Contacts of the helix formed by residues 156 - 166 (chain D) 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 GLU 156 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D ARG* 3.4 31.4 + - - +
154D VAL 4.8 3.8 - - - +
155D PHE* 1.3 72.6 - - - +
157D ARG* 1.3 66.6 + - - +
158D GLU* 4.1 22.4 - - + +
159D GLU* 2.9 35.8 + - + +
160D ILE* 3.2 12.6 - - - +
184D TYR* 3.9 0.2 - - - -
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Residues in contact with ARG 157 (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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155D PHE 3.7 0.2 + - - -
156D GLU* 1.3 73.0 - - - +
158D GLU* 1.3 60.6 + - + +
159D GLU 3.4 0.5 + - - -
160D ILE* 3.4 5.4 + - - +
161D GLU* 3.1 54.5 + - - +
184D TYR* 3.3 22.1 + - + +
187D PHE* 3.3 40.6 - - + -
190D LYS* 6.4 0.2 - - - +
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Residues in contact with GLU 158 (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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156D GLU* 4.1 23.2 - - + +
157D ARG* 1.3 76.9 - - + +
159D GLU* 1.3 61.7 + - + +
160D ILE 3.4 0.2 - - - -
161D GLU* 3.8 14.8 - - - +
162D ARG* 3.0 47.4 + - - +
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Residues in contact with GLU 159 (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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129D LEU 4.8 0.2 - - - +
130D ARG* 3.1 27.1 + - - +
131D ILE* 2.7 51.8 + - + +
153D HIS* 5.9 0.2 - - - -
155D PHE* 3.5 15.0 - - - -
156D GLU* 2.9 42.4 + - + +
158D GLU* 1.3 74.8 - - + +
160D ILE* 1.3 69.0 + - + +
162D ARG* 3.3 19.4 + - - +
163D ILE* 3.3 13.3 + - - +
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Residues in contact with ILE 160 (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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131D ILE* 4.8 3.6 - - + -
144D ILE* 4.8 10.8 - - + -
146D ASN* 5.1 1.1 - - - +
155D PHE* 3.6 26.0 - - + +
156D GLU 3.2 18.4 - - - +
157D ARG 3.8 5.4 - - - +
159D GLU* 1.3 79.5 - - + +
161D GLU* 1.3 57.8 + - - +
163D ILE* 3.4 5.3 + - - +
164D LEU* 2.8 48.4 + - + +
170D VAL* 4.7 10.1 - - + +
172D LEU* 3.8 30.7 - - + -
184D TYR* 4.1 31.4 - - + +
187D PHE* 5.2 1.3 - - + -
194D LEU* 5.3 2.9 - - + -
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Residues in contact with GLU 161 (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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157D ARG* 3.1 49.3 + - - +
158D GLU* 3.8 14.9 - - - +
160D ILE* 1.3 72.9 - - - +
162D ARG* 1.3 61.9 + - - +
164D LEU* 3.9 7.4 - - - -
165D LYS* 2.7 49.5 + - - +
187D PHE* 3.4 26.5 - - + -
191D TYR* 3.9 17.5 + - - +
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Residues in contact with ARG 162 (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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133D GLU* 6.0 2.0 - - - +
158D GLU* 3.0 40.6 + - - +
159D GLU* 3.3 12.8 - - - +
160D ILE 3.2 0.2 - - - -
161D GLU* 1.3 83.3 + - - +
163D ILE* 1.3 66.4 + - + +
165D LYS* 2.6 51.2 + - - +
166D THR* 3.3 10.2 + - - -
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Residues in contact with ILE 163 (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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102D PHE* 3.9 13.2 - - + -
131D ILE* 3.5 34.1 - - + -
134D VAL* 5.0 10.5 - - + -
136D VAL* 5.5 4.7 - - + -
142D VAL* 3.4 29.8 - - + -
144D ILE* 3.7 23.6 - - + -
159D GLU 3.3 7.7 + - - +
160D ILE 3.9 4.9 - - - +
162D ARG* 1.3 81.7 - - + +
164D LEU* 1.3 60.2 + - - +
166D THR* 2.8 39.9 - - + +
167D GLY 4.0 0.2 + - - -
168D ALA* 4.3 3.4 + - + +
170D VAL* 3.9 7.2 - - + -
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Residues in contact with LEU 164 (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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160D ILE* 2.8 36.0 + - + +
161D GLU* 3.4 6.3 - - - +
163D ILE* 1.3 77.7 - - - +
165D LYS* 1.3 59.3 + - - +
166D THR 3.0 4.9 + - - -
167D GLY* 3.1 6.8 + - - -
170D VAL* 3.4 24.4 - - + +
187D PHE* 4.1 9.0 - - + -
191D TYR* 3.4 45.8 - - + -
193D ASN* 2.9 55.0 + - - +
194D LEU* 3.9 15.7 - - + -
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Residues in contact with LYS 165 (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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161D GLU* 2.7 29.2 + - + +
162D ARG* 2.6 48.0 + - - +
164D LEU* 1.3 71.8 - - - +
166D THR* 1.3 60.2 - - - +
167D GLY* 3.1 1.8 + - - -
191D TYR* 3.9 24.7 - - + +
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Residues in contact with THR 166 (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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134D VAL 5.6 0.7 + - - -
136D VAL* 3.1 30.0 + - + +
137D GLY* 3.9 9.2 - - - -
138D GLU 4.5 0.9 + - - -
162D ARG 3.3 6.9 + - - -
163D ILE* 2.8 26.4 + - + +
164D LEU 3.0 1.2 - - - -
165D LYS* 1.3 78.3 - - - +
167D GLY* 1.3 57.2 + - - +
168D ALA* 3.2 28.4 + - + +
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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