Contacts of the helix formed by residues 217 - 228 (chain C) in PDB entry 1UU1
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 SER 217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C ASN* 4.0 4.3 - - - +
188C LEU* 4.5 5.0 - - - +
192C GLU* 3.7 31.8 + - - -
194C LEU 4.4 3.2 + - - -
216C ALA* 1.3 76.9 - - - +
218C GLU* 1.3 56.0 + - - +
219C LYS* 3.5 6.0 + - - -
220C PHE* 2.7 37.4 + - - +
221C ILE* 2.9 10.7 + - - +
1D MET* 3.4 17.3 - - - +
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Residues in contact with GLU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C SER* 3.7 8.3 + - - -
77C ASN* 3.3 49.4 - - + +
78C ASN* 3.6 16.3 + - - +
216C ALA 3.6 1.6 + - - -
217C SER* 1.3 72.1 - - - +
219C LYS* 1.3 65.1 + - + +
221C ILE* 3.8 0.7 - - - +
222C ASP* 2.9 27.7 + - - +
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Residues in contact with LYS 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLU* 4.7 10.1 - - - +
217C SER* 3.1 9.5 - - - +
218C GLU* 1.3 78.9 - - + +
220C PHE* 1.3 63.2 + - - +
222C ASP* 3.8 6.5 - - - +
223C ALA* 3.2 22.3 + - - +
1D MET* 4.1 19.6 - - + +
2D ASN* 4.3 16.0 + - - +
4D LEU 5.4 1.3 + - - +
5D ASP* 3.3 40.2 + - - +
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Residues in contact with PHE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C MET* 3.1 42.2 - - + -
95C MET* 3.8 24.2 - - + -
96C PHE* 4.1 14.8 - + - -
169C PHE* 3.3 36.3 - + + -
195C ALA* 4.4 1.1 - - + -
214C VAL* 4.0 11.9 - - + -
216C ALA* 3.4 25.6 - - + -
217C SER* 2.7 21.7 + - - +
219C LYS* 1.3 72.0 - - - +
221C ILE* 1.3 60.8 + - + +
222C ASP 3.1 1.8 - - - -
223C ALA* 3.0 4.9 + - - +
224C TYR* 2.8 50.9 + + + +
1D MET* 5.0 1.9 - - + +
4D LEU* 5.8 1.3 - - + -
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Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LYS 5.3 0.2 - - - +
77C ASN* 3.2 31.0 - - - +
78C ASN* 3.4 27.8 - - - +
79C VAL 4.1 11.9 - - - +
80C SER* 3.7 21.5 - - - +
214C VAL* 3.8 15.9 - - + +
216C ALA 3.8 9.6 - - - +
217C SER 2.9 9.3 + - - +
218C GLU 3.8 3.1 - - - +
220C PHE* 1.3 86.2 - - + +
222C ASP* 1.3 57.8 + - - +
224C TYR* 3.3 4.7 + - + +
225C ASN* 2.9 42.7 + - - +
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Residues in contact with ASP 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C GLU 2.9 17.8 + - - +
219C LYS* 3.8 7.0 - - - +
221C ILE* 1.3 76.9 - - - +
223C ALA* 1.3 66.1 + - - +
225C ASN* 3.2 15.2 + - - +
226C ARG* 3.1 45.0 + - - +
8D ALA* 3.4 15.8 - - - +
14D TYR* 5.3 4.2 + - - +
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C MET* 3.7 3.8 - - + -
219C LYS 3.2 14.7 + - - +
220C PHE* 3.0 5.6 + - - +
222C ASP* 1.3 82.0 - - - +
224C TYR* 1.3 61.3 + - - +
226C ARG* 3.2 11.0 + - - +
227C VAL* 3.2 23.4 + - - +
4D LEU* 3.5 37.7 - - + +
7D ILE* 3.8 16.1 - - + +
8D ALA* 5.1 2.7 - - + -
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Residues in contact with TYR 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C SER* 3.5 20.9 - - - -
81C VAL 2.9 28.6 + - - -
82C GLY* 3.6 5.2 - - - -
87C GLU* 4.2 3.3 + - - -
88C ILE* 3.1 31.1 + - + +
91C VAL* 2.8 41.0 - - + +
95C MET* 3.7 13.2 - - - +
214C VAL* 4.1 7.2 - - + -
220C PHE* 2.8 37.6 + + + +
221C ILE* 3.4 4.9 - - + +
223C ALA* 1.3 78.4 - - - +
225C ASN* 1.3 71.5 + - - +
227C VAL* 3.3 1.2 + - - +
228C ARG* 3.2 40.1 + - + +
232C ASN* 4.1 0.9 + - - -
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Residues in contact with ASN 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PRO* 5.4 1.0 - - - +
79C VAL 5.3 0.3 - - - +
80C SER* 2.5 29.8 + - - -
221C ILE* 2.9 32.3 + - - +
222C ASP* 3.2 8.6 + - - +
224C TYR* 1.3 81.2 - - - +
226C ARG* 1.3 58.6 + - - +
228C ARG* 2.7 42.0 - - - +
229C LEU 5.7 0.2 - - - -
230C PRO* 5.8 0.3 - - - +
14D TYR* 3.7 45.8 - - + +
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Residues in contact with ARG 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ASP* 3.1 40.4 + - - +
223C ALA* 3.2 9.8 + - - +
224C TYR 3.1 0.8 - - - -
225C ASN* 1.3 79.2 - - - +
227C VAL* 1.3 58.8 + - - +
228C ARG 4.3 2.9 - - - +
7D ILE* 4.5 1.8 - - + -
8D ALA* 3.0 46.6 + - - +
11D ALA* 2.8 28.8 + - + +
12D TYR 3.1 18.6 - - - +
13D PRO* 3.2 44.2 - - + +
14D TYR* 4.0 7.4 - - + +
111D ILE* 5.4 4.3 - - - +
115D ALA* 3.4 18.4 - - - +
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL* 4.5 6.3 - - + +
94C LEU* 4.5 17.5 - - + +
95C MET* 3.8 30.5 - - + -
223C ALA 3.2 16.9 + - - +
224C TYR 3.3 2.8 + - - +
226C ARG* 1.3 77.9 - - - +
228C ARG* 1.3 60.8 + - - +
7D ILE* 4.0 21.3 - - + -
10D ARG* 5.0 0.2 - - - +
11D ALA* 5.6 0.4 - - + -
90D TYR* 2.6 38.6 + - - +
115D ALA* 3.2 34.4 - - - +
116D VAL* 4.7 0.9 - - - -
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Residues in contact with ARG 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PRO* 2.8 36.8 - - - +
80C SER* 3.7 1.4 + - - -
81C VAL 4.2 0.7 - - - -
87C GLU* 5.2 2.0 - - - +
91C VAL* 4.1 21.0 - - + +
224C TYR* 3.2 40.7 + - + +
225C ASN* 2.7 35.1 - - - +
226C ARG 4.3 2.4 - - - +
227C VAL* 1.3 82.2 - - - +
229C LEU* 1.3 79.5 + - - +
230C PRO* 3.1 13.4 + - - +
232C ASN* 2.7 42.8 - - - +
14D TYR* 3.1 26.7 + - - -
90D TYR* 4.0 7.6 - - - -
112D PHE* 5.3 2.3 - - - -
115D ALA* 5.6 0.3 - - - +
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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