Contacts of the helix formed by residues 111 - 128 (chain D) in PDB entry 3U8Z
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 GLN 111 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLY 2.8 27.5 + - - -
56D LEU* 3.7 2.3 - - - +
57D ARG* 2.7 62.6 + - - +
58D GLU* 3.2 24.0 + - + +
109D LEU 3.9 3.0 - - - +
110D VAL* 1.4 79.8 - - + +
112D GLU* 1.3 63.3 + - - +
113D ILE* 3.3 11.7 - - + +
114D THR* 3.3 16.7 + - - +
115D GLN* 3.3 20.7 + - - +
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Residues in contact with GLU 112 (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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52B ARG* 4.3 8.4 - - - +
55B GLY* 3.6 25.5 - - - +
57B ARG* 3.3 26.4 - - + +
110D VAL 3.9 2.0 + - - -
111D GLN* 1.3 69.7 - - - +
113D ILE* 1.3 55.8 + - - +
115D GLN* 3.2 17.7 + - - +
116D HIS* 2.7 42.1 + - - +
201D ASP* 3.0 43.0 - - + +
204D GLU* 3.0 24.1 - - - +
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG 4.6 2.7 - - - +
53B THR 3.3 27.1 - - - +
54B LEU 3.9 2.2 - - - -
55B GLY* 3.8 20.7 + - - +
54D LEU* 3.4 37.0 - - + +
55D GLY 4.1 0.9 - - - +
56D LEU* 3.8 25.8 - - + -
111D GLN* 4.0 17.5 - - + +
112D GLU* 1.3 77.4 + - - +
114D THR* 1.4 60.3 + - - +
116D HIS* 3.5 6.5 + - + -
117D LEU* 3.0 55.0 + - + +
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Residues in contact with THR 114 (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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56D LEU* 3.5 12.5 - - + +
58D GLU* 2.8 32.5 + - + +
61D PHE* 3.9 10.1 - - + -
62D PHE* 3.5 32.5 - - + -
109D LEU* 3.8 23.6 - - + -
111D GLN* 3.3 12.8 - - - +
112D GLU 3.4 0.4 - - - -
113D ILE* 1.4 75.3 - - - +
115D GLN* 1.3 56.7 + - - +
117D LEU* 3.5 0.7 + - - +
118D PHE* 3.0 37.3 + - + -
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Residues in contact with GLN 115 (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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109D LEU* 4.0 15.8 + - + +
111D GLN 3.3 12.0 + - - +
112D GLU* 3.3 33.8 - - - +
114D THR* 1.3 76.0 - - - +
116D HIS* 1.3 57.8 + - - +
119D PHE* 2.9 29.8 + - - +
201D ASP* 2.9 31.3 + - - +
202D GLU* 5.5 0.4 - - - +
204D GLU* 3.4 11.9 - - + +
205D MET* 3.4 39.8 - - + +
208D LEU* 3.6 8.7 - - + +
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Residues in contact with HIS 116 (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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52B ARG* 3.2 49.3 + - + +
53B THR* 4.6 0.7 - - - -
30D ASP* 2.7 37.1 + - - -
112D GLU* 2.7 30.9 + - - +
113D ILE* 3.7 10.3 - - + +
115D GLN* 1.3 70.6 - - - +
117D LEU* 1.3 64.6 + - - +
119D PHE* 3.3 3.9 + + - +
120D LEU* 3.1 45.4 + - + +
204D GLU* 2.8 35.0 + - - +
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Residues in contact with LEU 117 (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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28D THR* 4.5 18.2 - - - -
29D MET* 4.2 12.7 - - + +
30D ASP* 3.9 20.9 - - - +
54D LEU* 4.4 7.6 - - + -
56D LEU* 4.7 5.2 - - + -
62D PHE* 4.0 22.0 - - + -
96D PHE* 3.7 31.2 - - + +
113D ILE* 3.0 43.0 + - + +
114D THR 3.9 3.4 - - - +
116D HIS* 1.3 75.7 - - - +
118D PHE* 1.3 60.8 + - - +
120D LEU* 3.6 4.7 + - + +
121D GLN* 3.2 25.5 + - - +
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Residues in contact with PHE 118 (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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61D PHE* 3.7 17.7 - + + -
62D PHE* 3.7 21.3 - + - -
98D ALA* 3.5 24.7 - - + -
100D PHE 3.2 23.3 - - - -
101D TYR* 3.7 22.9 - + - -
102D PRO* 3.6 22.7 - - + -
109D LEU* 3.7 35.4 - - + -
114D THR* 3.0 26.0 + - + +
115D GLN 4.0 1.3 - - - +
117D LEU* 1.3 73.5 - - - +
119D PHE* 1.3 65.2 + - - +
121D GLN* 3.3 4.6 + - + -
122D VAL* 2.9 31.7 + - + +
208D LEU* 3.9 10.3 - - + -
217D TYR* 4.8 2.2 - - - -
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Residues in contact with PHE 119 (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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115D GLN 2.9 19.6 + - - +
116D HIS* 3.3 4.7 + + - +
118D PHE* 1.3 74.4 - - - +
120D LEU* 1.3 72.5 + - + +
122D VAL* 4.0 1.0 - - - +
123D LYS* 2.9 64.2 + - + +
145D ALA* 4.2 8.1 - - - -
148D ALA* 3.7 21.3 - - + -
203D ALA 4.9 0.2 - - - -
204D GLU* 3.5 47.3 - - + +
207D TYR* 3.4 48.5 - + + -
208D LEU* 3.8 9.8 - - - +
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Residues in contact with LEU 120 (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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29D MET* 3.4 38.4 - - + +
30D ASP* 3.4 35.9 - - - +
116D HIS* 3.1 37.9 + - + +
117D LEU* 3.6 2.0 + - - +
119D PHE* 1.3 93.9 - - + +
121D GLN* 1.3 61.1 + - - +
123D LYS* 3.6 17.5 + - - +
124D LYS* 3.1 22.9 + - - +
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Residues in contact with GLN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D MET* 3.8 15.6 - - + +
62D PHE* 5.3 1.7 - - - -
97D LEU* 3.5 28.3 - - + +
98D ALA* 2.8 52.0 + - - +
101D TYR* 3.0 24.3 + - - +
117D LEU 3.2 18.9 + - - +
118D PHE* 3.8 5.2 - - + +
120D LEU* 1.3 77.4 - - - +
122D VAL* 1.4 62.1 + - + +
124D LYS* 3.5 4.9 + - - +
125D GLN* 3.3 34.0 + - - +
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Residues in contact with VAL 122 (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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101D TYR* 4.0 21.5 - - + -
118D PHE* 2.9 23.1 + - + +
119D PHE 4.1 0.7 - - - +
121D GLN* 1.4 70.9 - - - +
123D LYS* 1.3 61.5 + - - +
125D GLN* 3.1 13.3 + - - +
126D ILE* 3.0 30.5 + - + +
131D ILE* 4.2 7.6 - - + -
207D TYR* 4.4 4.7 - - + -
208D LEU* 3.9 13.9 - - + -
211D ALA* 3.6 31.2 - - + -
217D TYR* 3.6 28.9 - - + +
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Residues in contact with LYS 123 (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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119D PHE* 2.9 54.8 + - + +
120D LEU* 3.9 18.6 + - - +
122D VAL* 1.3 75.7 - - - +
124D LYS* 1.4 56.3 + - - +
126D ILE* 3.1 2.8 + - - +
127D LEU* 2.9 57.6 + - + +
145D ALA* 4.0 19.3 - - + -
207D TYR* 3.4 24.8 - - + +
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Residues in contact with LYS 124 (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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29D MET* 3.8 22.0 - - + +
120D LEU 3.1 17.8 + - - +
121D GLN 3.7 5.6 - - - +
122D VAL 3.3 0.4 - - - -
123D LYS* 1.4 75.3 - - - +
125D GLN* 1.3 58.5 + - + +
127D LEU* 3.4 7.2 + - + +
128D ASP* 2.9 60.2 + - - +
130D LYS* 5.1 7.8 - - - +
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Residues in contact with GLN 125 (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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101D TYR* 3.0 32.2 + - - -
121D GLN* 3.3 28.6 + - - +
122D VAL* 3.1 12.4 + - - +
124D LYS* 1.3 74.8 - - + +
126D ILE* 1.3 63.7 + - - +
128D ASP* 4.5 1.8 - - - -
129D GLU 3.2 0.7 + - - -
130D LYS* 2.9 51.7 + - + -
131D ILE* 3.2 37.1 + - + +
218D GLY 5.4 1.2 + - - -
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Residues in contact with ILE 126 (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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122D VAL* 3.0 24.9 + - + +
123D LYS 3.1 7.4 + - - +
125D GLN* 1.3 74.6 - - - +
127D LEU* 1.3 71.4 + - + +
129D GLU* 3.2 18.0 + - - +
131D ILE* 3.9 24.7 - - + +
133D CYS* 4.4 15.8 - - + +
138D SER* 6.1 1.8 - - - -
141D LEU* 4.0 20.9 - - + -
207D TYR* 3.5 22.4 - - + +
211D ALA* 4.8 2.9 - - + -
214D LEU* 3.6 31.9 - - + -
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Residues in contact with LEU 127 (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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123D LYS* 2.9 47.5 + - + +
124D LYS* 4.0 6.1 - - + +
126D ILE* 1.3 86.1 - - + +
128D ASP* 1.4 60.5 + - - +
129D GLU* 3.2 10.8 + - - +
207D TYR* 5.3 0.7 - - - +
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Residues in contact with ASP 128 (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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124D LYS* 2.9 48.4 + - - +
125D GLN 4.2 1.3 - - - +
127D LEU* 1.4 76.0 - - - +
129D GLU* 1.4 71.3 + - - +
130D LYS* 3.5 40.6 + - + +
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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