Contacts of the strand formed by residues 164 - 169 (chain K) in PDB entry 1QDU
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 TYR 164 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220E LEU* 4.0 22.7 - - + +
163K GLY* 1.3 75.7 - - - -
165K CYS* 1.3 60.5 + - - +
166K LEU* 3.8 4.3 - - + -
198K PHE* 3.8 2.1 - - - -
199K GLU* 3.2 32.1 - - + +
201K LYS* 4.0 27.1 - - + -
218K TYR* 3.7 23.1 - + + -
221K MET* 3.5 31.1 - - + -
222K ASP 6.0 1.6 - - - -
224K HIS* 3.8 26.0 + + - -
227K MET* 3.5 27.8 - - + +
229K CYS 4.3 2.4 + - - -
230K PHE* 3.6 11.8 - - + -
231K ILE 3.1 23.2 + - - +
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Residues in contact with CYS 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K TYR* 1.3 73.8 - - - +
166K LEU* 1.3 70.2 + - - +
167K ILE* 3.3 21.1 + - - +
193K PHE* 4.0 30.3 - - - -
198K PHE* 4.1 15.0 - - + -
199K GLU 2.9 9.0 + - - +
200K ILE* 3.9 20.2 - - + -
201K LYS* 3.4 15.4 + - - -
231K ILE* 3.0 22.0 - - + -
233K CYS* 4.3 3.8 - - - -
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Residues in contact with LEU 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K TYR* 4.4 3.4 - - + -
165K CYS* 1.3 75.6 - - - +
167K ILE* 1.3 62.1 + - - +
168K ILE* 3.9 6.3 - - + +
201K LYS* 3.7 12.1 - - + +
203K HIS* 5.4 0.7 - - - +
214K ILE* 3.4 33.0 - - + -
215K LEU* 3.8 22.7 - - + -
218K TYR* 3.5 39.9 - - + -
230K PHE* 3.4 28.3 - - + -
231K ILE 2.9 9.3 + - - +
232K CYS* 3.5 12.9 - - - -
233K CYS* 2.8 26.0 + - - +
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Residues in contact with ILE 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K CYS* 3.5 17.9 - - - +
166K LEU* 1.3 80.3 - - - +
168K ILE* 1.3 57.9 + - - +
169K ASN* 3.1 22.1 + - + +
186K ALA* 4.0 16.2 - - + +
189K LEU* 3.8 24.9 - - + -
190K THR* 3.7 26.9 - - - +
200K ILE* 3.9 12.3 - - + -
201K LYS 3.3 8.7 + - - -
202K PRO* 3.7 12.6 - - + +
203K HIS* 3.2 19.3 + - - +
233K CYS* 3.4 14.4 - - + +
235K LEU* 4.7 7.9 - - + -
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Residues in contact with ILE 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K LEU* 5.0 7.0 - - + -
167K ILE* 1.3 72.8 - - - +
169K ASN* 1.3 58.0 + - - +
170K ASN* 3.9 18.4 - - - +
203K HIS* 3.7 8.1 - - + +
206K CYS* 4.2 10.8 - - - -
211K ILE* 3.6 51.4 - - + +
214K ILE* 4.4 27.1 - - + -
215K LEU* 4.8 8.5 - - + -
232K CYS* 5.4 1.3 - - - -
233K CYS 2.7 13.0 + - - +
234K ILE* 3.4 23.1 - - + -
235K LEU* 2.9 26.0 + - - +
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Residues in contact with ASN 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K ILE* 3.1 11.6 + - + +
168K ILE* 1.3 72.3 - - - +
170K ASN* 1.3 67.4 + - - +
171K HIS* 4.1 6.2 + - - +
182K THR* 3.2 36.4 + - - +
183K HIS* 3.9 5.5 + - - +
186K ALA* 3.5 26.1 - - + +
203K HIS 2.9 13.0 + - - +
204K HIS* 3.2 22.9 + - + +
205K ASP* 2.9 21.5 + - - +
235K LEU* 3.7 14.4 - - + +
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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