Contacts of the helix formed by residues 211 - 221 (chain A) in PDB entry 1UXI
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 LYS 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ASP* 3.1 36.9 + - - +
207A GLU* 3.1 38.6 + - + +
208A ARG* 3.3 5.4 - - - +
210A ARG* 1.3 78.1 - - + +
212A GLY* 1.3 64.3 + - - +
213A GLY 3.4 2.7 - - - -
214A GLY* 3.2 7.6 + - - +
215A GLU* 3.1 20.8 + - - +
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.7 22.0 + - - -
155A PHE* 5.1 1.3 - - - -
208A ARG 2.7 14.8 + - - -
209A THR* 2.9 12.2 + - - -
210A ARG 3.3 0.4 - - - -
211A LYS* 1.3 76.7 - - - +
213A GLY* 1.3 63.3 + - - +
215A GLU* 3.2 24.6 + - - +
216A ILE* 3.4 12.1 + - - +
48B GLU* 5.2 0.5 - - - +
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Residues in contact with GLY 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ARG* 3.8 8.6 - - - +
151A ARG* 3.5 25.5 - - - +
179A MET* 6.3 0.2 - - - +
209A THR 4.8 0.2 + - - -
210A ARG 5.0 0.2 + - - -
211A LYS 3.4 1.0 - - - -
212A GLY* 1.3 74.6 - - - +
214A GLY* 1.3 62.0 + - - +
216A ILE* 3.3 5.9 + - - +
217A VAL* 3.1 24.3 + - - +
225A ALA 5.4 0.3 + - - -
1311A FUM 3.3 27.3 - - - +
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Residues in contact with GLY 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ARG* 4.1 21.7 - - - +
88A ARG* 4.9 0.4 - - - +
211A LYS* 3.2 9.8 + - - -
213A GLY* 1.3 73.4 - - - +
215A GLU* 1.3 61.1 + - - +
217A VAL* 3.7 6.0 - - - +
218A ASN* 2.7 41.4 + - - -
1311A FUM 4.1 0.8 + - - -
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PHE* 4.1 6.6 - - - -
208A ARG* 3.0 46.2 + - - +
211A LYS* 3.1 13.2 + - + +
212A GLY* 3.2 12.6 + - - +
214A GLY* 1.3 78.3 - - - +
216A ILE* 1.3 62.9 + - - +
218A ASN* 3.5 7.3 + - - +
219A LEU* 3.2 30.8 + - + +
44B LEU* 3.6 26.3 - - + +
48B GLU* 4.5 0.5 - - - +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.8 9.2 - - - +
212A GLY 3.9 5.2 - - - +
213A GLY 3.3 6.8 + - - +
214A GLY 3.3 0.2 - - - -
215A GLU* 1.3 75.2 - - - +
217A VAL* 1.3 61.1 + - - +
219A LEU* 2.8 24.6 + - + +
220A LEU* 2.8 30.1 + - + +
225A ALA* 3.6 43.5 - - + +
41B GLY 4.4 13.5 - - - +
44B LEU* 4.2 16.4 - - + -
45B ASP* 3.9 18.4 - - + +
48B GLU* 3.4 26.9 - - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ARG* 4.2 12.3 - - + +
83A LYS* 3.6 10.8 - - - +
84A PRO* 3.4 34.8 - - + +
213A GLY 3.1 19.2 + - - +
214A GLY* 3.7 11.2 - - - +
216A ILE* 1.3 75.3 - - - +
218A ASN* 1.3 60.0 + - - +
221A LYS* 2.8 29.5 + - - -
223A GLY 3.7 12.3 - - - +
224A SER* 3.6 28.3 - - - -
1311A FUM 3.9 12.3 - - - +
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Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 3.5 28.9 - - - +
85A GLY 4.5 3.3 + - - -
214A GLY* 2.7 29.9 + - - +
215A GLU* 3.8 7.9 - - - +
217A VAL* 1.3 77.7 - - - +
219A LEU* 1.3 62.5 + - + +
221A LYS* 3.6 21.7 + - - +
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A GLU* 3.2 25.8 + - + +
216A ILE* 2.8 9.5 + - - +
218A ASN* 1.3 80.1 - - + +
220A LEU* 1.3 65.7 + - - +
221A LYS* 3.3 11.2 + - - +
36B GLU 4.2 0.7 - - - +
37B GLY* 3.2 39.9 - - - +
38B VAL 3.6 0.9 + - - -
40B GLN* 4.1 20.9 - - + +
41B GLY* 3.7 23.1 - - - +
44B LEU* 4.4 14.8 - - + -
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ILE* 2.8 39.0 + - + +
219A LEU* 1.3 70.4 - - - +
221A LYS* 1.3 68.2 + - - +
222A THR* 2.9 15.5 + - - +
223A GLY* 3.5 19.3 - - - +
224A SER 3.7 24.5 - - - +
225A ALA* 4.5 0.4 - - - -
226A TYR* 4.3 14.6 - - + -
37B GLY 4.7 0.2 - - - -
38B VAL* 3.8 22.9 + - + +
41B GLY* 4.0 3.4 - - - -
42B LYS* 3.8 40.2 - - + +
45B ASP* 5.6 1.6 - - + +
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Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS* 4.4 3.3 - - - +
84A PRO* 3.3 32.5 - - + +
217A VAL 2.8 22.2 + - - -
218A ASN* 3.6 17.4 + - - +
219A LEU* 3.5 17.9 + - - +
220A LEU* 1.3 71.8 - - - +
222A THR* 1.3 64.7 + - + +
223A GLY 3.5 1.5 + - - -
35B VAL* 6.3 1.8 - - + -
36B GLU* 3.6 24.3 + - - +
37B GLY* 4.3 2.8 - - - -
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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