Contacts of the strand formed by residues 211 - 215 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168G TYR* 3.1 24.8 + - - -
169G TYR 3.2 10.3 - - - -
171G LEU* 4.3 4.7 - - - -
189G PHE* 3.6 10.1 - - - -
210G ARG* 1.3 76.2 - - - +
212G ILE* 1.3 63.6 + - - -
224G VAL* 2.9 30.1 + - - +
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Residues in contact with ILE 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G TYR* 3.4 4.6 - - - -
169G TYR* 2.7 48.8 + - + +
171G LEU* 4.0 11.2 - - + -
174G MET* 5.3 0.2 - - - -
182G LEU* 4.2 21.8 - - + -
187G PHE* 3.5 20.2 - - + +
188G LEU* 3.5 35.2 - - + -
189G PHE* 3.5 20.9 - - + -
211G GLY* 1.3 78.1 - - - -
213G TRP* 1.3 65.1 + - - +
214G HIS* 5.0 2.0 - - + -
221G LEU* 3.7 24.5 - - + -
222G ILE 3.7 3.6 - - - -
223G TRP* 4.2 1.3 - - + -
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Residues in contact with TRP 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157G LEU* 3.4 44.6 + - + +
158G SER* 5.7 0.6 - - - +
160G LEU* 3.7 20.2 - - + -
164G LEU 3.2 28.9 - - - -
166G GLY* 3.7 16.7 + - - +
167G ARG 3.2 33.8 - - - +
168G TYR* 3.8 15.3 - - + -
169G TYR* 5.1 0.2 - - - -
212G ILE* 1.3 77.5 - - - +
214G HIS* 1.3 66.1 + - - +
215G ASN* 3.8 17.0 - - + -
220G PHE* 3.5 33.7 - + - -
221G LEU* 3.3 5.2 - - - +
222G ILE* 2.8 58.6 + - + +
224G VAL* 5.6 0.4 - - + -
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Residues in contact with HIS 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G ARG* 3.1 29.8 + - + -
169G TYR* 3.3 37.9 + + - -
182G LEU* 4.1 11.1 - - + +
185G ASP* 5.2 1.0 + - - -
187G PHE* 3.7 36.4 - + + -
212G ILE* 5.0 2.2 - - + -
213G TRP* 1.3 83.2 - - - +
215G ASN* 1.3 84.9 + - - +
216G ASN* 5.1 4.5 - - - -
218G LYS* 4.3 24.5 - - + +
220G PHE 3.2 12.8 - - - +
221G LEU* 4.3 4.5 - - + -
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Residues in contact with ASN 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G ASP 3.0 25.3 + - - +
164G LEU* 4.0 10.4 - - - +
165G ALA 3.1 15.9 - - - +
166G GLY* 3.7 1.8 - - - -
213G TRP* 3.8 7.0 - - + -
214G HIS* 1.3 91.4 + - - +
216G ASN* 1.3 63.3 + - - +
217G GLU* 3.5 5.5 - - - +
218G LYS* 3.0 7.0 + - - -
219G SER* 2.8 46.3 + - - -
220G PHE* 3.1 23.2 + - + +
247G ARG* 4.6 3.8 - - - +
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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