Contacts of the helix formed by residues 148 - 165 (chain D) in PDB entry 1TU8
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 148 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D LEU* 3.5 23.3 - - - -
87D ILE* 3.6 33.1 - - - +
142D ILE* 4.5 2.8 - - - +
143D LEU* 4.1 14.6 + - - +
147D ILE* 1.3 79.0 - - - +
149D TYR* 1.3 65.7 + - - +
150D ALA* 3.7 7.4 + - - +
151D ASP* 2.9 33.1 + - - +
152D TYR* 3.8 5.0 - - - -
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Residues in contact with TYR 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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20D PHE* 4.0 10.8 - - + -
67D LEU* 3.5 40.9 - - + +
68D ARG* 3.7 29.2 - - + +
71D ALA* 3.4 29.6 - - + -
76D LEU* 3.1 18.9 + - - +
77D ASN* 3.3 23.9 + - - -
87D ILE* 3.5 17.6 - - + +
88D ASP* 3.3 32.8 + - - +
91D CYS* 3.9 23.6 - - + -
148D SER* 1.3 74.2 - - - +
150D ALA* 1.3 64.3 + - - +
152D TYR* 3.3 24.5 + - - +
153D ALA 3.7 6.2 + - - -
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Residues in contact with ALA 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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87D ILE* 3.6 32.3 - - + +
90D PHE* 4.8 0.7 - - + -
91D CYS* 4.0 18.2 - - + +
94D VAL* 5.4 1.4 - - + +
142D ILE* 3.7 18.7 - - + +
148D SER* 3.2 9.0 + - - +
149D TYR* 1.3 88.2 - - + +
151D ASP* 1.3 61.5 + - - +
153D ALA* 3.1 4.2 + - - +
154D LEU* 3.0 23.0 + - - +
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Residues in contact with ASP 151 (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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141D LEU* 3.6 11.5 - - - +
142D ILE* 2.9 36.0 + - - +
143D LEU 5.1 0.2 + - - -
146D LYS 4.3 0.9 - - - +
147D ILE* 3.4 15.4 - - + -
148D SER* 2.9 37.0 + - - +
150D ALA* 1.3 77.7 - - - +
152D TYR* 1.3 57.4 + - - +
155D PHE* 2.9 30.7 + - - +
178D PHE* 3.3 21.8 - - + -
182D MET* 3.9 17.5 - - + -
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Residues in contact with TYR 152 (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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16D PRO* 3.6 20.1 - - + +
19D LEU* 3.8 22.0 - - + +
20D PHE* 3.7 29.2 - + + -
23D ASP* 2.5 47.1 + - + +
24D GLN* 3.0 19.8 + - - +
67D LEU* 5.6 0.7 - - + -
76D LEU* 3.6 22.6 - - + +
147D ILE* 3.7 9.6 - - + +
148D SER 3.8 6.7 - - - -
149D TYR 3.3 13.6 + - - +
150D ALA 3.2 0.6 - - - -
151D ASP* 1.3 74.8 - - - +
153D ALA* 1.3 62.8 + - - +
155D PHE* 3.5 3.4 + + - +
156D GLU* 3.1 24.9 + - - +
182D MET* 3.7 22.7 - - + -
188D LEU* 4.4 3.4 - - + -
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Residues in contact with ALA 153 (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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16D PRO* 4.0 23.9 - - + +
67D LEU* 4.8 2.5 - - + -
91D CYS* 3.7 27.1 - - - -
94D VAL* 3.6 16.5 - - + +
95D ARG* 6.3 1.1 - - + -
149D TYR 3.7 4.0 + - - +
150D ALA 3.1 8.1 + - - +
152D TYR* 1.3 75.8 - - - +
154D LEU* 1.3 65.7 + - - +
156D GLU* 3.4 3.1 + - - +
157D GLU* 3.0 24.6 + - - +
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Residues in contact with LEU 154 (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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90D PHE* 3.9 27.1 - - + -
94D VAL* 4.1 23.7 - - + +
128D PHE* 4.5 11.7 - - + -
132D LEU* 4.8 3.8 - - + -
142D ILE* 4.1 11.7 - - + -
150D ALA 3.0 15.2 + - - +
151D ASP 3.9 3.1 - - - +
153D ALA* 1.3 75.7 - - - +
155D PHE* 1.3 62.9 + - - +
157D GLU* 3.2 4.0 + - + -
158D LEU* 2.9 48.8 + - + +
175D LEU* 4.4 14.8 - - + -
178D PHE* 3.6 31.4 - - + -
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Residues in contact with PHE 155 (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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19D LEU* 3.9 34.5 - - + -
151D ASP 2.9 19.1 + - - +
152D TYR* 3.6 3.4 - - - +
154D LEU* 1.3 77.1 - - - +
156D GLU* 1.3 61.9 + - - +
158D LEU* 3.3 4.3 + - - +
159D ASP* 2.9 24.9 + - + +
178D PHE* 3.7 7.5 - - - -
179D HIS* 3.1 48.7 - + - -
182D MET* 3.6 27.8 - - + -
183D LYS* 3.8 23.1 - - + -
188D LEU* 4.1 17.7 - - + -
192D CYS* 4.0 18.6 - - - -
195D ARG* 5.0 3.6 - - - -
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Residues in contact with GLU 156 (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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11D ARG* 3.0 45.4 + - - +
12D GLY 4.7 3.7 - - - +
15D GLU* 3.4 27.3 - - + +
16D PRO* 4.2 14.6 - - + -
19D LEU* 3.8 11.6 - - + +
98D HIS* 5.7 4.6 - - + -
152D TYR 3.1 14.4 + - - +
153D ALA 3.8 3.6 - - - +
155D PHE* 1.3 80.1 - - - +
157D GLU* 1.3 63.6 + - - +
159D ASP* 3.2 3.2 + - - +
160D VAL* 2.9 40.6 + - + +
195D ARG* 3.4 14.4 + - - -
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Residues in contact with GLU 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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94D VAL* 3.7 22.9 - - + +
97D LEU* 4.0 18.8 - - + -
98D HIS* 2.6 54.1 + - - +
101D TYR* 4.1 2.1 - - - +
153D ALA 3.0 16.3 + - - +
154D LEU* 3.2 6.9 + - + +
156D GLU* 1.3 80.5 - - - +
158D LEU* 1.3 64.1 + - + +
160D VAL* 3.5 6.7 - - - +
161D HIS* 2.8 57.3 + - - +
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Residues in contact with LEU 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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97D LEU* 6.2 0.9 - - + -
125D LEU* 3.9 27.4 - - + -
128D PHE* 6.0 0.4 - - + -
154D LEU* 2.9 36.1 + - + +
155D PHE* 3.8 3.6 - - - +
157D GLU* 1.3 78.5 - - + +
159D ASP* 1.3 56.4 + - - +
161D HIS* 3.4 4.2 + - - +
162D GLN* 3.0 33.7 + - - +
168D CYS* 4.9 0.5 - - - -
169D LEU* 4.0 21.6 - - + +
175D LEU* 3.6 38.1 - - + +
178D PHE* 3.8 24.2 - - + -
179D HIS* 4.0 9.9 - - + -
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Residues in contact with ASP 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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11D ARG* 2.8 29.9 + - - +
155D PHE* 2.9 21.9 + - + +
156D GLU* 3.2 8.3 + - - +
158D LEU* 1.3 74.7 - - - +
160D VAL* 1.3 65.2 + - - +
162D GLN* 3.2 5.2 + - - +
163D ILE* 3.1 30.9 + - - +
179D HIS* 2.9 33.3 + - + -
183D LYS* 4.9 8.1 + - - +
192D CYS* 5.9 0.2 - - - -
195D ARG* 3.4 15.3 + - - -
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Residues in contact with VAL 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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11D ARG* 3.6 9.9 - - - +
98D HIS* 5.3 4.7 - - + -
101D TYR* 4.0 24.1 + - + +
156D GLU* 2.9 42.2 + - + +
157D GLU* 3.5 24.9 - - - +
159D ASP* 1.3 74.7 - - - +
161D HIS* 1.3 73.4 + - - +
163D ILE* 3.3 12.1 + - - +
164D LEU* 3.2 20.1 + - - +
202D VAL* 3.7 28.0 - - + -
208D GLN* 5.9 0.7 - - - +
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Residues in contact with HIS 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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97D LEU* 3.9 14.8 - - + +
101D TYR* 3.5 25.1 - + + -
116D TYR* 2.7 29.9 + + - -
121D LEU* 3.3 33.6 - - + +
125D LEU* 5.5 4.5 - - + -
157D GLU* 2.8 52.9 + - - +
158D LEU* 3.9 5.2 - - + +
160D VAL* 1.3 81.0 - - + +
162D GLN* 1.3 56.9 + - - +
164D LEU* 3.2 8.3 + - + +
165D ASP* 2.9 28.4 + - - +
168D CYS* 3.6 17.0 - - - +
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Residues in contact with GLN 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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158D LEU 3.0 17.7 + - - +
159D ASP* 3.2 6.2 + - - +
161D HIS* 1.3 74.8 - - - +
163D ILE* 1.3 63.3 + - + +
165D ASP 3.5 6.3 - - - +
166D PRO* 3.1 42.4 + - + +
168D CYS* 4.0 13.5 - - - -
169D LEU* 3.5 28.1 - - + +
176D LYS* 4.9 14.3 - - - +
179D HIS* 2.9 35.5 + - - -
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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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11D ARG* 3.7 26.7 - - - +
159D ASP* 3.1 21.5 + - - +
160D VAL* 3.5 10.5 - - - +
161D HIS 3.3 0.2 - - - -
162D GLN* 1.3 78.1 - - - +
164D LEU* 1.3 64.3 + - - +
166D PRO* 4.3 6.8 - - - +
196D ASP* 6.2 0.2 - - - +
202D VAL* 4.0 15.0 - - + -
208D GLN* 3.9 41.0 - - + +
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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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101D TYR* 4.3 10.3 - - + -
104D MET* 3.7 32.5 - - + -
105D ILE* 4.4 4.3 - - + -
109D TYR* 4.4 3.8 - - + -
113D LYS* 4.0 27.3 + - + -
116D TYR* 3.8 25.1 - - + -
117D ILE* 3.9 22.9 - - + +
121D LEU* 5.1 1.6 - - + -
160D VAL 3.2 12.6 + - - +
161D HIS* 3.2 15.7 + - + +
163D ILE* 1.3 80.1 - - - +
165D ASP* 1.3 57.8 + - - +
166D PRO* 4.1 2.5 - - - +
208D GLN 3.9 26.0 - - - -
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Residues in contact with ASP 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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117D ILE* 3.3 42.0 - - + +
121D LEU* 4.9 2.6 - - + +
161D HIS 2.9 16.7 + - - +
162D GLN* 3.3 3.1 - - - -
164D LEU* 1.3 78.5 - - + +
166D PRO* 1.3 69.2 - - - +
167D HIS* 3.3 17.5 + - - +
168D CYS* 3.0 40.3 + - + +
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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