Contacts of the strand formed by residues 347 - 352 (chain A) in PDB entry 6VW1
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 THR 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A HIS* 3.5 22.0 + - + +
346A PRO* 1.3 79.5 - - - +
348A ALA* 1.3 59.8 + - - +
349A TRP* 2.8 30.3 + - + +
358A ILE* 3.5 6.1 - - - +
359A LEU* 2.9 42.9 + - - +
375A GLU* 3.8 7.1 - - - +
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Residues in contact with ALA 348 (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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347A THR* 1.3 73.8 - - - +
349A TRP* 1.3 62.8 + - - +
350A ASP* 3.8 1.9 + - - +
357A ARG 3.7 4.7 - - - -
358A ILE* 4.4 2.9 - - + -
375A GLU* 3.5 18.5 + - - +
378A HIS* 3.6 28.0 - - + +
379A ILE* 3.7 22.7 - - + +
382A ASP* 4.4 5.6 - - - +
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Residues in contact with TRP 349 (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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44A SER* 3.8 9.4 - - - -
47A SER* 3.2 33.4 - - - -
48A TRP* 3.4 51.4 - + + -
51A ASN* 3.9 26.7 - - + -
347A THR* 2.8 38.3 + - + -
348A ALA* 1.3 74.2 - - - +
350A ASP* 1.3 59.8 + - - +
351A LEU* 3.7 22.6 + - + -
356A PHE* 3.4 6.4 - - - -
357A ARG* 2.9 40.4 + - + +
359A LEU* 3.7 10.9 - - + +
379A ILE* 3.7 5.3 - - - +
382A ASP* 4.8 0.2 - - - -
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Residues in contact with ASP 350 (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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40A PHE* 3.6 16.5 - - - -
348A ALA 3.8 3.0 + - - +
349A TRP* 1.3 69.4 - - - +
351A LEU* 1.3 60.5 + - - +
352A GLY* 3.3 15.2 + - - -
355A ASP 3.9 3.3 - - - +
356A PHE* 3.4 24.2 - - - -
382A ASP* 3.5 24.8 - - + +
385A TYR* 3.9 24.1 + - - +
393A ARG* 4.9 12.6 - - - +
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Residues in contact with LEU 351 (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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37A GLU 5.3 0.2 - - - +
40A PHE* 3.4 20.2 - - - -
41A TYR* 3.4 17.9 - - + +
44A SER* 3.7 37.1 + - - +
45A LEU* 4.0 13.9 - - + -
48A TRP* 4.8 5.6 - - + -
349A TRP* 3.8 23.8 - - + +
350A ASP* 1.3 73.7 - - - +
352A GLY* 1.3 58.0 + - - +
355A ASP* 2.9 42.4 + - + +
357A ARG* 3.6 45.3 - - + +
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Residues in contact with GLY 352 (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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37A GLU* 3.9 9.6 - - - -
40A PHE* 5.0 5.2 - - - -
41A TYR* 3.1 15.3 - - - -
350A ASP* 3.2 16.5 + - - -
351A LEU* 1.3 77.5 - - - +
353A LYS* 1.3 73.4 + - - +
354A GLY 3.1 4.5 - - - -
355A ASP* 3.0 12.1 + - - +
390A PHE* 6.2 0.7 - - - -
393A ARG* 5.2 6.5 - - - -
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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