Contacts of the helix formed by residues 194 - 199 (chain E) in PDB entry 1QK1
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 194 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193E VAL* 1.3 83.1 - - - +
195E PRO* 1.3 67.0 - - - +
196E LEU* 3.1 24.4 + - - +
197E LEU* 3.0 37.7 + - - +
198E THR* 3.1 12.5 + - - +
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Residues in contact with PRO 195 (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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191A LYS* 5.5 6.5 - - - +
58E ASN* 3.3 20.6 + - - +
193E VAL 3.2 7.4 - - - +
194E SER* 1.3 85.5 - - - +
196E LEU* 1.3 66.9 + - + +
197E LEU 3.1 0.4 - - - -
198E THR* 3.5 12.8 - - - +
199E ALA* 3.1 28.8 + - - +
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Residues in contact with LEU 196 (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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54E THR* 2.7 26.0 + - - +
58E ASN* 3.3 35.4 - - + +
66E THR* 3.9 34.1 - - + +
70E VAL* 5.5 0.5 - - - +
194E SER* 3.1 13.4 - - - +
195E PRO* 1.3 83.0 - - + +
197E LEU* 1.3 69.9 + - + +
200E ALA* 3.7 9.7 + - - +
202E MET* 4.5 0.5 - - - +
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Residues in contact with LEU 197 (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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192E PRO* 4.2 28.3 - - + -
194E SER* 3.0 21.1 + - - +
196E LEU* 1.3 90.3 - - + +
198E THR* 1.3 64.8 + - - +
199E ALA 3.3 1.3 - - - -
200E ALA* 3.2 10.0 + - - +
202E MET* 3.2 52.1 + - + +
226E GLU* 6.1 0.7 - - - +
227E GLU* 4.3 30.3 - - + +
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Residues in contact with THR 198 (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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192E PRO* 3.6 26.2 - - + +
193E VAL* 4.3 6.5 + - - +
194E SER 3.1 10.6 + - - +
195E PRO* 3.5 16.1 + - - +
197E LEU* 1.3 76.6 - - - +
199E ALA* 1.3 59.6 + - - +
200E ALA 3.0 0.2 - - - -
201E GLY* 3.0 19.6 + - - +
202E MET 4.7 2.7 - - - +
203E ALA* 4.4 17.2 + - + -
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Residues in contact with ALA 199 (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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53E GLN* 4.1 19.6 - - - +
54E THR* 4.0 12.7 + - - +
57E ASP* 3.8 22.4 - - + +
58E ASN* 4.0 13.9 - - - +
195E PRO* 3.1 17.9 + - + +
198E THR* 1.3 81.5 + - - +
200E ALA* 1.3 57.7 + - - +
201E GLY 3.2 1.4 + - - -
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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