Contacts of the helix formed by residues 147 - 161 (chain B) in PDB entry 3UGV
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 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LYS* 1.3 79.2 - - - +
148B PRO* 1.3 76.7 - - - +
149B ALA* 4.0 4.3 + - - +
150B GLU* 3.1 33.8 + - - +
151B VAL* 3.0 17.0 + - - +
176B ARG* 5.3 0.9 - - - +
181B VAL* 5.7 0.2 - - - -
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Residues in contact with PRO 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B SER* 1.3 87.6 - - - +
149B ALA* 1.3 64.4 + - - +
151B VAL* 3.2 2.4 + - - +
152B ALA* 2.9 24.3 + - - +
181B VAL* 4.1 19.3 - - + -
184B GLU* 3.7 27.8 - - + +
185B THR* 3.6 40.4 - - + +
188B ALA* 4.2 13.9 - - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B SER* 3.4 5.2 + - - +
148B PRO* 1.3 80.4 - - - +
150B GLU* 1.3 64.0 + - + +
152B ALA* 3.3 6.6 + - - +
153B ALA* 3.1 22.0 + - - +
188B ALA* 5.5 1.6 - - - -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LYS* 3.9 31.9 + - + +
147B SER* 3.1 35.3 + - - +
148B PRO 3.3 0.2 - - - -
149B ALA* 1.3 79.1 - - + +
151B VAL* 1.3 62.7 + - - +
153B ALA* 3.3 6.1 + - - +
154B GLU* 3.1 24.3 + - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.5 25.1 - - + +
144B TRP 3.6 18.2 - - - +
146B LYS* 3.2 37.7 - - + +
147B SER 3.0 6.4 + - - +
148B PRO 3.7 4.0 - - - +
150B GLU* 1.3 75.6 - - - +
152B ALA* 1.3 58.1 + - - +
154B GLU* 3.3 5.4 + - - -
155B ALA* 2.9 25.6 + - - +
172B LEU* 4.0 8.7 - - + -
176B ARG* 3.8 5.8 - - - +
185B THR* 3.6 20.9 - - + -
189B VAL* 3.6 13.7 - - + -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PRO 2.9 13.2 + - - +
149B ALA* 3.5 12.1 - - - +
151B VAL* 1.3 77.1 - - - +
153B ALA* 1.3 64.1 + - - +
155B ALA* 3.2 16.0 + - - +
156B VAL* 3.4 12.3 + - - +
188B ALA* 3.5 29.8 - - + +
189B VAL* 4.2 12.1 - - - +
192B ALA* 3.8 10.2 - - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ALA 3.1 10.8 + - - +
150B GLU* 3.7 8.7 - - - +
152B ALA* 1.3 78.4 - - - +
154B GLU* 1.3 63.6 + - - +
156B VAL* 3.2 23.0 + - - +
157B GLU* 3.6 14.4 + - - +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 3.5 32.2 + - - +
142B GLY* 3.5 10.7 - - - -
143B LEU* 3.0 31.9 + - + -
144B TRP* 4.7 1.0 + - - -
146B LYS* 2.9 27.8 + - - -
150B GLU 3.1 15.7 + - - +
151B VAL* 3.7 5.2 - - - +
153B ALA* 1.3 76.1 - - - +
155B ALA* 1.3 64.4 - - - +
157B GLU* 3.1 18.5 + - - +
158B LEU* 2.9 26.0 + - + +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.8 12.7 - - + +
151B VAL 2.9 13.8 + - - +
152B ALA* 3.4 11.7 - - - +
153B ALA 3.2 0.2 - - - -
154B GLU* 1.3 76.9 - - - +
156B VAL* 1.3 56.8 + - - +
158B LEU* 3.0 6.5 + - - +
159B LYS* 2.8 30.7 + - - +
170B LEU* 4.0 9.8 - - + +
189B VAL* 4.0 21.8 - - + +
193B VAL* 3.8 18.4 - - + +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA 3.6 13.9 - - - +
153B ALA* 3.4 11.7 - - - +
154B GLU 3.2 0.4 - - - -
155B ALA* 1.3 78.5 - - - +
157B GLU* 1.3 62.9 + - + +
159B LYS* 3.6 4.0 + - - +
160B ALA* 3.3 20.5 + - + +
192B ALA* 4.0 26.9 - - + +
193B VAL* 3.8 8.7 - - + +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 3.2 30.6 + - - +
153B ALA* 3.8 15.0 - - - +
154B GLU* 3.1 17.9 + - - +
156B VAL* 1.3 77.1 - - + +
158B LEU* 1.3 64.8 + - - +
160B ALA* 3.0 9.0 + - - +
161B GLU* 3.0 25.6 + - + +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 3.9 17.7 - - - +
139B ASN* 3.1 32.3 + - - +
141B ASN* 3.9 12.8 - - + +
142B GLY 3.7 23.6 - - - +
143B LEU* 4.0 27.1 - - + -
154B GLU* 2.9 21.9 + - + +
155B ALA* 3.0 7.4 + - - +
157B GLU* 1.3 74.5 - - - +
159B LYS* 1.3 68.7 + - - +
160B ALA 3.2 0.3 + - - -
161B GLU* 3.0 31.1 + - - +
167B PHE* 3.2 6.6 - - - -
170B LEU* 3.8 15.3 - - + -
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ALA 2.8 17.5 + - - +
156B VAL* 3.9 5.2 - - - +
158B LEU* 1.3 70.1 - - - +
160B ALA* 1.3 62.4 + - - +
162B GLY 3.2 4.9 + - - -
165B THR 4.0 15.4 + - - +
166B GLY* 3.2 7.1 - - - -
167B PHE* 2.9 55.6 + - - +
168B LYS* 4.7 2.8 - - - +
170B LEU* 3.8 13.5 - - + +
193B VAL* 4.2 27.1 - - + +
196B ASP* 5.4 2.8 - - - +
197B THR* 2.8 33.0 + - + +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 3.3 10.9 + - + +
157B GLU* 3.0 13.1 + - - +
159B LYS* 1.3 75.1 - - - +
161B GLU* 1.3 55.8 + - - +
162B GLY 2.8 11.5 + - - -
163B GLN* 2.9 21.5 + - - +
166B GLY* 5.1 2.5 - - - -
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 4.5 4.9 + - - +
21B ARG* 3.2 26.7 + - - +
139B ASN* 2.8 30.5 + - - +
141B ASN* 3.0 19.8 + - - -
157B GLU 3.0 14.6 + - - +
158B LEU* 3.0 22.9 + - - +
160B ALA* 1.3 74.7 - - - +
162B GLY* 1.3 57.3 + - - +
163B GLN* 3.2 13.9 + - - +
167B PHE* 3.8 3.1 - - + -
325B TRP* 4.3 8.9 - - + -
327B SER* 4.7 2.1 + - - -
339B LEU* 3.2 17.2 - - - +
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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