Contacts of the helix formed by residues 162 - 169 (chain E) in PDB entry 1KD1
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 VAL 162 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU 4.7 0.4 - - - -
131E PHE* 4.4 12.1 - - + -
133E ARG* 4.3 17.3 - - + -
138E VAL* 4.3 12.6 - - + -
157E LEU* 2.9 16.6 + - + +
160E LEU* 3.2 22.7 - - + +
161E ASP* 1.3 79.0 - - - +
163E HIS* 1.3 66.3 + - - +
164E ALA 3.1 3.7 + - - -
165E ASP* 3.3 15.0 + - - +
192E ILE* 3.1 32.2 - - + +
232E LEU* 3.5 21.5 - - + -
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Residues in contact with HIS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A A 5.8 2.5 - - - -
154E VAL* 3.7 33.7 + - + +
157E LEU* 3.2 10.7 + - - +
158E GLU* 3.7 39.0 + - + +
161E ASP* 3.7 0.6 - - - +
162E VAL* 1.3 79.5 - - - +
164E ALA* 1.3 56.7 + - - +
166E ILE* 2.8 51.1 + - + +
167E ASP* 3.1 33.0 + - - -
207E LEU* 5.4 0.4 - - + -
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Residues in contact with ALA 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU* 3.7 30.4 - - + +
131E PHE* 4.5 5.6 - - - +
132E ASP* 4.8 9.4 - - - +
161E ASP 5.2 1.7 - - - +
162E VAL 3.1 1.0 - - - +
163E HIS* 1.3 78.3 - - - +
165E ASP* 1.3 62.3 + - - +
167E ASP* 3.2 18.2 + - - +
168E ARG* 3.0 16.5 + - - +
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Residues in contact with ASP 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E HIS* 2.9 29.0 - - - -
130E GLU* 3.0 40.1 + - - +
162E VAL 3.3 9.8 + - - +
163E HIS 3.0 0.8 + - - -
164E ALA* 1.3 75.3 - - - +
166E ILE* 1.3 60.7 + - - +
168E ARG* 2.9 39.4 + - - +
169E ALA* 3.0 5.4 + - - +
191E SER* 3.0 28.0 - - - -
192E ILE* 3.4 7.9 + - + +
232E LEU* 3.9 8.5 - - + -
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Residues in contact with ILE 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A A 6.1 0.9 - - - +
157E LEU* 3.4 33.9 - - + -
163E HIS* 2.8 29.1 + - + +
165E ASP* 1.3 74.9 - - - +
167E ASP* 1.3 67.3 + - - +
169E ALA 3.2 1.9 + - - -
170E ASP* 3.0 22.8 + - + +
191E SER* 4.3 6.3 - - - +
192E ILE* 4.2 14.6 - - + -
194E PHE* 5.1 1.1 - - + -
207E LEU* 3.6 28.7 - - + -
208E ALA* 3.9 38.6 - - + +
210E ALA* 5.6 0.4 - - + -
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Residues in contact with ASP 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E HIS* 3.1 36.5 + - - -
164E ALA* 3.2 19.2 - - - +
165E ASP 3.1 0.2 - - - -
166E ILE* 1.3 77.8 - - - +
168E ARG* 1.3 62.7 + - - +
170E ASP* 3.3 20.8 + - - +
171E GLU* 4.0 8.8 - - - +
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Residues in contact with ARG 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309A U 3.8 11.7 + - - -
1310A U 2.6 42.9 + - - +
127E ARG* 5.0 0.4 - - - +
128E GLY* 3.5 23.5 + - - -
129E HIS* 3.5 19.8 + - - +
130E GLU* 4.1 14.8 - - + -
164E ALA 3.0 10.9 + - - +
165E ASP* 2.9 29.9 + - - +
167E ASP* 1.3 80.0 - - - +
169E ALA* 1.3 55.3 + - - +
170E ASP 3.1 4.0 + - - -
171E GLU* 3.6 21.5 + - - +
189E PRO* 3.7 22.4 - - + +
190E ALA 2.4 33.6 + - - -
191E SER* 4.1 1.0 - - - +
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Residues in contact with ALA 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ASP 3.0 5.7 + - - +
166E ILE 3.2 2.4 + - - +
168E ARG* 1.3 73.5 - - + +
170E ASP* 1.3 54.6 + - - +
171E GLU 3.0 8.5 + - - +
188E ARG* 2.8 29.6 + - - -
189E PRO* 3.5 33.4 - - + +
190E ALA 5.1 0.2 - - - +
191E SER* 3.7 14.4 - - - -
208E ALA* 3.4 27.8 - - - +
209E GLY* 3.7 4.0 - - - -
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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