Contacts of the helix formed by residues 154 - 171 (chain D) in PDB entry 3HUU
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 TYR 154 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LYS* 3.4 54.0 + - + +
89D TYR* 3.7 25.7 - + + -
90D SER 3.4 17.5 - - - +
91D LEU* 3.9 26.8 - - + +
150D GLU* 6.1 1.6 - - - -
151D SER 5.1 3.4 - - - -
152D GLY* 3.6 11.0 - - - -
153D HIS* 1.3 86.4 - - - +
155D ALA* 1.3 65.8 + - - +
156D VAL* 3.3 14.7 + - + -
157D THR* 3.3 11.7 + - - +
158D GLU* 3.2 17.9 + - - +
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D SER* 3.1 36.1 + - - +
91D LEU* 4.7 1.0 - - - +
112D LYS* 4.4 16.8 - - + +
114D LEU* 3.8 23.1 - - + +
153D HIS 3.5 3.0 + - - -
154D TYR* 1.3 71.4 - - - +
156D VAL* 1.3 57.9 + - - +
158D GLU* 3.2 7.5 + - - +
159D ASP* 2.8 36.9 + - - +
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LYS* 5.2 7.0 - - - +
90D SER* 4.9 1.2 + - - +
126D ASN* 3.9 16.8 - - - +
150D GLU* 5.2 4.3 - - - +
154D TYR* 4.2 13.0 - - + -
155D ALA* 1.3 78.7 - - - +
157D THR* 1.3 81.6 + - - +
159D ASP* 3.3 4.5 + - - +
160D ARG* 3.1 62.9 + - - +
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Residues in contact with THR 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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147D PHE* 4.8 0.7 - - - -
149D GLN* 3.3 35.0 - - + +
150D GLU* 3.3 46.0 + - + +
151D SER 5.2 1.0 + - - -
152D GLY 5.5 4.3 - - - +
154D TYR* 3.3 15.4 + - - +
156D VAL* 1.3 82.2 - - - +
158D GLU* 1.3 64.5 + - - +
160D ARG* 3.6 6.4 + - - +
161D SER* 3.3 22.7 + - - -
207D SER* 3.8 12.6 - - - +
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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
----------------------------------------------------------
149D GLN* 5.1 8.0 + - - +
153D HIS* 5.3 6.3 - - - +
154D TYR 3.2 10.3 + - - +
155D ALA* 3.2 12.5 + - - +
157D THR* 1.3 77.1 - - - +
159D ASP* 1.3 67.1 + - - +
161D SER* 2.8 28.2 + - - -
162D VAL* 3.1 32.2 + - - +
165D LYS* 4.3 6.6 + - - -
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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
----------------------------------------------------------
112D LYS* 2.7 50.5 + - - +
123D ASP* 4.5 5.0 - - - +
126D ASN* 3.5 30.0 + - + +
127D ILE* 3.6 23.2 - - + +
155D ALA 2.8 20.5 + - - +
156D VAL* 3.6 1.7 - - - +
158D GLU* 1.3 80.3 - - - +
160D ARG* 1.3 62.0 + - - +
162D VAL* 3.2 7.9 + - - +
163D GLY 3.0 18.5 + - - -
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Residues in contact with ARG 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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124D ASN* 5.2 0.6 - - - +
126D ASN* 2.8 39.5 + - + +
130D ALA* 3.1 19.6 - - + +
147D PHE* 3.8 16.1 - - + -
150D GLU* 5.2 2.0 + - - -
156D VAL* 3.1 35.9 + - - +
157D THR* 4.1 3.4 - - - +
158D GLU 3.3 0.4 - - - -
159D ASP* 1.3 74.1 - - - +
161D SER* 1.3 64.1 + - - +
164D PHE* 3.0 21.7 + - - +
207D SER* 2.7 36.5 + - - +
208D ASP* 4.5 8.9 + - - +
235D PHE* 3.4 40.1 - - + +
236D ASN* 5.9 0.6 - - - +
253D ILE* 4.0 30.3 - - - +
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Residues in contact with SER 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PHE* 3.8 15.2 - - - -
149D GLN* 3.4 26.0 + - - -
157D THR 3.3 10.9 + - - -
158D GLU* 2.8 26.5 + - - -
160D ARG* 1.3 77.0 - - - +
162D VAL* 1.3 55.9 + - - +
164D PHE* 3.3 2.6 + - - +
165D LYS* 2.9 49.1 + - - +
177D CYS* 3.9 12.8 - - - -
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ILE* 4.2 24.5 - - + -
158D GLU* 3.1 36.5 + - - +
159D ASP* 3.4 11.2 - - - +
161D SER* 1.3 82.2 + - - +
163D GLY* 1.3 60.2 + - - +
165D LYS* 3.5 14.6 + - - +
166D GLN* 2.9 33.8 + - + +
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Residues in contact with GLY 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ILE* 3.3 34.5 - - - -
130D ALA* 4.2 0.4 - - - -
131D TYR* 3.6 19.2 - - - -
159D ASP 3.0 11.2 + - - -
160D ARG 3.3 2.9 + - - -
161D SER 3.3 0.2 - - - -
162D VAL* 1.3 73.6 - - - +
164D PHE* 1.3 64.8 + - - +
166D GLN* 3.4 4.7 + - - +
167D TYR* 3.1 17.8 + - - +
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Residues in contact with PHE 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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130D ALA* 3.9 3.4 - - + +
134D THR* 3.5 27.4 - - + +
145D ILE* 3.5 44.9 - - + -
147D PHE* 3.5 31.4 - + + -
160D ARG 3.0 13.1 + - - +
161D SER 3.5 7.2 - - - +
163D GLY* 1.3 74.1 - - - +
165D LYS* 1.3 75.0 + - + +
167D TYR* 3.2 3.6 + - - +
168D CYS* 3.1 44.2 + - - -
175D ASN* 3.7 20.2 - - - -
176D ASP 3.5 21.3 - - - -
177D CYS* 4.6 2.0 - - + -
205D ILE* 4.0 9.6 - - + -
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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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149D GLN* 5.6 0.4 + - - -
158D GLU* 4.3 6.1 + - - -
161D SER* 2.9 45.9 + - - +
162D VAL* 3.7 16.3 - - - +
164D PHE* 1.3 89.0 - - + +
166D GLN* 1.3 62.4 + - - +
168D CYS* 3.5 1.9 + - - +
169D ASP* 3.1 25.3 + - - +
175D ASN* 4.1 32.7 + - + +
177D CYS* 4.7 14.8 - - + -
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Residues in contact with GLN 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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127D ILE* 4.1 22.2 - - - +
131D TYR* 3.5 22.2 - - + -
162D VAL* 2.9 25.7 + - + +
163D GLY 3.5 5.2 - - - +
164D PHE 3.2 0.2 - - - -
165D LYS* 1.3 77.8 - - - +
167D TYR* 1.3 62.8 + - - +
169D ASP* 3.5 5.6 + - - +
170D ASP* 3.1 35.8 + - - +
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Residues in contact with TYR 167 (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 TYR* 3.4 50.0 - + + +
134D THR* 3.5 29.6 - - + -
135D GLN* 3.5 24.4 + - + +
138D TYR* 3.3 43.1 - + + +
139D HIS* 3.7 13.2 - - - -
163D GLY 3.1 9.9 + - - +
164D PHE 3.2 7.6 + - - +
166D GLN* 1.3 77.0 - - - +
168D CYS* 1.3 66.2 + - - +
170D ASP* 2.9 13.9 + - - +
171D VAL* 3.0 43.1 + - + +
173D ILE* 4.7 1.3 - - + -
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Residues in contact with CYS 168 (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 THR* 4.4 2.7 - - - -
145D ILE* 5.4 0.2 - - - -
164D PHE* 3.1 46.7 + - - +
165D LYS 3.8 0.9 - - - +
167D TYR* 1.3 77.9 - - - +
169D ASP* 1.3 57.5 + - - +
172D LYS* 2.9 23.7 + - - -
173D ILE* 2.9 50.6 + - + +
174D SER 3.3 20.2 - - - +
175D ASN* 3.7 15.3 - - + -
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Residues in contact with ASP 169 (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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165D LYS 3.1 18.8 + - - +
166D GLN* 3.6 7.0 - - - +
168D CYS* 1.3 75.6 - - - +
170D ASP* 1.3 73.3 + - - +
172D LYS* 3.1 31.6 + - - +
173D ILE 5.3 0.2 - - - -
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Residues in contact with ASP 170 (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 TYR* 2.6 37.5 + - - +
166D GLN* 3.1 22.6 + - - +
167D TYR* 2.9 10.1 + - - +
169D ASP* 1.3 85.7 - - - +
171D VAL* 1.3 61.5 + - + +
172D LYS* 2.8 19.3 + - - +
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Residues in contact with VAL 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D TYR* 3.7 31.5 + - + +
167D TYR* 3.0 48.7 + - + +
170D ASP* 1.3 78.3 - - + +
172D LYS* 1.3 72.1 + - - +
173D ILE* 3.6 37.4 - - + +
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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
------------------------------------------------------------
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