Contacts of the helix formed by residues 150 - 164 (chain D) in PDB entry 1UMD
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 THR 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D MET* 3.7 7.1 - - - +
149D SER* 1.3 87.6 + - - +
151D PRO* 1.3 70.2 - - - +
152D TYR* 3.7 3.5 + - - +
153D ASP* 2.7 30.3 + - - +
154D ALA* 2.9 28.8 + - - +
180D VAL* 6.0 0.2 - - - -
182D GLU* 3.5 13.2 + - - +
199D ARG* 3.8 29.2 + - - +
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Residues in contact with PRO 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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4D MET 3.5 25.6 - - - +
5D THR 3.8 8.5 - - - +
6D MET* 3.6 28.0 - - + +
9D ALA* 3.2 10.2 - - + +
150D THR* 1.3 82.9 - - - +
152D TYR* 1.3 60.6 + - - +
154D ALA* 3.2 1.4 + - + -
155D LYS* 3.1 20.1 + - - +
176D LEU 5.8 0.9 - - - +
180D VAL* 3.8 23.1 - - + +
182D GLU* 3.3 22.4 - - + +
184D VAL* 3.6 15.4 - - + +
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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
----------------------------------------------------------
150D THR* 4.0 2.7 - - - +
151D PRO* 1.3 76.7 - - - +
153D ASP* 1.3 69.4 + - - +
156D GLY 3.2 9.4 + - - -
182D GLU* 3.0 28.5 + - - +
183D GLU 4.2 6.7 - - - +
184D VAL* 3.7 4.8 - - - +
185D PRO* 3.8 25.6 - - + -
189D TYR* 2.8 64.1 + + - +
191D LEU* 3.7 29.5 - - + +
199D ARG* 6.2 1.1 - - - -
237D ARG* 5.8 0.2 - - - -
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Residues in contact with ASP 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D VAL* 4.1 10.8 - - + -
149D SER* 4.7 0.8 + - - +
150D THR* 2.7 20.9 + - - +
152D TYR* 1.3 80.7 - - - +
154D ALA* 1.3 59.2 + - - +
157D LEU* 2.8 48.8 + - + +
191D LEU* 3.4 10.8 - - - +
199D ARG* 2.3 37.6 + - - -
235D ASP* 4.3 0.9 - - - +
237D ARG* 2.8 34.4 + - - -
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D MET* 3.8 19.3 - - + -
9D ALA* 4.4 2.7 - - + -
10D LEU* 3.6 25.7 - - + +
148D VAL* 4.0 17.0 - - + +
150D THR 2.9 14.1 + - - +
151D PRO* 3.4 10.1 - - + +
153D ASP* 1.3 75.6 - - - +
155D LYS* 1.3 62.6 + - - +
158D LEU* 3.0 29.5 + - - +
170D PHE* 3.8 1.4 - - - -
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Residues in contact with LYS 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ALA* 3.6 24.4 - - + +
12D ARG* 4.2 12.7 - - + +
13D ALA* 3.8 7.0 - - + +
16D GLU* 2.7 41.5 + - - +
151D PRO 3.1 9.4 + - - +
154D ALA* 1.3 80.5 - - - +
156D GLY* 1.3 63.8 + - - +
159D LYS* 3.1 42.3 + - + +
184D VAL* 3.8 12.6 - - + -
185D PRO 2.7 22.2 + - - -
186D GLU* 3.3 5.3 + - - +
187D GLU 3.2 14.6 + - - -
189D TYR* 3.6 29.8 - - + +
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Residues in contact with GLY 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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152D TYR 3.2 8.5 + - - -
153D ASP 3.9 1.1 - - - -
155D LYS* 1.3 80.1 - - - +
157D LEU* 1.3 56.8 + - - +
159D LYS* 3.7 0.7 + - - +
160D ALA* 3.2 18.5 + - - +
189D TYR* 3.6 28.7 - - - -
190D THR* 3.5 3.3 - - - -
191D LEU* 3.2 30.4 + - - -
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Residues in contact with LEU 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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146D VAL* 4.0 15.7 - - + +
148D VAL* 3.9 18.8 - - + -
153D ASP* 2.8 23.4 + - + +
156D GLY* 1.3 70.1 - - - -
158D LEU* 1.3 59.9 + - - +
159D LYS 3.2 1.1 - - - -
160D ALA* 3.2 2.4 + - - +
161D ALA* 2.8 29.5 + - - +
170D PHE* 3.8 15.5 - - + -
191D LEU* 3.6 32.1 - - + +
192D PRO 3.7 19.5 - - - +
193D ILE* 4.0 15.8 - - + +
237D ARG* 4.0 34.5 - - + +
238D THR* 5.1 1.6 - - - +
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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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10D LEU* 3.8 38.8 - - + +
13D ALA* 4.1 9.9 - - + -
14D LEU* 4.0 18.8 - - + -
78D VAL* 5.0 0.9 - - + -
114D VAL* 4.3 21.5 - - + -
116D ARG* 4.4 15.0 - - - -
154D ALA 3.0 19.2 + - - +
157D LEU* 1.3 76.9 - - - +
159D LYS* 1.3 61.8 + - - +
161D ALA* 3.3 2.0 + - + -
162D ILE* 3.0 42.9 + - + +
170D PHE* 3.6 28.1 - - + -
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Residues in contact with LYS 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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13D ALA* 3.7 15.9 - - + -
16D GLU* 2.8 31.4 + - - +
17D GLU* 2.6 38.7 + - + +
155D LYS* 3.1 30.5 + - + +
156D GLY 3.8 3.8 - - - +
158D LEU* 1.3 77.4 - - - +
160D ALA* 1.3 61.9 + - - +
162D ILE* 3.3 3.3 + - - +
163D ARG* 3.2 34.5 + - - +
188D ASP* 2.6 29.8 + - - -
189D TYR 3.1 30.7 - - - +
190D THR* 4.2 6.3 - - + -
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Residues in contact with ALA 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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156D GLY 3.2 9.2 + - - +
157D LEU 3.5 8.1 - - - +
159D LYS* 1.3 80.0 - - - +
161D ALA* 1.3 57.5 + - - +
163D ARG* 3.2 6.9 + - - +
164D ASP* 2.9 28.8 + - - +
190D THR* 4.4 10.7 - - - +
191D LEU 3.2 26.9 - - - +
193D ILE* 3.9 16.5 - - + +
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Residues in contact with ALA 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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113D LEU 5.4 0.2 - - - +
114D VAL* 3.6 26.3 - - + +
146D VAL* 6.0 0.2 - - + -
157D LEU 2.8 17.2 + - - +
158D LEU* 3.5 9.2 - - - +
160D ALA* 1.3 77.6 - - - +
162D ILE* 1.3 61.6 + - - +
164D ASP* 3.1 22.3 + - - +
166D ASP 4.9 0.2 - - - +
168D VAL* 4.0 25.3 - - + +
170D PHE* 4.5 5.6 - - + -
193D ILE* 3.7 12.1 - - + +
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Residues in contact with ILE 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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13D ALA 4.7 1.8 - - - +
14D LEU* 4.1 18.4 - - + -
17D GLU* 3.7 35.7 - - + +
24D VAL* 3.8 31.0 - - + -
76D ARG* 3.3 30.1 + - + +
78D VAL* 3.9 27.8 - - + -
112D PRO 5.6 1.2 - - - +
114D VAL* 4.0 11.0 - - + -
158D LEU* 3.0 26.3 + - + +
159D LYS 3.7 4.5 - - - +
160D ALA 3.3 0.2 - - - -
161D ALA* 1.3 76.2 - - - +
163D ARG* 1.3 56.9 + - + +
164D ASP 4.0 1.0 - - - +
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Residues in contact with ARG 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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17D GLU* 2.9 37.6 + - - +
20D LYS* 2.9 31.3 - - - +
76D ARG* 3.1 19.0 + - - +
159D LYS* 3.2 17.4 + - - +
160D ALA* 3.8 5.8 - - - +
162D ILE* 1.3 76.7 - - + +
164D ASP* 1.3 64.7 + - - +
165D GLU* 3.2 8.3 + - - +
188D ASP* 3.0 26.1 + - - -
190D THR* 3.4 27.3 - - - +
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Residues in contact with ASP 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 3.6 6.7 + - - -
112D PRO* 4.3 7.1 - - - +
113D LEU 5.6 0.5 - - - +
144D LYS* 2.7 31.6 + - - +
160D ALA 2.9 16.5 + - - +
161D ALA* 3.1 19.3 + - - +
162D ILE 4.0 0.9 - - - +
163D ARG* 1.3 79.0 - - - +
165D GLU* 1.3 62.7 + - - +
166D ASP* 2.9 47.4 + - - +
168D VAL* 4.5 1.1 - - + -
193D ILE* 3.8 13.7 - - + +
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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