Contacts of the helix formed by residues 145 - 159 (chain D) in PDB entry 4RDU
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 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D ILE 3.6 1.8 + - - -
144D TYR* 1.3 75.9 - - - +
146D SER* 1.3 59.2 + - - +
147D PHE* 3.6 10.9 + - - +
148D GLN* 3.0 42.2 + - - +
149D LEU* 2.9 28.7 + - - +
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Residues in contact with SER 146 (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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157A GLN 5.5 6.1 - - - -
160A GLN* 3.9 22.8 + - - +
145D SER* 1.3 71.3 - - - +
147D PHE* 1.3 59.4 + - - +
149D LEU* 4.0 10.6 - - - +
150D ALA* 3.0 31.5 + - - +
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Residues in contact with PHE 147 (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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145D SER* 3.2 9.9 + - - +
146D SER* 1.3 82.9 + - - +
148D GLN* 1.3 66.8 + - + +
150D ALA* 3.9 4.3 - - - +
151D ALA* 3.3 23.9 + - + +
173D SER 4.4 11.0 - - - -
174D LEU* 3.6 30.5 - - + -
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Residues in contact with GLN 148 (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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142D THR* 5.5 0.5 - - - +
143D ILE 4.4 1.9 - - - +
144D TYR* 3.5 21.8 - - + -
145D SER* 3.0 39.8 + - - +
147D PHE* 1.3 80.9 - - + +
149D LEU* 1.3 66.8 + - - +
151D ALA* 3.4 1.9 + - - +
152D LEU* 3.0 30.9 + - - +
174D LEU* 3.0 40.6 + - + +
175D GLY 4.4 3.6 + - - -
176D LEU* 3.4 25.9 - - + +
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Residues in contact with LEU 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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157A GLN 4.9 4.5 - - - +
158A LYS* 3.9 22.4 - - + +
160A GLN* 6.1 1.6 - - + -
144D TYR* 3.4 38.8 - - + +
145D SER 2.9 21.6 + - - +
146D SER* 4.0 7.6 - - - +
147D PHE 3.4 0.2 - - - -
148D GLN* 1.3 77.5 - - - +
150D ALA* 1.3 59.0 + - - +
152D LEU* 3.3 4.0 + - + +
153D GLN* 2.8 52.1 + - - +
184D TRP* 4.0 20.2 - - - +
6F A 4.3 6.7 - - - +
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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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160A GLN* 3.5 28.7 - - + +
161A TYR* 3.4 15.4 - - + -
146D SER 3.0 19.6 + - - +
147D PHE* 3.9 6.1 - - + +
149D LEU* 1.3 79.2 - - - +
151D ALA* 1.3 55.7 + - - +
153D GLN* 3.9 9.2 + - - -
154D ARG* 2.9 31.7 + - - +
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Residues in contact with ALA 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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147D PHE* 3.3 14.6 + - + +
148D GLN 3.8 1.6 - - - +
149D LEU 3.3 0.2 - - - -
150D ALA* 1.3 78.7 - - - +
152D LEU* 1.3 62.7 + - - +
154D ARG* 3.9 5.0 - - - +
155D ARG* 3.1 23.9 + - - +
170D LEU* 4.8 8.1 - - + +
174D LEU* 3.5 35.7 - - + -
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Residues in contact with LEU 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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144D TYR* 4.4 18.4 - - + -
148D GLN 3.0 26.1 + - - +
149D LEU* 3.7 6.3 - - + +
151D ALA* 1.3 75.7 - - - +
153D GLN* 1.3 58.4 + - - +
155D ARG* 3.4 5.6 + - - +
156D PHE* 2.9 29.6 + - - +
170D LEU* 4.4 5.8 - - + -
174D LEU* 3.9 16.6 - - + -
176D LEU* 4.4 5.2 - - + -
181D VAL* 4.2 21.3 - - + -
184D TRP* 3.6 48.1 - - + +
185D PHE* 4.0 23.3 - - + -
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Residues in contact with GLN 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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158A LYS 2.9 25.9 + - - +
159A THR* 3.5 16.9 + - + +
160A GLN* 2.9 24.9 + - - +
161A TYR* 3.5 21.1 + - + +
149D LEU* 2.8 38.9 + - - +
150D ALA* 3.8 4.4 - - - +
152D LEU* 1.3 74.9 - - - +
154D ARG* 1.3 64.3 + - - +
156D PHE* 3.4 5.4 + - - +
157D GLN* 3.2 24.4 + - - +
184D TRP* 3.7 23.8 - - + -
188D LYS* 4.8 9.9 - - - +
5F T 5.7 1.6 + - - -
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Residues in contact with ARG 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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161A TYR* 3.8 31.7 - - + +
3B A 4.1 14.6 + - - +
4B C 3.5 36.6 + - - +
150D ALA 2.9 19.0 + - - +
151D ALA* 3.9 6.1 - - - +
153D GLN* 1.3 75.0 - - - +
155D ARG* 1.3 64.2 + - - +
157D GLN* 2.8 58.8 + - - +
158D LYS* 3.6 41.0 + - - +
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Residues in contact with ARG 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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151D ALA 3.1 18.4 + - - +
152D LEU 3.7 4.0 - - - +
154D ARG* 1.3 78.1 - - - +
156D PHE* 1.3 55.5 + - - +
158D LYS* 2.9 26.7 + - - +
159D THR* 2.9 37.7 + - + +
162D LEU* 4.0 7.2 - - + -
166D GLU* 3.0 42.5 + - - +
169D GLU* 6.1 4.6 - - - +
170D LEU* 3.9 42.6 - - + +
185D PHE* 4.1 3.6 - - + -
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Residues in contact with PHE 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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163A ALA* 4.5 13.7 - - + -
152D LEU 2.9 17.6 + - - +
153D GLN* 3.6 7.2 - - - +
154D ARG 3.3 0.4 - - - -
155D ARG* 1.3 73.2 - - - +
157D GLN* 1.3 60.7 + - + +
159D THR 3.4 6.2 - - - +
160D GLN* 2.8 55.7 + - + -
184D TRP* 4.1 9.2 - + + -
185D PHE* 3.7 23.1 - + + -
188D LYS* 3.5 42.4 - - + -
189D ARG* 3.8 27.6 - - + -
192D ILE* 3.7 27.8 - - + -
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Residues in contact with GLN 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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161A TYR* 3.8 15.2 - - - +
162A LEU 2.8 31.2 + - - +
163A ALA* 4.9 6.1 - - - +
3B A 3.5 10.9 + - - -
4B C 2.8 29.5 + - - +
153D GLN 3.2 11.6 + - - +
154D ARG* 2.8 50.0 + - - +
155D ARG 3.1 0.8 - - - -
156D PHE* 1.3 79.3 - - + +
158D LYS* 1.3 60.0 + - - +
160D GLN* 3.7 6.3 + - - +
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Residues in contact with LYS 158 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C C 5.0 3.0 + - - -
14C G 4.0 21.4 + - - +
154D ARG* 3.7 56.3 - - - +
155D ARG* 2.9 25.5 + - - +
157D GLN* 1.3 79.0 - - - +
159D THR* 1.3 65.5 + - + +
160D GLN* 3.9 4.1 + - - +
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Residues in contact with THR 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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155D ARG* 2.9 27.1 + - - +
156D PHE* 3.4 9.2 - - - -
157D GLN 3.6 0.4 - - - -
158D LYS* 1.3 81.4 - - + +
160D GLN* 1.3 67.1 + - - +
161D TYR 2.7 22.2 + - - +
162D LEU* 3.8 12.3 - - + -
166D GLU* 3.5 26.7 + - - +
185D PHE* 3.5 6.1 - - - -
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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