Contacts of the strand formed by residues 365 - 372 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A GLY* 3.3 21.0 - - - -
363A PRO* 4.1 0.7 - - - +
364A VAL* 1.3 73.6 - - + +
366A THR* 1.3 69.7 + - - +
412A GLU* 4.2 26.5 - - + +
413A ILE 3.6 4.7 - - - +
414A PRO* 3.7 18.2 - - + -
447A ILE* 3.7 43.1 - - + +
673A LEU* 3.8 28.7 - - + -
690A ARG* 4.2 22.7 - - - +
692A HIS* 4.2 15.5 - - + +
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Residues in contact with THR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A LEU* 4.6 19.3 - - + -
359A VAL* 4.8 0.9 - - + -
360A HIS 3.3 19.5 - - - +
361A PRO* 3.8 11.4 - - + +
362A GLY 3.7 5.4 + - - +
365A ILE* 1.3 76.2 + - - +
367A ARG* 1.3 70.5 + - - +
368A PHE* 4.0 9.8 - - + -
411A ILE 3.4 1.0 - - - +
412A GLU* 3.4 2.4 - - - -
413A ILE* 2.8 43.3 + - - +
415A ASN* 2.9 33.0 + - - +
447A ILE* 5.8 0.4 - - - -
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Residues in contact with ARG 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A VAL* 4.1 0.5 - - - +
360A HIS* 3.2 50.0 + - + +
366A THR* 1.3 83.7 - - - +
368A PHE* 1.3 76.6 + - - +
369A GLU* 4.2 2.4 - - - +
400A VAL* 3.5 26.9 - - - +
403A ILE* 3.4 37.9 - - - +
410A GLY* 4.2 7.0 - - - -
411A ILE 3.3 7.4 - - - +
412A GLU* 3.3 30.5 + - + +
447A ILE* 3.7 37.3 - - + +
448A GLY* 6.2 0.4 - - - -
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Residues in contact with PHE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A LEU* 4.5 12.3 - - + -
339A MET* 3.7 28.3 - - + -
340A SER* 3.7 26.2 - - - -
343A LEU* 4.4 10.8 - - + -
356A VAL* 4.8 5.4 - - + -
358A SER 3.8 3.6 - - - -
359A VAL* 4.2 19.5 - - + -
366A THR* 4.0 7.4 - - + -
367A ARG* 1.3 88.6 - - - +
369A GLU* 1.3 62.1 + - - +
370A ILE* 3.0 22.9 + - + +
409A VAL 3.6 0.2 - - - +
410A GLY* 3.5 5.2 - - - -
411A ILE* 2.9 43.1 + - + +
413A ILE* 3.6 38.1 - - + -
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Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A VAL* 3.6 1.2 - - - +
357A ASP* 2.6 40.2 + - + +
358A SER* 2.7 36.9 + - - +
360A HIS* 2.4 42.1 + - + -
367A ARG* 4.2 5.0 + - - +
368A PHE* 1.3 70.0 - - - +
370A ILE* 1.3 54.2 + - - +
403A ILE* 4.6 13.7 - - + +
406A LYS* 4.8 15.8 + - - +
408A THR* 4.1 18.0 + - - +
409A VAL 4.2 4.3 - - - -
410A GLY* 5.1 1.1 - - - -
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LEU* 4.0 11.7 - - + -
347A LEU* 4.6 4.7 - - + -
354A VAL* 3.7 27.6 - - + -
355A SER 3.4 4.3 - - - +
356A VAL* 3.8 27.1 - - + +
368A PHE* 3.0 17.1 + - + +
369A GLU* 1.3 79.1 - - - +
371A GLN* 1.3 60.1 + - - +
372A PRO* 3.7 2.6 - - - +
381A ILE* 5.4 7.2 - - + -
408A THR* 3.3 11.4 - - - -
409A VAL* 3.1 44.0 + - + +
411A ILE* 3.7 30.5 - - + -
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Residues in contact with GLN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A VAL* 3.6 2.4 - - - -
355A SER* 3.0 37.1 + - - +
357A ASP* 4.7 11.5 + - + +
370A ILE* 1.3 72.8 - - - +
372A PRO* 1.3 85.9 - - - +
373A ALA* 3.8 1.3 + - - -
406A LYS* 5.0 0.2 - - - +
407A THR* 2.5 37.9 + - - -
408A THR* 3.4 18.6 - - + +
390B ARG* 3.2 22.7 + - - -
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Residues in contact with PRO 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A GLU 3.9 3.6 - - - +
354A VAL* 3.6 16.6 - - + -
370A ILE 3.7 9.0 - - - +
371A GLN* 1.3 112.8 - - - +
373A ALA* 1.3 67.1 + - - +
374A ALA 3.9 0.2 - - - -
376A VAL* 3.7 30.3 - - + +
378A VAL* 6.0 0.7 - - + -
381A ILE* 6.2 2.9 - - + -
409A VAL* 4.2 15.3 - - + +
390B ARG* 3.4 34.7 + - - +
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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