Contacts of the strand formed by residues 211 - 215 (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 GLY 211 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168E TYR* 3.1 24.8 + - - -
169E TYR 3.2 10.5 - - - -
171E LEU* 4.3 4.7 - - - -
189E PHE* 3.6 8.5 - - - -
210E ARG* 1.3 77.0 - - - +
212E ILE* 1.3 65.0 + - - -
224E VAL* 2.9 30.6 + - - +
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Residues in contact with ILE 212 (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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168E TYR* 3.4 3.6 - - - -
169E TYR* 2.7 52.0 + - + +
171E LEU* 4.0 11.0 - - + -
182E LEU* 4.2 22.7 - - + -
187E PHE* 3.5 20.2 - - + +
188E LEU* 3.5 35.2 - - + -
189E PHE* 3.6 20.9 - - + -
211E GLY* 1.3 77.5 - - - -
213E TRP* 1.3 66.4 + - - +
214E HIS* 5.0 1.6 - - + -
221E LEU* 3.7 23.8 - - + -
222E ILE 3.7 2.9 - - - -
223E TRP* 4.2 1.3 - - + -
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Residues in contact with TRP 213 (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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157E LEU* 3.4 46.5 + - + +
158E SER* 5.7 0.2 - - - +
160E LEU* 3.7 19.7 - - + -
164E LEU 3.2 28.0 - - - -
166E GLY* 3.7 15.6 + - - +
167E ARG 3.2 34.5 - - - +
168E TYR* 3.8 15.5 - - + -
169E TYR* 5.1 0.2 - - - -
212E ILE* 1.3 76.4 - - - +
214E HIS* 1.3 65.3 + - - +
215E ASN* 3.8 9.6 - - + -
220E PHE* 3.5 39.0 - + - -
221E LEU* 3.4 5.5 - - - +
222E ILE* 2.8 60.4 + - + +
224E VAL* 5.6 0.4 - - + -
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Residues in contact with HIS 214 (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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166E GLY* 3.2 1.0 - - - -
167E ARG* 3.1 30.4 + - + -
169E TYR* 3.3 38.2 + + - -
182E LEU* 4.1 10.7 - - + +
185E ASP* 5.3 1.2 + - - -
187E PHE* 3.7 37.9 - + + -
212E ILE* 5.0 2.7 - - + -
213E TRP* 1.3 84.4 - - - +
215E ASN* 1.3 84.0 + - - +
216E ASN* 5.1 4.7 - - - -
218E LYS* 4.3 22.8 - - + +
220E PHE 3.1 12.6 - - - +
221E LEU* 4.3 4.7 - - + -
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Residues in contact with ASN 215 (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 ASP 3.0 24.9 + - - +
164E LEU* 4.0 10.8 - - - +
165E ALA 3.2 15.3 - - - +
166E GLY* 3.7 1.8 - - - -
213E TRP* 3.8 7.8 - - + -
214E HIS* 1.3 90.1 + - - +
216E ASN* 1.3 65.6 + - - +
217E GLU* 3.5 5.6 - - - +
218E LYS* 3.0 7.8 + - - -
219E SER* 2.8 46.5 + - - -
220E PHE* 3.1 22.5 + - + +
247E ARG* 4.6 3.4 - - - +
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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