Contacts of the strand formed by residues 220 - 224 (chain D) 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 PHE 220 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LEU* 5.1 2.2 - - + -
164D LEU* 4.1 13.2 - - + -
187D PHE* 6.0 0.9 - - - -
213D TRP* 3.5 27.2 - + - -
214D HIS* 3.1 7.5 - - - +
215D ASN* 3.1 40.5 + - + +
218D LYS 3.7 0.6 - - - -
219D SER* 1.3 82.3 - - - +
221D LEU* 1.3 60.5 + - - +
222D ILE* 4.3 15.9 - - + -
232D VAL* 3.7 30.7 - - + -
233D ILE 3.4 11.7 - - - -
234D SER* 4.3 7.2 - - - -
247D ARG* 4.2 23.1 - - + -
248D PHE* 4.3 11.2 - + - -
251D GLY* 3.7 33.9 - - - -
252D LEU* 4.3 1.1 - - + -
255D VAL* 5.0 5.4 - - + -
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D HIS 4.8 2.0 - - - +
187D PHE* 3.8 39.7 - - + -
212D ILE* 3.8 13.9 - - + -
213D TRP 3.4 12.6 - - - +
214D HIS* 4.3 4.0 - - + -
220D PHE* 1.3 74.3 - - - +
222D ILE* 1.3 77.7 + - - +
223D TRP* 3.5 40.2 - - + +
231D ARG 3.8 0.5 - - - +
232D VAL* 4.5 0.2 - - - +
233D ILE* 2.8 63.3 + - + +
235D MET* 4.8 11.7 - - + -
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Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D VAL* 4.9 1.8 - - + -
157D LEU* 3.7 33.0 - - + -
212D ILE* 3.7 1.9 - - - -
213D TRP* 2.7 58.0 + - + +
220D PHE* 4.3 14.4 - - + -
221D LEU* 1.3 80.5 - - - +
223D TRP* 1.3 75.9 + - - +
224D VAL* 4.0 13.8 + - + +
230D THR* 4.4 14.8 - - + -
231D ARG 3.3 7.4 - - - +
232D VAL* 4.2 21.8 - - + -
255D VAL* 4.7 8.7 - - + -
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Residues in contact with TRP 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ARG* 6.2 0.9 - - - -
186D HIS 5.1 3.4 - - - -
187D PHE* 2.9 32.0 + - - -
188D LEU 3.9 7.0 - - - -
189D PHE* 3.5 43.7 - + + -
211D GLY 3.9 1.8 - - - -
212D ILE* 4.3 4.0 - - + -
221D LEU* 3.5 27.1 - - + +
222D ILE* 1.3 80.8 - - - +
224D VAL* 1.3 61.9 + - - +
225D ASN 3.9 0.3 + - - -
226D GLU* 3.6 36.0 + - + -
228D ASP 4.8 0.5 - - - +
229D HIS 3.7 0.3 - - - +
230D THR* 3.2 8.0 - - - -
231D ARG* 2.9 46.7 + - + +
233D ILE* 4.8 13.0 - - + -
400D PO4 5.5 5.8 - - - -
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Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL* 4.5 4.0 - - + -
150D GLU* 4.1 20.4 - - + +
153D VAL* 4.0 24.7 - - + -
154D VAL* 5.6 0.9 - - + -
157D LEU* 5.3 1.6 - - + -
168D TYR* 4.1 23.1 - - + +
189D PHE* 4.1 2.5 - - - -
209D ALA 4.2 4.3 - - - +
210D ARG* 3.3 5.2 - - - +
211D GLY 2.9 35.4 + - - +
213D TRP* 5.6 0.2 - - + -
222D ILE* 4.3 12.3 - - + +
223D TRP* 1.3 75.6 - - - +
225D ASN* 1.3 88.9 + - - +
226D GLU 3.4 2.1 + - - -
229D HIS 3.5 7.6 - - - +
230D THR* 4.9 0.4 - - + -
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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