Contacts of the helix formed by residues 145 - 159 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ILE 3.7 2.0 + - - -
144A TYR* 1.3 75.7 - - - +
146A SER* 1.3 66.2 + - - +
147A PHE* 3.6 10.1 + - - +
148A GLN* 3.2 34.3 + - - +
149A LEU* 3.0 22.3 + - - +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TYR 4.0 0.6 + - - -
145A SER* 1.3 72.6 - - - +
147A PHE* 1.3 57.0 + - - +
149A LEU* 3.8 10.1 - - - +
150A ALA* 2.9 32.1 + - - +
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER* 3.1 9.0 + - - +
146A SER* 1.3 77.2 + - - +
148A GLN* 1.3 70.2 + - + +
150A ALA* 3.5 5.3 + - + +
151A ALA* 3.1 32.2 + - + +
173A SER 4.6 9.9 - - - -
174A LEU* 3.8 28.7 - - + -
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A THR* 5.5 0.2 - - - +
143A ILE 4.2 2.8 - - - +
144A TYR* 3.5 22.7 - - + -
145A SER* 3.1 34.2 + - - +
147A PHE* 1.3 82.9 - - + +
149A LEU* 1.3 60.1 + - - +
151A ALA* 3.3 2.1 + - - +
152A LEU* 2.9 38.5 + - + +
174A LEU* 2.9 40.5 + - + +
175A GLY 4.4 3.2 + - - -
176A LEU* 3.5 23.9 - - + +
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TYR* 3.4 47.6 - - + +
145A SER 3.0 17.2 + - - +
146A SER* 3.9 8.5 - - - +
148A GLN* 1.3 76.6 - - - +
150A ALA* 1.3 56.5 + - - +
152A LEU* 3.8 3.3 - - + +
153A GLN* 2.9 44.8 + - + +
184A TRP* 4.0 19.1 - - + +
6C A 4.2 7.4 - - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER 2.9 18.6 + - - +
147A PHE* 3.8 7.2 - - + +
148A GLN 3.3 0.2 - - - -
149A LEU* 1.3 76.3 - - - +
151A ALA* 1.3 57.6 + - - +
153A GLN* 3.7 4.9 - - - +
154A ARG* 2.8 31.9 + - - +
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE* 3.1 23.7 + - + +
148A GLN 3.6 1.6 - - - +
150A ALA* 1.3 79.1 - - - +
152A LEU* 1.3 55.9 + - - +
154A ARG* 4.0 5.0 - - - +
155A ARG* 3.0 29.1 + - - +
170A LEU* 4.9 5.3 - - + +
174A LEU* 3.5 30.5 - - + -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TYR* 4.4 20.2 - - + -
148A GLN 2.9 29.0 + - - +
149A LEU* 3.8 3.4 - - - +
151A ALA* 1.3 68.5 - - - +
153A GLN* 1.3 61.2 - - - +
155A ARG* 3.3 6.3 + - - +
156A PHE* 2.8 30.0 + - - +
170A LEU* 4.1 9.4 - - + -
174A LEU* 3.9 17.3 - - + -
176A LEU* 4.5 4.9 - - + -
181A VAL* 4.5 14.4 - - + -
184A TRP* 3.7 49.6 - - + +
185A PHE* 4.0 23.2 - - + -
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Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 2.9 33.8 + - + +
150A ALA* 3.8 5.4 - - - +
152A LEU* 1.3 76.5 - - - +
154A ARG* 1.3 61.1 + - - +
156A PHE* 3.2 3.8 + - - +
157A GLN* 3.1 27.5 + - + +
184A TRP* 3.6 20.4 - - + -
188A LYS* 3.0 36.3 + - - +
5C T 5.2 7.5 + - - -
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA 2.8 22.6 + - - +
151A ALA* 4.0 5.6 - - - +
153A GLN* 1.3 73.7 - - - +
155A ARG* 1.3 63.6 - - - +
157A GLN* 3.3 30.2 + - - +
158A LYS* 3.9 7.5 + - + +
14E G 4.7 17.0 - - - +
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Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA 3.0 18.9 + - - +
152A LEU 3.6 4.0 - - - +
154A ARG* 1.3 75.3 - - - +
156A PHE* 1.3 59.8 + - - +
158A LYS* 3.0 7.9 + - - -
159A THR* 2.8 45.7 + - - +
162A LEU* 4.3 7.6 - - + +
166A GLU* 3.6 32.7 + - - +
169A GLU* 5.0 9.7 + - - -
170A LEU* 4.1 42.7 - - + +
185A PHE* 4.3 9.2 - - + -
191D LYS* 3.6 25.4 - - - +
4F C 5.5 4.4 + - - -
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU 2.8 16.7 + - - +
153A GLN* 3.2 5.8 + - - +
155A ARG* 1.3 78.6 - - - +
157A GLN* 1.3 65.2 + - + +
158A LYS 3.2 0.7 + - - -
159A THR 3.3 20.3 + - - +
160A GLN* 3.8 47.1 + - + +
184A TRP* 4.0 11.0 - + + -
185A PHE* 3.6 24.2 - + + -
188A LYS* 3.7 43.5 - - + -
189A ARG* 3.7 33.0 - - + -
192A ILE* 4.1 15.5 - - + -
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLN 3.1 15.5 + - - +
154A ARG* 3.4 19.8 - - - +
156A PHE* 1.3 78.6 - - + +
158A LYS* 1.3 64.1 + - + +
160A GLN* 5.8 0.7 + - - +
146D SER* 5.5 6.2 - - - -
149D LEU* 4.9 6.6 - - - +
14E G 3.7 34.3 + - - +
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 4.7 8.3 - - + +
155A ARG* 3.0 10.0 + - - +
156A PHE 4.1 0.4 - - - -
157A GLN* 1.3 84.8 - - + +
159A THR* 1.3 63.1 + - - +
160A GLN* 4.2 1.3 - - - -
149D LEU* 3.9 19.0 - - + +
153D GLN* 2.9 17.3 + - - -
12E T 5.4 3.2 + - - -
13E C 5.6 12.0 + - - -
14E G 6.1 5.8 - - - -
3F A 4.7 10.7 + - - -
4F C 3.8 44.5 + - - +
5F T 4.0 19.4 + - - +
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ARG* 2.8 36.0 + - - +
156A PHE* 3.3 11.9 - - - -
158A LYS* 1.3 79.7 + - - +
160A GLN* 1.3 58.3 + - - +
161A TYR 3.1 23.6 - - - +
162A LEU* 3.6 19.5 - - + -
166A GLU* 4.0 13.5 - - - +
185A PHE* 3.2 20.4 - - - -
153D GLN* 3.5 11.4 + - - +
188D LYS* 4.8 3.4 + - - +
191D LYS* 4.8 2.8 + - - -
5F T 4.4 6.8 + - - -
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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