Contacts of the helix formed by residues 170 - 181 (chain E) in PDB entry 1KR2
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 170 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E GLU* 4.2 21.9 + - - +
97E LYS* 5.1 9.7 - - - +
169E TRP* 1.3 71.8 - - - +
171E SER* 1.3 62.0 + - - +
172E GLU* 3.8 26.3 + - - +
173E ASP* 2.8 59.9 + - + +
174E ILE* 3.2 7.4 + - - +
273E ASN* 3.7 23.6 - - + +
813E TAD 4.6 1.8 + - - -
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Residues in contact with SER 171 (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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169E TRP 3.4 4.0 + - - -
170E LYS* 1.3 72.5 - - - +
172E GLU* 1.3 73.7 + - - +
174E ILE* 3.3 16.2 + - - +
175E THR* 3.0 25.8 + - - -
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Residues in contact with GLU 172 (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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170E LYS* 3.2 28.1 + - - +
171E SER* 1.3 94.8 + - - +
173E ASP* 1.3 62.6 + - - +
175E THR* 3.6 7.2 + - - -
176E GLN* 3.1 41.6 + - - +
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Residues in contact with ASP 173 (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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94E GLU* 3.6 21.8 - - - +
96E LEU* 3.1 32.1 - - + +
169E TRP* 5.1 5.4 - - + -
170E LYS* 2.8 55.7 + - + +
172E GLU* 1.3 79.8 - - - +
174E ILE* 1.3 56.2 + - - +
176E GLN* 3.3 3.5 + - - +
177E ILE* 2.9 40.8 + - + +
813E TAD 4.5 5.7 + - - +
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Residues in contact with ILE 174 (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 PHE* 3.9 56.1 - - + +
169E TRP* 3.9 28.5 - - + +
170E LYS 3.2 10.5 + - - +
171E SER* 3.6 15.3 - - - +
173E ASP* 1.3 73.2 - - - +
175E THR* 1.3 68.4 + - - +
177E ILE* 3.2 9.0 + - - +
178E VAL* 3.0 27.3 + - + +
202E VAL* 4.1 15.3 - - + -
203E LEU* 4.0 15.9 - - + -
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Residues in contact with THR 175 (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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171E SER* 3.0 14.1 + - - -
172E GLU* 3.8 10.7 - - - -
174E ILE* 1.3 78.9 - - - +
176E GLN* 1.3 60.3 + - + +
178E VAL* 3.3 7.8 - - - +
179E ALA* 2.8 36.9 + - + +
202E VAL* 3.5 27.5 - - + +
206E HIS* 4.5 11.0 - - - +
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Residues in contact with GLN 176 (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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96E LEU* 3.7 18.9 - - + +
100E ARG* 3.7 22.2 + - - -
172E GLU* 3.1 37.3 + - - +
173E ASP* 3.8 4.3 + - - +
174E ILE 3.2 0.2 - - - -
175E THR* 1.3 80.0 - - + +
177E ILE* 1.3 59.5 + - - +
179E ALA* 4.7 0.9 - - - -
180E ASN* 2.9 52.4 + - - +
181E TYR* 3.7 5.0 - - + -
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Residues in contact with ILE 177 (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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95E THR* 4.6 3.8 - - + -
96E LEU* 3.9 31.0 - - + +
99E LEU* 3.9 21.5 - - + -
153E LEU* 4.4 3.4 - - + -
163E PHE* 5.2 5.8 - - + -
169E TRP* 3.8 30.3 - - + -
173E ASP* 2.9 28.3 + - + +
174E ILE* 3.2 7.8 + - - +
176E GLN* 1.3 77.9 - - - +
178E VAL* 1.3 60.3 + - + +
181E TYR* 3.0 16.0 + - - +
182E GLY 2.8 25.7 + - - +
183E LEU* 4.1 25.8 - - + -
813E TAD 5.5 0.2 - - - +
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Residues in contact with VAL 178 (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 PHE* 4.7 4.3 - - + -
174E ILE 3.0 21.3 + - - +
175E THR* 3.3 11.0 - - - +
177E ILE* 1.3 81.2 - - + +
179E ALA* 1.3 60.8 + - - +
182E GLY* 3.8 6.3 + - - +
183E LEU* 4.3 17.9 - - + -
202E VAL* 4.6 7.0 - - + +
203E LEU* 3.8 26.9 - - + -
206E HIS* 4.0 27.9 - - + +
209E ASN* 3.0 31.9 - - - +
210E ILE* 3.9 17.5 - - + -
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Residues in contact with ALA 179 (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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175E THR* 2.8 26.9 + - + +
176E GLN* 4.7 0.7 - - - -
178E VAL* 1.3 74.6 - - - +
180E ASN* 1.3 69.8 + - - +
206E HIS* 3.5 34.1 - - + +
209E ASN* 3.5 12.9 - - - +
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Residues in contact with ASN 180 (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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150E LYS* 5.8 3.6 - - - +
176E GLN* 2.9 42.6 + - - +
179E ALA* 1.3 86.0 - - - +
181E TYR* 1.3 80.0 + - + +
209E ASN* 5.0 0.7 - - - -
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Residues in contact with TYR 181 (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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96E LEU* 3.7 26.0 - - + -
99E LEU* 3.9 42.6 - - + -
100E ARG* 3.3 35.1 + - - +
103E GLN* 3.9 22.7 - - + +
150E LYS* 5.6 1.2 - - - +
151E VAL* 3.6 21.4 - - + +
152E LYS* 2.7 39.8 + - - +
176E GLN* 3.7 10.5 - - + -
177E ILE* 3.0 12.5 + - - +
179E ALA 3.6 1.0 - - - -
180E ASN* 1.3 99.2 - - + +
182E GLY* 1.3 56.3 + - - +
209E ASN* 4.2 2.9 - - - -
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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