Contacts of the strand formed by residues 365 - 372 (chain E) in PDB entry 6T8G
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362E GLY* 3.3 24.1 + - - -
364E VAL* 1.3 89.3 - - + +
366E THR* 1.3 73.9 + - - +
367E ARG* 4.5 2.2 - - + +
412E GLU* 3.8 27.1 - - + -
413E ILE 3.3 11.2 - - - +
414E PRO* 3.8 22.4 - - + -
447E ILE* 3.7 34.5 + - + +
673E LEU* 4.5 0.7 - - + -
690E ARG* 3.4 33.0 - - - +
692E HIS* 4.0 14.6 + - - +
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Residues in contact with THR 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E LEU* 4.5 10.6 - - + +
359E VAL* 4.3 4.3 - - + -
360E HIS 3.3 18.6 - - - +
361E PRO* 3.8 11.2 - - + +
362E GLY 4.1 4.2 + - - -
365E ILE* 1.3 79.8 + - - +
367E ARG* 1.3 61.6 + - - +
368E PHE* 3.6 31.7 + - + -
411E ILE 3.7 0.9 - - - +
412E GLU* 3.4 1.2 - - - -
413E ILE* 2.7 38.8 + - - +
415E ASN* 3.0 28.3 + - - -
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Residues in contact with ARG 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359E VAL* 3.7 1.0 - - - -
360E HIS* 2.9 48.0 + - + +
365E ILE* 4.3 3.2 - - + +
366E THR* 1.3 72.5 - - - +
368E PHE* 1.3 68.4 + - - +
369E GLU* 3.7 27.3 + - + +
400E VAL* 4.9 8.6 - - - +
403E ILE* 3.3 47.3 - - - +
404E PRO* 5.0 4.8 - - - +
410E GLY* 4.8 7.6 - - - -
411E ILE 3.5 5.4 - - - +
412E GLU* 4.2 25.5 + - + -
447E ILE* 3.4 38.4 + - + +
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Residues in contact with PHE 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E LEU* 4.7 7.2 - - + -
339E MET* 3.6 33.0 - - + -
340E SER* 4.5 12.6 - - - -
343E LEU* 3.7 25.4 - - + -
356E VAL* 5.2 3.1 - - + -
358E SER 3.9 2.7 - - - -
359E VAL* 3.7 24.0 - - + -
366E THR* 3.6 28.3 - - + -
367E ARG* 1.3 77.9 - - - +
369E GLU* 1.3 61.7 + - - +
370E ILE* 3.0 25.9 + - + +
411E ILE* 2.6 36.1 + - + +
413E ILE* 3.6 28.5 - - + -
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Residues in contact with GLU 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E ASP* 3.1 9.2 + - - +
358E SER* 2.5 55.7 + - - +
360E HIS* 2.9 34.6 + - + -
367E ARG* 3.7 24.8 + - + +
368E PHE* 1.3 70.8 - - - +
370E ILE* 1.3 58.8 + - - +
403E ILE* 5.1 9.2 - - + +
406E LYS* 4.8 16.8 + - - +
408E THR* 3.8 25.2 + - + +
409E VAL 4.4 3.6 - - - -
410E GLY* 5.1 0.9 - - - -
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Residues in contact with ILE 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E LEU* 4.6 8.5 - - + -
347E LEU* 5.4 1.8 - - + -
354E VAL* 3.7 26.0 - - + -
355E SER 4.0 3.6 - - - +
356E VAL* 3.7 33.7 - - + +
357E ASP 4.0 0.2 - - - +
368E PHE* 3.0 20.4 + - + +
369E GLU* 1.3 77.2 - - - +
371E GLN* 1.3 63.6 + - - +
372E PRO* 3.8 3.4 - - + +
381E ILE* 5.6 7.0 - - + -
408E THR* 3.3 3.6 - - - -
409E VAL* 2.8 55.0 + - + +
411E ILE* 3.7 24.5 - - + -
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Residues in contact with GLN 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E VAL* 3.3 7.2 - - - +
355E SER* 3.3 29.0 + - - +
357E ASP* 4.3 14.1 - - + +
370E ILE* 1.3 75.7 - - - +
372E PRO* 1.3 82.5 + - + +
407E THR* 3.5 29.6 + - - +
408E THR* 4.3 12.6 - - + +
346F LYS* 5.4 8.1 - - - +
390F ARG* 5.3 1.3 - - - +
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Residues in contact with PRO 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E GLU 3.8 2.9 - - - +
354E VAL* 3.8 15.4 - - + -
370E ILE* 3.8 8.7 - - + +
371E GLN* 1.3 104.9 + - + +
373E ALA* 1.3 70.4 + - - +
376E VAL* 3.7 18.6 - - + +
377E LYS 5.7 1.8 - - - +
378E VAL* 6.0 0.4 - - + -
381E ILE* 5.9 8.7 - - + -
407E THR 4.5 1.1 - - - +
409E VAL* 4.1 13.0 - - + -
390F ARG* 3.4 38.6 - - - +
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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