Contacts of the strand formed by residues 238 - 244 (chain j) in PDB entry 6QX2
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 ARG 238 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232j ARG* 3.1 16.3 - - - +
233j ALA* 3.7 4.5 - - - -
236j THR* 2.8 24.0 + - - +
237j GLY* 1.3 84.5 - - - +
239j GLY* 1.3 57.8 + - - +
333j VAL 3.3 7.9 - - - +
334j ASN* 3.8 21.7 + - - +
345j LEU* 3.9 23.3 - - + +
2019o T 3.7 26.8 + - - +
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Residues in contact with GLY 239 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229j GLY 4.1 8.3 - - - -
232j ARG* 4.6 10.3 - - - -
233j ALA* 4.0 14.7 - - - +
238j ARG* 1.3 74.4 - - - +
240j SER* 1.3 60.7 + - - -
332j GLY* 3.8 0.9 - - - -
333j VAL* 2.9 35.3 + - - +
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Residues in contact with SER 240 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229j GLY* 3.1 23.0 - - - -
232j ARG* 4.9 6.7 + - - +
239j GLY* 1.3 71.3 - - - -
241j ILE* 1.3 57.5 + - - +
242j GLN* 3.5 15.9 + - - +
330j SER* 2.6 25.5 + - - -
331j PHE 3.9 3.6 - - - -
332j GLY* 4.7 2.5 - - - -
2019o T 4.6 6.4 + - - -
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Residues in contact with ILE 241 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184j PRO* 4.9 0.4 - - + -
216j PRO* 3.7 25.4 - - + -
218j PHE* 4.9 1.6 - - + -
224j ILE* 3.8 39.3 - - + -
229j GLY* 4.0 3.1 - - - -
230j ILE* 3.9 32.5 - - + +
233j ALA* 4.6 2.2 - - + -
234j TYR* 6.0 1.6 - - + -
239j GLY 4.8 0.2 - - - +
240j SER* 1.3 75.9 + - - +
242j GLN* 1.3 65.0 + - - +
243j MET* 3.6 6.8 + - + -
330j SER* 3.4 1.4 - - - -
331j PHE* 2.7 46.1 + - + +
333j VAL* 3.5 28.3 - - + -
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Residues in contact with GLN 242 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224j ILE* 3.4 5.9 - - - +
225j LEU* 3.0 48.8 + - + +
240j SER* 3.5 14.6 + - - +
241j ILE* 1.3 69.4 - - - +
243j MET* 1.3 61.1 + - - +
328j GLN* 3.2 35.3 + - - +
329j THR 4.0 5.5 - - - +
330j SER* 3.4 26.6 + - - -
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Residues in contact with MET 243 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218j PHE* 3.5 42.4 - - + -
223j LEU 3.3 8.1 - - - +
224j ILE* 4.7 1.1 - - + +
241j ILE* 4.3 9.0 - - + +
242j GLN* 1.3 73.1 - - - +
244j ARG* 1.3 60.1 + - - +
265j PRO* 3.9 15.7 - - + -
266j PHE* 3.7 37.0 - - + +
328j GLN* 3.4 9.2 - - - +
329j THR* 2.8 58.9 + - + +
330j SER 4.0 0.7 - - - +
331j PHE* 4.0 21.8 - - + +
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Residues in contact with ARG 244 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222j GLY* 3.8 2.8 - - - -
223j LEU* 2.7 50.6 + - + +
225j LEU* 3.7 38.8 - - + +
243j MET* 1.3 74.5 - - - +
245j SER* 1.3 64.9 - - - +
246j ARG 3.7 0.2 + - - -
265j PRO* 4.4 5.1 - - - +
319j ASN* 5.6 4.0 + - - -
322j TYR* 3.4 56.2 - - + +
327j LEU 3.8 3.1 - - - -
328j GLN* 3.0 29.3 + - + +
251t GLU* 4.5 16.1 - - - +
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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