Contacts of the strand formed by residues 238 - 244 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232L ARG* 3.1 32.3 + - - +
233L ALA* 3.7 3.6 - - - -
236L THR* 2.8 24.5 + - - +
237L GLY* 1.3 86.0 - - - +
239L GLY* 1.3 58.2 - - - +
333L VAL 3.3 7.8 + - - +
334L ASN* 3.1 36.4 + - - +
345L LEU* 3.9 21.1 - - + -
2018N C 4.0 16.6 + - - -
2019N T 3.1 30.6 + - - -
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Residues in contact with GLY 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229L GLY 4.1 7.6 - - - -
232L ARG* 3.8 18.5 - - - +
233L ALA* 4.0 14.7 - - - +
238L ARG* 1.3 74.0 - - - +
240L SER* 1.3 61.8 + - - -
241L ILE 4.1 0.2 - - - -
332L GLY* 3.8 1.8 - - - -
333L VAL* 2.9 35.8 + - - +
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Residues in contact with SER 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229L GLY* 3.1 22.3 - - - -
232L ARG* 4.3 7.5 - - - +
239L GLY* 1.3 73.4 - - - -
241L ILE* 1.3 60.6 + - - +
242L GLN* 3.5 24.0 + - - +
330L SER* 3.7 12.0 - - - -
331L PHE 3.9 4.7 + - - -
332L GLY* 4.7 4.6 - - - -
2019N T 6.5 1.1 - - - -
2020N T 4.3 5.5 + - - -
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Residues in contact with ILE 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L PRO* 4.9 0.9 - - + -
216L PRO* 3.7 25.8 - - + -
218L PHE* 4.9 1.8 - - + -
224L ILE* 3.8 38.6 - - + -
229L GLY* 4.0 3.8 - - - +
230L ILE* 3.9 30.5 - - + +
233L ALA* 4.6 2.7 - - + -
234L TYR* 6.0 1.8 - - + -
239L GLY 4.9 0.2 - - - +
240L SER* 1.3 77.5 + - - +
242L GLN* 1.3 63.4 + - - +
243L MET* 3.6 7.2 + - + -
330L SER* 3.4 1.6 - - - -
331L PHE* 2.7 47.0 + - + +
333L VAL* 3.5 28.7 - - + -
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Residues in contact with GLN 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224L ILE* 3.4 6.0 - - - +
225L LEU* 3.0 47.9 + - + +
240L SER* 3.5 15.2 + - - +
241L ILE* 1.3 71.1 - - - +
243L MET* 1.3 62.3 + - - +
328L GLN* 3.2 34.4 + - - +
329L THR 4.0 5.2 - - - +
330L SER* 3.4 27.3 + - - -
2020N T 4.5 3.6 + - - -
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Residues in contact with MET 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L PHE* 3.5 42.8 - - + -
223L LEU 3.3 7.6 - - - +
224L ILE* 4.7 0.9 - - + +
241L ILE* 3.6 8.9 + - + +
242L GLN* 1.3 74.2 - - - +
244L ARG* 1.3 61.3 + - - +
265L PRO* 3.9 15.7 - - + -
266L PHE* 3.7 37.7 - - + +
328L GLN* 3.4 9.8 - - - +
329L THR* 2.8 57.8 + - + +
330L SER 4.0 1.8 - - - +
331L PHE* 4.0 20.6 - - + -
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Residues in contact with ARG 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A GLU* 4.8 13.5 - - - +
255A GLY* 6.3 1.2 - - - -
222L GLY* 3.8 2.5 - - - -
223L LEU* 2.7 43.4 + - + +
225L LEU* 3.6 39.9 - - + +
243L MET* 1.3 75.7 - - - +
245L SER* 1.3 65.2 + - - +
246L ARG 3.7 0.2 + - - -
265L PRO* 4.4 4.5 - - - -
319L ASN* 5.7 2.6 + - - -
322L TYR* 3.4 58.1 - - + +
327L LEU 3.8 3.4 - - - +
328L GLN* 3.0 28.6 + - + +
489L GLN* 5.7 2.2 + - - -
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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