Contacts of the strand formed by residues 204 - 209 (chain R) in PDB entry 2QKK
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 LYS 204 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C C 5.8 2.2 + - - -
138R ASP* 3.9 29.9 + - + +
139R PHE* 3.3 35.9 - - + -
140R VAL* 3.1 21.4 + - - +
202R ILE* 3.6 6.4 - - + +
203R ASN* 1.3 101.4 - - - +
205R LEU* 1.3 63.6 + - - +
254R MET* 4.8 0.4 - - - -
255R ASP* 3.2 32.6 + - + +
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Residues in contact with LEU 205 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139R PHE* 3.8 6.0 - - - -
140R VAL* 2.7 26.9 - - + +
142R VAL* 3.7 27.1 - - + -
164R TRP* 3.9 22.4 - - + -
194R ILE* 5.2 5.8 - - - +
197R ALA* 4.2 14.4 - - + -
202R ILE* 5.7 0.9 - - + +
204R LYS* 1.3 78.1 - - - +
206R VAL* 1.3 62.7 + - - +
207R LEU* 3.5 14.5 + - + -
254R MET* 4.6 8.7 - - - -
255R ASP 3.2 3.6 + - - -
256R ILE* 3.4 38.1 - - + +
257R GLN 3.0 20.1 + - - -
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Residues in contact with VAL 206 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 3.6 26.7 - - + -
136R MET* 3.9 8.5 - - - -
139R PHE* 3.6 22.9 - - + -
140R VAL 3.0 3.6 + - - -
141R VAL* 3.6 21.6 - - + +
142R VAL* 3.1 26.9 + - - +
205R LEU* 1.3 70.6 - - - +
207R LEU* 1.3 61.3 + - - +
208R TYR* 3.6 26.8 + - + +
257R GLN* 3.4 14.4 - - + +
259R MET* 3.8 17.7 - - + -
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Residues in contact with LEU 207 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142R VAL* 3.5 22.7 - - + -
144R THR* 3.5 31.6 - - + +
190R ALA* 4.1 5.8 - - + -
193R ALA* 4.2 5.2 - - + -
194R ILE* 4.0 22.0 - - + -
205R LEU* 3.5 11.6 + - + -
206R VAL* 1.3 71.8 - - - +
208R TYR* 1.3 63.1 + - - +
209R THR* 3.7 2.6 + - - +
256R ILE* 3.7 28.3 - - + -
257R GLN 2.9 10.1 + - - +
258R TRP* 3.7 32.1 - - + -
259R MET 3.0 23.4 + - - +
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Residues in contact with TYR 208 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136R MET* 3.0 28.0 - - + +
141R VAL* 3.6 28.5 - - + -
142R VAL 3.0 7.3 + - - +
143R TYR* 3.5 41.9 - + + +
144R THR* 3.1 27.0 + - - +
206R VAL* 3.6 23.1 - - + +
207R LEU* 1.3 72.3 - - - +
209R THR* 1.3 60.3 + - - +
259R MET* 3.0 33.2 - - + +
260R HIS 4.8 0.9 - - - -
261R VAL* 3.4 29.8 - - + -
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Residues in contact with THR 209 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144R THR* 3.1 29.1 + - - -
186R GLU* 4.4 8.0 + - - +
190R ALA* 5.7 1.5 - - - +
207R LEU* 4.6 5.8 - - - +
208R TYR* 1.3 77.1 - - - +
210R ASN* 1.3 63.7 + - - +
211R SER* 3.5 30.9 + - - +
214R THR* 4.8 7.9 + - + +
215R ILE* 3.9 18.5 - - + +
258R TRP* 4.8 9.0 - - + -
259R MET 3.1 3.5 + - - +
260R HIS* 3.4 20.6 + - - +
261R VAL* 4.0 6.0 - - - +
270R ASN* 5.2 0.7 - - - +
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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