Contacts of the strand formed by residues 258 - 263 (chain C) in PDB entry 3QKJ
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 MET 258 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C TYR* 3.6 10.2 - - - -
219C ASP* 4.8 0.2 - - - +
254C ALA* 3.9 5.9 - - + +
255C MET* 3.0 27.6 + - + +
256C SER 3.7 8.3 - - - +
257C GLY* 1.3 81.3 - - - +
259C ARG* 1.3 76.0 + - - +
271C GLU* 3.7 44.9 - - + +
272C VAL* 3.5 6.3 - - - -
273C SER* 3.5 37.5 - - - +
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Residues in contact with ARG 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C TYR* 3.6 41.3 + - - -
219C ASP* 2.8 44.3 + - - -
221C LYS* 3.3 13.1 + - - +
222C GLU 3.0 20.9 + - - +
223C PHE* 2.8 25.6 + - + -
243C VAL* 4.3 8.1 - - + -
254C ALA* 4.7 2.0 - - - -
257C GLY 4.1 4.6 - - - -
258C MET* 1.3 90.4 + - - +
260C TRP* 1.3 68.2 + - - +
261C VAL* 3.8 0.7 + - + +
270C SER 3.6 0.5 - - - +
271C GLU* 3.5 2.6 - - - -
272C VAL* 2.7 37.1 + - - +
274C ALA* 3.9 17.7 - - + +
277C LEU* 4.0 20.6 - - + -
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Residues in contact with TRP 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C TYR* 2.9 15.6 + - - +
243C VAL* 3.5 8.3 - - - +
244C VAL* 3.0 40.3 + - + +
245C SER 4.7 0.2 - - - +
246C TRP* 3.4 22.4 - - + -
249C THR* 3.8 19.5 - - + -
251C LYS* 3.6 40.2 - - + -
252C ARG* 2.7 53.9 + - + -
254C ALA* 3.4 24.4 - - + +
259C ARG* 1.3 73.6 - - - +
261C VAL* 1.3 60.3 + - - +
269C PHE* 4.2 2.5 - - + -
270C SER* 3.4 29.8 - - - -
271C GLU* 3.5 30.1 - - + -
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Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 4.3 4.5 - - + -
241C ALA* 3.9 15.3 - - + -
242C MET 3.2 8.1 - - - +
243C VAL* 4.3 12.3 - - + -
244C VAL* 4.3 4.0 - - - +
259C ARG* 4.4 5.6 - - + +
260C TRP* 1.3 79.9 - - - +
262C GLN* 1.3 58.8 + - - +
263C TRP* 3.9 31.0 - - + -
268C LYS 3.9 0.3 - - - +
269C PHE* 3.3 5.7 - - - +
270C SER 2.9 39.6 + - - +
272C VAL* 3.9 8.5 - - + -
277C LEU* 4.0 34.8 - - + -
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Residues in contact with GLN 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A GLN* 4.3 1.8 + - - +
254A ALA 2.9 25.3 + - - -
255A MET* 3.4 24.6 - - + +
256A SER* 2.9 25.6 + - - -
241C ALA* 3.2 3.3 - - - -
242C MET 2.8 30.3 + - - +
244C VAL* 4.0 12.3 - - + +
261C VAL* 1.3 73.7 - - - +
263C TRP* 1.3 63.0 + - - +
267C GLY* 3.0 33.6 + - - +
268C LYS 3.3 3.8 - - - +
269C PHE* 3.4 32.6 - - + -
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Residues in contact with TRP 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A MET* 3.7 2.8 - - - +
231C GLY* 3.6 32.8 - - - -
233C ILE* 3.8 29.6 - - + -
239C TRP* 3.4 38.1 - - + -
240C PRO 3.8 6.5 - - - -
241C ALA* 3.7 18.8 - - + -
261C VAL* 3.9 17.2 - - + +
262C GLN* 1.3 71.0 - - - +
264C PHE* 1.3 64.0 + - - +
266C ASP* 3.5 12.8 - - - +
267C GLY* 2.9 31.9 + - - -
268C LYS* 2.9 33.0 + - + -
270C SER* 2.8 32.5 + - - +
272C VAL* 4.3 2.5 - - + -
356C BTB 3.5 38.7 - - - -
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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