Contacts of the strand formed by residues 365 - 370 (chain B) in PDB entry 6T8O
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 ILE 365 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B GLY* 3.3 24.8 - - - -
364B VAL* 1.3 89.2 - - + +
366B THR* 1.3 81.1 + - - +
367B ARG* 4.5 0.9 - - - +
412B GLU* 4.3 12.8 - - + -
413B ILE 3.4 10.5 - - - +
414B PRO* 3.7 24.0 - - + -
415B ASN* 4.0 1.8 - - - +
447B ILE* 3.7 34.1 + - + +
673B LEU* 6.2 3.1 - - + -
690B ARG* 3.3 48.2 - - - +
692B HIS* 4.9 2.4 + - + +
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Residues in contact with THR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 4.6 12.6 - - + +
359B VAL* 4.7 0.7 - - + -
360B HIS 3.3 17.3 - - - +
361B PRO* 3.8 10.7 - - + +
362B GLY 4.2 3.7 + - - +
365B ILE* 1.3 84.8 + - - +
367B ARG* 1.3 59.0 + - - +
368B PHE* 3.6 34.2 + - + -
411B ILE 3.4 2.8 - - - +
412B GLU* 3.6 1.6 - - - -
413B ILE* 2.9 37.4 + - - +
415B ASN* 3.9 22.5 + - - -
447B ILE 5.6 0.2 - - - -
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Residues in contact with ARG 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B HIS* 2.8 65.6 + - + +
365B ILE* 4.5 2.1 - - + +
366B THR* 1.3 72.3 - - - +
368B PHE* 1.3 71.1 + - - +
369B GLU* 4.0 8.2 + - + +
400B VAL* 4.8 12.9 - - - +
403B ILE* 4.9 14.2 - - - +
410B GLY* 4.8 8.3 - - - -
411B ILE 3.5 8.1 - - - +
412B GLU* 3.5 30.2 + - + +
447B ILE* 3.5 44.0 + - + +
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Residues in contact with PHE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B LEU* 4.5 6.5 - - + -
339B MET* 3.6 37.0 - - + -
340B SER* 3.8 17.0 - - - -
343B LEU* 3.6 23.6 - - + -
356B VAL* 5.1 3.6 - - + -
358B SER 4.2 2.2 - - - +
359B VAL* 3.6 35.2 - - + -
366B THR* 3.6 19.7 - - + -
367B ARG* 1.3 78.8 - - - +
369B GLU* 1.3 61.6 + - - +
370B ILE* 3.1 23.0 + - + +
409B VAL 3.5 0.5 - - - +
411B ILE* 2.9 35.4 + - + +
413B ILE* 3.6 21.3 - - + -
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Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B VAL* 4.2 0.3 - - - -
357B ASP* 3.0 27.7 + - - +
358B SER* 2.8 31.7 + - - +
360B HIS* 2.8 38.7 + - + -
367B ARG* 4.0 6.8 + - + -
368B PHE* 1.3 68.5 - - - +
370B ILE* 1.3 61.6 + - - +
403B ILE* 3.7 25.1 - - + +
406B LYS* 4.0 25.7 + - - +
408B THR* 3.9 22.4 + - + +
409B VAL 3.7 7.0 - - - -
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 3.8 19.1 - - + -
354B VAL* 3.7 24.7 - - + -
355B SER 3.8 3.1 - - - +
356B VAL* 3.7 26.9 - - + +
368B PHE* 3.8 13.5 - - + +
369B GLU* 1.3 73.7 - - - +
371B GLN* 1.3 60.3 + - - +
372B PRO* 3.3 15.3 - - + +
381B ILE* 5.2 9.6 - - + -
408B THR* 3.5 5.3 - - - -
409B VAL* 3.0 56.5 + - + +
411B ILE* 3.7 23.6 - - + -
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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