Contacts of the helix formed by residues 163 - 174 (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 ALA 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A TYR 4.0 0.6 + - - -
162A LEU* 1.3 75.6 - - - +
164A LEU* 1.3 66.8 + - - +
165A PRO* 3.3 6.7 - - + -
166A GLU* 2.9 21.5 + - - +
167A ARG* 3.0 18.8 + - - +
156D PHE* 4.5 20.0 - - + -
157D GLN* 4.9 9.2 - - - +
188D LYS* 5.0 1.5 - - - +
192D ILE* 3.8 24.5 - - + -
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Residues in contact with LEU 164 (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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162A LEU 3.9 2.0 + - - +
163A ALA* 1.3 69.7 - - - +
165A PRO* 1.3 72.7 - - + +
167A ARG* 3.1 44.1 + - - +
168A ALA* 2.9 23.6 + - - +
178A GLN* 4.1 3.7 - - - +
2B G 5.9 3.6 - - - +
3B A 4.3 17.7 - - - +
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Residues in contact with PRO 165 (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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163A ALA* 3.5 12.6 - - + -
164A LEU* 1.3 95.8 - - + +
166A GLU* 1.3 55.5 + - - +
168A ALA* 3.5 6.8 + - + +
169A GLU* 3.0 28.9 + - - +
192D ILE* 3.8 15.7 - - + -
195D ILE* 3.8 26.0 - - + +
196D MET* 3.8 36.3 - - + -
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Residues in contact with GLU 166 (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* 3.6 25.2 + - - +
159A THR* 4.0 5.9 - - - +
161A TYR 4.3 0.5 - - - +
162A LEU* 3.7 11.9 - - + +
163A ALA* 2.9 32.1 + - + +
165A PRO* 1.3 76.2 - - - +
167A ARG* 1.3 60.0 + - - +
169A GLU* 3.9 4.6 - - - +
170A LEU* 3.0 30.7 + - - +
188D LYS* 2.7 32.7 + - - -
191D LYS* 2.9 22.0 + - - +
192D ILE* 4.0 7.7 - - + +
195D ILE* 3.8 20.4 - - + -
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Residues in contact with ARG 167 (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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162A LEU* 3.9 21.5 - - + -
163A ALA 3.0 12.6 + - - +
164A LEU* 3.1 29.3 + - - +
166A GLU* 1.3 75.9 - - - +
168A ALA* 1.3 65.4 + - - +
170A LEU* 3.4 1.4 + - - +
171A ALA* 3.0 28.1 + - - +
178A GLN* 2.9 51.5 + - + +
181A VAL* 4.1 18.2 - - + +
182A LYS* 3.8 28.0 - - - +
3B A 2.9 34.3 + - - -
4B C 5.1 1.4 + - - -
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Residues in contact with ALA 168 (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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164A LEU 2.9 15.9 + - - +
165A PRO* 3.7 7.9 - - + +
167A ARG* 1.3 78.1 - - - +
169A GLU* 1.3 61.4 + - - +
171A ALA* 3.8 1.2 - - - +
172A ALA* 3.1 25.5 + - - +
178A GLN* 3.6 27.9 + - - +
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Residues in contact with GLU 169 (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* 5.0 9.7 + - - -
165A PRO 3.0 17.6 + - - +
166A GLU* 3.9 5.6 - - - +
168A ALA* 1.3 75.6 - - - +
170A LEU* 1.3 58.3 + - - +
172A ALA* 3.6 5.4 + - - +
173A SER* 3.1 29.2 + - - -
191D LYS* 6.0 0.3 - - - -
195D ILE* 3.9 38.9 - - + +
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Residues in contact with LEU 170 (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* 4.9 6.7 - - + +
152A LEU* 4.1 7.0 - - + -
155A ARG* 4.1 39.3 - - + +
162A LEU* 4.0 8.5 - - + -
166A GLU 3.0 18.6 + - - +
167A ARG 3.8 2.9 - - - +
169A GLU* 1.3 75.6 + - - +
171A ALA* 1.3 65.5 + - - +
173A SER* 2.7 26.9 + - - +
174A LEU* 3.3 34.4 + - + +
181A VAL* 3.9 14.1 - - + -
185A PHE* 3.8 28.3 - - + -
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Residues in contact with ALA 171 (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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167A ARG 3.0 18.4 + - - +
168A ALA 3.8 2.9 - - - +
170A LEU* 1.3 76.5 - - - +
172A ALA* 1.3 63.0 + - - +
174A LEU* 3.0 7.8 + - - -
176A LEU* 2.9 41.1 + - - +
178A GLN* 3.7 21.3 - - + +
181A VAL* 3.6 25.3 - - + +
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Residues in contact with ALA 172 (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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168A ALA 3.1 17.6 + - - +
169A GLU* 4.0 4.9 - - - +
171A ALA* 1.3 75.9 - - - +
173A SER* 1.3 61.4 + - - +
174A LEU 3.1 1.6 + - - -
175A GLY* 3.3 10.4 + - - -
176A LEU 4.1 2.7 + - - +
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Residues in contact with SER 173 (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* 4.6 8.1 - - - -
169A GLU* 3.1 16.6 + - - -
170A LEU* 2.7 27.1 + - - +
172A ALA* 1.3 75.5 - - - +
174A LEU* 1.3 71.3 + - - +
175A GLY 3.6 0.2 - - - -
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Residues in contact with LEU 174 (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* 3.8 28.0 - - + -
148A GLN* 2.9 40.7 + - + +
151A ALA* 3.5 27.4 - - + -
152A LEU* 3.9 28.5 - - + -
170A LEU* 3.3 33.9 - - + +
171A ALA 3.0 3.6 + - - +
173A SER* 1.3 86.4 - - - +
175A GLY* 1.3 61.6 + - - +
176A LEU* 3.5 18.6 + - + -
181A VAL* 5.4 0.4 - - + -
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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
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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