Contacts of the helix formed by residues 163 - 178 (chain A) in PDB entry 1DUS
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 LYS 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A THR* 1.3 92.7 - - + +
164A GLN* 1.3 69.7 + - + +
165A GLY 3.4 0.6 + - - +
166A ALA* 4.1 1.2 - - - +
167A LYS* 2.9 40.1 + - - +
190A ARG* 4.0 5.7 - - - +
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Residues in contact with GLN 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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163A LYS* 1.3 85.2 - - + +
165A GLY* 1.3 58.7 + - - +
167A LYS* 3.5 35.5 + - - +
168A SER* 2.8 32.1 + - - -
171A LYS* 5.8 3.8 - - - +
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Residues in contact with GLY 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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136A LYS* 5.7 6.1 - - - -
160A ILE* 3.8 12.9 - - - +
161A GLN 4.3 4.7 - - - -
162A THR 3.7 6.7 + - - -
163A LYS 3.2 1.2 - - - -
164A GLN* 1.3 75.4 - - - +
166A ALA* 1.3 63.2 + - - +
168A SER* 3.4 4.1 + - - -
169A LEU* 3.1 24.3 + - - +
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Residues in contact with ALA 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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160A ILE* 3.6 28.9 - - + +
161A GLN 3.8 5.7 + - - -
162A THR* 4.0 13.0 - - - -
163A LYS 3.6 2.5 + - - +
165A GLY* 1.3 75.5 - - - +
167A LYS* 1.3 57.6 + - - +
169A LEU* 3.4 0.9 + - - -
170A ALA* 2.8 31.5 + - - +
190A ARG* 3.5 34.5 - - + -
192A LEU* 3.7 6.8 - - + +
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Residues in contact with LYS 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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163A LYS* 2.9 28.6 + - - +
164A GLN* 3.5 36.4 + - - +
165A GLY 3.2 0.2 - - - -
166A ALA* 1.3 75.3 - - - +
168A SER* 1.3 64.8 + - - +
170A ALA* 3.4 6.4 + - - +
171A LYS* 3.0 39.3 + - - +
190A ARG* 4.3 26.2 - - - +
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Residues in contact with SER 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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136A LYS* 3.0 37.8 + - - +
140A HIS* 5.0 5.4 + - - -
164A GLN 2.8 21.5 + - - -
165A GLY 3.8 3.6 - - - -
167A LYS* 1.3 72.8 - - - +
169A LEU* 1.3 63.5 + - - +
171A LYS* 3.4 14.4 + - - +
172A TYR* 3.2 20.6 + - - +
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Residues in contact with LEU 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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130A PRO* 5.3 3.8 - - + -
139A LEU* 4.5 22.9 - - + -
140A HIS* 4.6 9.2 - - + +
143A ILE* 3.0 37.0 - - + -
158A VAL* 3.9 29.8 - - + -
160A ILE* 3.8 28.0 - - + -
165A GLY 3.1 17.1 + - - +
166A ALA 3.8 3.1 - - - +
168A SER* 1.3 75.6 - - - +
170A ALA* 1.3 66.2 + - - +
172A TYR* 3.1 5.2 + - + +
173A MSE 2.9 29.7 + - - +
192A LEU* 4.3 1.3 - - + -
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Residues in contact with ALA 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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166A ALA 2.8 21.6 + - - +
167A LYS* 3.7 7.9 - - - +
168A SER 3.3 0.2 - - - -
169A LEU* 1.3 71.5 - - - +
171A LYS* 1.3 57.3 + - - +
173A MSE 3.1 3.9 + - - +
174A LYS* 2.9 30.1 + - - +
180A VAL* 3.7 22.0 - - + +
182A THR* 5.7 1.3 - - - +
192A LEU* 4.0 25.5 - - + +
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Residues in contact with LYS 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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164A GLN* 5.8 3.8 - - - +
167A LYS* 3.0 32.5 + - - +
168A SER* 3.5 12.9 - - - +
169A LEU 3.2 0.2 - - - -
170A ALA* 1.3 77.2 - - + +
172A TYR* 1.3 56.0 + - - +
174A LYS* 3.4 14.8 + - - +
175A ASP* 2.9 36.9 + - - +
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Residues in contact with TYR 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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140A HIS* 3.4 70.8 + + + +
143A ILE* 3.5 22.2 - - + -
144A GLU* 3.2 25.8 + - - +
168A SER 3.2 8.8 + - - +
169A LEU* 3.1 9.7 + - + +
171A LYS* 1.3 75.6 - - - +
173A MSE 1.3 61.2 + - - +
175A ASP* 3.1 18.3 + - + +
176A VAL* 2.9 47.3 + - + +
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Residues in contact with MSE 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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143A ILE* 3.9 31.4 - - + -
156A ILE* 4.0 18.8 - - + +
158A VAL* 4.0 17.0 - - + -
169A LEU* 2.9 20.5 + - + +
170A ALA 3.5 6.7 - - - +
172A TYR* 1.3 74.9 - - - +
174A LYS* 1.3 58.8 + - - +
177A PHE* 2.8 35.5 + - - +
179A ASN 4.1 1.8 - - - -
180A VAL* 3.9 5.2 - - + -
192A LEU* 3.8 45.3 - - + +
193A LYS 4.0 0.7 - - - -
194A SER* 3.4 50.9 - - - +
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Residues in contact with LYS 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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170A ALA 2.9 16.1 + - - +
171A LYS* 3.7 14.7 - - - +
173A MSE 1.3 74.2 - - - +
175A ASP* 1.3 65.6 + - - +
178A GLY* 2.8 33.0 + - - +
179A ASN* 3.9 25.8 - - - +
180A VAL* 3.9 15.4 - - + +
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Residues in contact with ASP 175 (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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171A LYS* 2.9 28.1 + - - +
172A TYR* 3.2 24.8 - - + +
174A LYS* 1.3 84.3 - - - +
176A VAL* 1.3 64.6 + - + +
178A GLY* 4.4 1.6 + - - -
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Residues in contact with VAL 176 (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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143A ILE* 4.0 4.9 - - + +
144A GLU* 4.2 26.5 - - + -
147A LYS* 3.0 38.1 + - + -
172A TYR* 2.9 52.3 + - + +
173A MSE 4.0 1.8 - - - +
175A ASP* 1.3 80.5 - - + +
177A PHE* 1.3 79.6 + - + +
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Residues in contact with PHE 177 (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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143A ILE* 3.6 32.1 - - + -
147A LYS* 3.5 44.7 + - + +
150A LEU* 3.6 23.1 - - + -
156A ILE* 3.7 23.3 - - + -
173A MSE 2.8 22.2 + - - +
176A VAL* 1.3 84.9 - - + +
178A GLY* 1.3 56.3 + - - +
179A ASN* 3.2 25.9 - - - +
194A SER* 3.6 13.7 - - - -
195A LYS 3.6 22.2 - - - +
196A LYS* 4.0 8.7 - - - -
197A LEU* 4.4 13.7 + - - +
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Residues in contact with GLY 178 (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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174A LYS* 2.8 27.4 + - - +
175A ASP 4.4 1.7 + - - -
176A VAL 3.6 1.0 - - - -
177A PHE* 1.3 73.5 - - - +
179A ASN* 1.3 64.7 + - - +
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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
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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