Contacts of the helix formed by residues 200 - 206 (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 SER 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ARG* 3.6 2.7 - - - -
196E PHE* 3.5 12.9 + - - -
197E ILE 3.2 4.9 + - - +
198E TYR 3.3 0.2 - - - -
199E GLU* 1.3 78.3 - - - +
201E ASP* 1.3 66.2 + - - +
202E VAL* 3.5 13.9 + - - +
203E LEU* 3.3 34.6 + - - +
204E TRP* 2.8 22.9 + - - +
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Residues in contact with ASP 201 (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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228A ARG* 4.2 0.5 - - - -
231A ARG* 2.8 48.2 + - - +
232A ARG* 2.9 30.7 + - - +
256A SER* 4.6 6.4 + - - -
199E GLU 4.0 2.4 + - - +
200E SER* 1.3 70.7 + - - +
202E VAL* 1.3 56.8 + - - +
204E TRP* 3.8 1.2 - - - +
205E LYS* 2.9 32.3 + - - +
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Residues in contact with VAL 202 (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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174E ILE* 4.1 24.2 - - + -
175E THR* 3.5 42.8 - - + +
178E VAL* 4.6 1.3 - - + +
200E SER* 3.5 11.0 + - - +
201E ASP* 1.3 78.7 - - - +
203E LEU* 1.3 71.0 + - + +
205E LYS* 3.4 6.3 + - + -
206E HIS* 3.2 39.2 + - + +
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Residues in contact with LEU 203 (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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160E LEU* 3.8 12.8 - - + -
163E PHE* 4.1 9.6 - - + -
174E ILE* 4.0 20.9 - - + -
178E VAL* 3.8 28.0 - - + -
196E PHE* 3.7 37.7 - - + -
197E ILE* 3.9 21.5 - - + +
200E SER* 3.2 24.2 + - - +
202E VAL* 1.3 79.2 - - + +
204E TRP* 1.3 68.0 + - - +
206E HIS* 3.0 5.2 + - - -
207E ARG* 2.9 22.0 + - - +
210E ILE* 3.7 12.1 - - + +
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Residues in contact with TRP 204 (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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232A ARG* 3.4 59.6 + - + +
234A GLN* 3.2 27.7 - - - +
34B TYR* 6.4 1.8 - + - -
216B TRP* 4.6 12.6 - + - -
194E GLN* 6.3 0.7 - - - -
197E ILE* 3.4 16.5 + - + +
198E TYR* 4.0 25.4 - + + -
200E SER 2.8 20.5 + - - +
201E ASP 3.8 2.0 - - - +
203E LEU* 1.3 72.8 - - - +
205E LYS* 1.3 67.2 + - - +
207E ARG* 2.7 80.7 + - - +
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Residues in contact with LYS 205 (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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201E ASP 2.9 18.5 + - - +
202E VAL* 3.5 8.5 - - + +
204E TRP* 1.3 84.8 - - + +
206E HIS* 1.3 85.8 + - + +
207E ARG* 3.7 8.3 + - - +
208E SER* 5.1 0.9 + - - -
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Residues in contact with HIS 206 (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* 4.5 9.5 - - + +
178E VAL* 4.0 34.3 - - + +
179E ALA* 3.5 30.4 - - + +
202E VAL* 3.2 31.7 + - + +
203E LEU 3.0 6.5 + - - +
205E LYS* 1.3 106.1 + - + +
207E ARG* 1.3 50.1 + - - +
208E SER* 3.0 8.1 - - - -
209E ASN* 2.7 33.5 + - + +
210E ILE* 3.7 5.5 + - - +
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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