEU* 4.0 4.9 - - + +
150D HIS* 3.2 26.2 + - - +
156D ILE* 5.0 4.3 - - + -
386D ALA 3.9 8.3 - - - +
387D PHE* 3.4 35.9 - - - +
388D TYR* 3.4 21.5 - - - +
389D VAL* 3.8 23.3 - - + +
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Residues in contact with GLN 147 (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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14C ARG* 4.8 1.6 + - - +
15C ASN* 3.5 45.1 + - - +
17C SER* 3.8 24.4 - - - +
18C PRO* 4.9 8.2 - - + +
290C VAL* 3.9 21.9 - - + +
143D SER* 2.8 23.8 + - - +
144D GLY* 4.0 3.1 - - - +
146D LEU* 1.3 83.5 + - - +
148D SER* 1.3 57.4 + - - +
150D HIS* 4.2 7.6 + - - +
151D PRO* 3.1 25.3 - - - +
386D ALA 5.3 5.5 + - - -
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Residues in contact with SER 148 (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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14C ARG* 5.0 2.3 + - - -
290C VAL* 3.8 22.7 + - - +
118D GLN* 5.5 1.1 - - - -
122D CYS* 4.0 19.3 - - - -
125D PHE* 3.4 25.5 - - - +
144D GLY 3.0 19.1 + - - -
145D THR* 3.0 6.9 + - - -
147D GLN* 1.3 78.1 - - - +
149D LEU* 1.3 61.8 + - - +
151D PRO* 3.4 11.0 - - - +
152D LEU* 3.5 17.9 - - - +
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Residues in contact with LEU 149 (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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125D PHE* 3.6 34.3 - - + -
129D ILE* 3.5 31.4 - - + -
135D VAL* 4.8 4.0 - - + -
137D LEU* 3.9 28.9 - - + -
145D THR* 2.8 30.4 + - - +
146D LEU* 3.5 3.6 + - + +
148D SER* 1.3 71.4 - - - +
150D HIS* 1.3 67.2 + - - +
151D PRO 3.5 0.2 - - - -
152D LEU* 3.2 18.1 + - - +
153D GLY 3.7 1.4 + - - -
154D CYS* 3.6 20.0 + - - +
156D ILE* 4.1 20.2 - - + -
193D PHE* 4.1 7.2 - - + -
195D TYR* 5.9 0.9 - - + -
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Residues in contact with HIS 150 (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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13C ALA* 3.0 41.9 + - + +
15C ASN* 3.6 20.9 + - - -
146D LEU 3.2 17.7 + - - +
147D GLN* 4.2 8.5 + - - +
149D LEU* 1.3 77.5 - - - +
151D PRO* 1.3 69.9 - - + +
152D LEU 3.2 0.9 + - - -
153D GLY* 3.2 13.3 + - - -
156D ILE* 5.7 3.8 - - - -
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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