Contacts of the strand formed by residues 220 - 224 (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 PHE 220 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G LEU* 5.1 2.2 - - + -
164G LEU* 4.1 13.9 - - + -
187G PHE* 6.1 0.4 - - - -
213G TRP* 3.5 26.7 - + - -
214G HIS* 3.2 7.7 - - - +
215G ASN* 3.1 41.1 + - + +
218G LYS 3.7 1.1 - - - -
219G SER* 1.3 81.0 - - - +
221G LEU* 1.3 60.5 + - - +
222G ILE* 4.3 16.2 - - + -
232G VAL* 3.7 28.7 - - + -
233G ILE 3.4 12.1 - - - -
234G SER* 4.3 9.6 - - - -
235G MET* 6.2 0.2 - - - -
247G ARG* 4.1 20.0 - - + -
248G PHE* 4.3 11.7 - + - -
251G GLY* 3.7 34.1 - - - -
252G LEU* 4.3 1.3 - - - -
255G VAL* 5.0 4.9 - - + -
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Residues in contact with LEU 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ARG* 6.2 0.2 - - - +
186G HIS 4.8 2.0 - - - +
187G PHE* 3.8 40.2 - - + -
212G ILE* 3.7 17.0 - - + -
213G TRP 3.3 12.1 - - - +
214G HIS* 4.3 4.3 - - + -
219G SER 4.3 0.2 - - - -
220G PHE* 1.3 73.8 - - - +
222G ILE* 1.3 77.2 + - - +
223G TRP* 3.6 36.8 - - + +
231G ARG 3.8 1.1 - - - +
232G VAL* 3.7 0.3 - - - +
233G ILE* 2.8 62.0 + - + +
235G MET* 4.9 11.0 - - + -
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Residues in contact with ILE 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G VAL* 4.9 2.0 - - + -
157G LEU* 3.7 33.2 - - + -
212G ILE* 3.7 1.6 - - - -
213G TRP* 2.8 55.6 + - + +
220G PHE* 4.3 16.8 - - + -
221G LEU* 1.3 81.1 - - - +
223G TRP* 1.3 76.1 + - - +
224G VAL* 4.0 13.9 + - + +
230G THR* 4.4 14.4 - - + -
231G ARG 3.3 7.0 - - - +
232G VAL* 4.3 22.7 - - + -
255G VAL* 4.7 9.0 - - + -
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Residues in contact with TRP 223 (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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125G ARG* 6.3 0.7 - - - -
186G HIS 5.1 2.9 - - - -
187G PHE* 2.9 31.4 + - - -
188G LEU 3.9 7.0 - - - -
189G PHE* 3.4 42.8 - + + -
211G GLY 3.9 1.6 - - - -
212G ILE* 4.2 4.3 - - + -
221G LEU* 3.6 27.3 - - + +
222G ILE* 1.3 80.4 - - - +
224G VAL* 1.3 62.4 + - - +
225G ASN 4.0 0.3 + - - -
226G GLU* 3.6 36.1 + - + -
228G ASP 4.9 0.2 - - - +
229G HIS 3.7 0.3 - - - +
230G THR* 3.2 8.3 - - - -
231G ARG* 2.9 49.6 + - + +
233G ILE* 4.9 13.0 - - + -
400G PO4 5.6 4.9 - - - -
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Residues in contact with VAL 224 (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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149G VAL* 4.6 5.6 - - + +
150G GLU* 4.1 19.5 - - + -
153G VAL* 4.1 24.5 - - + -
154G VAL* 5.6 0.9 - - + -
157G LEU* 5.2 1.8 - - + -
168G TYR* 4.1 24.0 - - + +
189G PHE* 4.2 2.3 - - - -
209G ALA 4.3 3.6 - - - +
210G ARG* 3.3 5.0 - - - +
211G GLY 2.9 35.2 + - - +
222G ILE* 4.3 12.1 - - + +
223G TRP* 1.3 73.5 - - - +
225G ASN* 1.3 89.8 + - - +
226G GLU 3.4 2.9 + - - -
229G HIS 3.5 7.2 - - - +
230G THR* 4.9 0.9 - - + -
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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
------------------------------------------------------------
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