Contacts of the strand formed by residues 366 - 372 (chain A) in PDB entry 6TAV
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 PHE 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A LYS 5.2 5.4 - - - -
355A VAL* 4.1 1.0 - - - -
356A ASP* 3.6 33.3 + - - +
363A ILE* 6.3 3.8 - - + -
364A PRO 4.5 5.6 - - - -
365A PHE* 1.4 98.1 - - - +
367A GLY* 1.3 57.8 + - - +
407A PHE 3.5 9.9 - - - +
408A SER* 4.1 9.4 - - - +
460A HIS* 4.3 10.8 - + - -
462A GLU* 3.2 37.7 - - + -
463A PRO* 3.9 15.0 - - + -
479A HIS* 4.7 10.3 - + - -
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Residues in contact with GLY 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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352A PHE* 6.0 0.2 - - - -
354A LYS 3.7 2.9 - - - -
355A VAL* 3.6 19.1 - - - -
365A PHE* 4.7 7.0 - - - -
366A PHE* 1.3 75.6 - - - +
368A GLN* 1.3 60.0 + - - -
369A VAL* 5.0 0.2 - - - -
406A GLN* 4.7 0.9 - - - -
407A PHE* 2.9 54.5 + - - +
408A SER* 4.9 0.2 - - - +
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Residues in contact with GLN 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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352A PHE* 3.6 2.1 - - - -
353A VAL* 3.2 47.2 + - + +
354A LYS* 3.2 39.6 + - + +
355A VAL* 3.4 11.3 - - - +
367A GLY* 1.3 70.3 - - - -
369A VAL* 1.4 69.6 + - - +
404A LEU* 3.6 31.3 - - + +
405A VAL 3.8 5.6 - - - +
406A GLN* 3.7 26.9 + - + +
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Residues in contact with VAL 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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350A LEU* 4.4 8.5 - - + -
351A SER 3.3 18.6 - - - +
352A PHE* 3.7 22.2 - - + +
353A VAL* 3.9 4.3 - - - -
368A GLN* 1.4 76.6 - - - +
370A ARG* 1.3 71.1 + - - +
404A LEU* 3.6 6.9 - - - +
405A VAL* 3.1 43.8 + - + +
407A PHE* 4.0 22.7 - - + -
421A VAL* 4.1 31.9 - - + -
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Residues in contact with ARG 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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350A LEU* 3.3 6.1 - - - +
351A SER* 2.8 39.6 + - - +
352A PHE 5.5 0.2 - - - +
353A VAL* 4.1 27.2 - - + +
369A VAL* 1.3 75.3 - - - +
371A LEU* 1.4 61.4 + - - +
372A VAL* 4.3 15.0 - - + +
378A PRO* 5.4 3.8 - - + +
402A HIS* 4.0 10.3 - - - +
403A GLY 3.1 19.5 - - - +
404A LEU* 4.1 17.3 - - + +
405A VAL* 5.9 0.7 - - - -
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Residues in contact with LEU 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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348A THR* 4.7 7.9 - - + -
349A LYS 3.8 8.1 - - - +
350A LEU* 4.2 4.9 - - + -
370A ARG* 1.4 71.6 - - - +
372A VAL* 1.3 71.4 + - - +
373A ASP* 3.6 19.1 - - - +
378A PRO* 3.3 23.4 - - - +
379A ILE* 3.7 27.6 - - + +
382A LYS* 5.5 5.6 - - + -
384A ILE* 4.8 2.5 - - + -
399A THR* 3.8 26.9 - - + +
403A GLY 2.9 12.7 + - - +
404A LEU* 4.8 0.4 - - - +
423A VAL* 3.4 38.8 - - + -
424A ASN* 5.3 3.4 - - - +
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Residues in contact with VAL 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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348A THR* 3.8 2.3 - - - +
349A LYS* 2.7 43.0 + - + +
350A LEU* 4.7 4.7 - - - -
351A SER* 5.1 6.5 - - - +
370A ARG* 4.3 25.1 - - + +
371A LEU* 1.3 86.6 - - - +
373A ASP* 1.3 79.1 + - - +
374A GLY 5.7 0.2 - - - +
376A GLY* 3.4 34.5 - - - +
377A VAL 3.5 6.3 - - - +
378A PRO* 5.7 1.1 - - + -
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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