Contacts of the helix formed by residues 172 - 185 (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 PHE 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D PRO* 3.3 31.0 - - + -
125D LEU* 3.7 20.0 - - + -
126D ALA* 3.6 25.1 - - + -
129D GLU* 3.4 31.2 - - + +
168D CYS 3.4 27.6 - - - -
169D LEU* 2.9 14.7 + - + +
170D ASP 3.2 0.2 - - - -
171D LYS* 1.3 113.6 - - + +
173D PRO* 1.3 60.0 - - - +
174D LEU 3.4 2.7 - - - -
175D LEU* 3.2 15.2 + - + +
176D LYS 3.0 22.7 + - - -
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Residues in contact with PRO 173 (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 GLU* 3.2 11.0 - - - +
169D LEU 4.8 0.4 - - - +
170D ASP 4.7 4.2 - - - +
171D LYS 3.4 10.5 - - - +
172D PHE* 1.3 84.4 - - - +
174D LEU* 1.3 64.4 + - + +
176D LYS* 3.8 8.5 - - + +
177D VAL* 2.9 40.1 + - + +
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Residues in contact with LEU 174 (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 GLU* 3.0 33.1 + - + +
132D LEU* 3.8 11.4 - - + +
133D ALA* 3.7 32.1 - - + +
137D ASN 3.7 13.9 - - - +
138D GLY* 3.6 25.0 - - - +
139D ARG* 4.4 10.8 - - + -
173D PRO* 1.3 81.0 - - + +
175D LEU* 1.3 57.7 + - - +
177D VAL* 3.5 5.3 + - + +
178D PHE* 2.9 30.1 + - - +
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Residues in contact with LEU 175 (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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125D LEU* 3.4 46.9 - - + +
128D PHE* 3.9 24.0 - - + -
129D GLU* 3.0 22.5 + - - +
132D LEU* 3.9 18.2 - - + -
154D LEU* 4.4 9.4 - - + -
158D LEU* 3.6 27.4 - - + +
169D LEU* 4.0 7.6 - - + -
172D PHE* 3.2 16.1 + - + +
174D LEU* 1.3 73.0 - - - +
176D LYS* 1.3 66.3 + - - +
178D PHE* 3.7 3.1 - - - +
179D HIS* 3.0 25.8 + - - +
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Residues in contact with LYS 176 (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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162D GLN* 4.9 12.8 - - - +
169D LEU* 3.8 33.3 - - + +
170D ASP* 5.0 12.8 - - - +
172D PHE 3.0 15.9 + - - +
173D PRO* 3.8 8.1 - - + +
174D LEU 3.3 0.2 - - - -
175D LEU* 1.3 76.2 - - - +
177D VAL* 1.3 66.0 + - + +
179D HIS* 3.3 5.4 + - + +
180D GLN* 3.1 22.7 + - + +
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Residues in contact with VAL 177 (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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138D GLY 6.0 0.7 - - - +
139D ARG* 5.0 7.0 - - - +
173D PRO* 2.9 30.3 + - + +
174D LEU* 3.9 5.6 - - + +
176D LYS* 1.3 76.2 - - + +
178D PHE* 1.3 59.3 + - - +
180D GLN* 3.3 6.3 + - - +
181D ARG* 2.9 53.0 + - - +
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Residues in contact with PHE 178 (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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132D LEU* 4.1 15.0 - - + -
138D GLY 5.4 1.3 + - - +
140D ASN 3.5 21.5 - - - +
141D LEU* 4.0 11.9 - - + -
142D ILE 4.5 1.6 - - - -
151D ASP* 3.3 43.3 - - - -
154D LEU* 3.6 33.7 - - + -
155D PHE* 3.7 15.5 - - - -
158D LEU* 3.8 14.6 - - + -
174D LEU 2.9 19.1 + - - +
175D LEU 3.7 2.9 - - - +
177D VAL* 1.3 74.4 - - - +
179D HIS* 1.3 68.5 + - - +
181D ARG* 3.2 6.9 + - - +
182D MET* 3.0 43.4 + - + +
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Residues in contact with HIS 179 (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* 3.1 33.6 + + - -
158D LEU* 4.0 16.2 - - + -
159D ASP* 2.9 34.5 + - + +
162D GLN* 2.9 39.6 + - + -
169D LEU* 4.3 4.3 - - + -
175D LEU 3.0 18.2 + - - +
176D LYS* 3.6 5.2 - - + +
177D VAL 3.3 0.2 - - - -
178D PHE* 1.3 82.5 - - - +
180D GLN* 1.3 66.5 + - + +
182D MET 3.6 0.2 + - - -
183D LYS* 3.2 33.0 + - + +
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Residues in contact with GLN 180 (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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176D LYS* 3.1 17.0 + - + +
177D VAL* 3.8 7.0 - - - +
179D HIS* 1.3 81.9 - - + +
181D ARG* 1.3 59.8 + - - +
183D LYS* 3.2 21.9 + - - +
184D ASP* 2.8 70.4 + - - +
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Residues in contact with ARG 181 (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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139D ARG* 2.8 28.7 + - - +
140D ASN* 3.2 38.4 + - - +
141D LEU* 4.4 9.0 - - + -
177D VAL* 2.9 38.2 + - - +
178D PHE* 3.2 8.1 + - - +
180D GLN* 1.3 76.6 - - - +
182D MET* 1.3 63.1 + - + +
184D ASP* 3.3 15.9 + - - +
185D ARG* 3.4 17.1 + - + +
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Residues in contact with MET 182 (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* 3.9 24.9 - - + -
147D ILE* 4.1 5.8 - - + -
151D ASP* 3.8 24.2 - - + +
152D TYR* 3.7 35.0 - - + -
155D PHE* 3.6 24.7 - - + -
178D PHE* 3.0 40.5 + - + +
181D ARG* 1.3 76.4 - - - +
183D LYS* 1.3 62.1 + - - +
185D ARG* 3.2 25.1 + - - +
188D LEU* 3.4 32.5 - - + +
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Residues in contact with LYS 183 (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* 3.8 18.5 - - + -
159D ASP* 4.9 7.0 + - - +
179D HIS* 3.2 34.0 + - + +
180D GLN* 3.2 24.0 + - - +
182D MET* 1.3 78.4 - - - +
184D ASP* 1.3 58.5 + - - +
188D LEU* 4.8 2.0 - - - -
189D LYS* 3.2 33.7 + - + +
192D CYS* 4.6 21.8 - - + -
196D ASP* 4.9 11.1 + - - -
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Residues in contact with ASP 184 (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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180D GLN* 2.8 50.8 + - - +
181D ARG* 3.7 8.1 - - - +
182D MET 3.2 0.4 - - - -
183D LYS* 1.3 76.6 - - - +
185D ARG* 1.3 65.7 + - - +
186D PRO* 3.2 8.7 - - - +
189D LYS* 4.5 18.8 + - - +
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Residues in contact with ARG 185 (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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23D ASP* 3.0 45.1 + - - +
24D GLN* 4.7 2.8 - - - +
141D LEU* 4.3 14.3 - - - +
147D ILE* 3.4 30.5 - - - +
181D ARG* 3.4 11.3 + - + +
182D MET* 3.2 37.5 + - - +
184D ASP* 1.3 74.9 - - - +
186D PRO* 1.3 70.4 - - + +
187D LYS 3.3 0.9 - - - -
188D LEU* 3.0 9.6 + - + -
189D LYS 2.8 24.9 + - - -
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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