Contacts of the strand formed by residues 343 - 349 (chain A) in PDB entry 6FD3
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 TYR 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ILE 4.8 0.2 + - - -
329A ILE* 4.1 19.9 - - + +
332A MET* 3.8 50.2 + - + +
333A ARG* 3.5 38.6 + - + -
336A LYS* 2.8 32.7 + - - +
341A VAL 3.3 5.5 + - - -
342A ASN* 1.3 75.0 + - - +
344A LEU* 1.3 71.5 + - - +
345A ASP* 3.3 29.7 + - - -
346A SER* 2.8 29.3 + - - -
355A VAL* 4.2 12.8 - - + -
356A VAL 4.2 1.3 - - - -
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Residues in contact with LEU 344 (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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307A GLN* 4.2 19.3 - - - +
309A VAL* 3.8 25.4 - - + -
336A LYS* 5.4 0.4 - - - +
342A ASN* 3.5 25.1 - - - +
343A TYR* 1.3 84.1 - - - +
345A ASP* 1.3 66.5 + - + +
356A VAL* 2.9 23.5 + - + +
357A MET* 3.7 25.1 - - - -
358A GLU* 3.9 4.3 - - + +
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Residues in contact with ASP 345 (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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275A SER* 2.5 31.9 + - - -
283A TYR* 4.9 3.8 - - - +
343A TYR* 3.3 20.1 + - - -
344A LEU* 1.3 80.8 - - + +
346A SER* 1.3 67.3 + - - +
347A TYR* 3.4 29.6 + - + +
355A VAL* 3.6 0.2 - - - -
356A VAL* 2.8 37.9 + - + +
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Residues in contact with SER 346 (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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273A ILE 4.1 0.2 + - - -
274A VAL* 3.5 22.2 - - - +
275A SER* 2.9 26.9 + - - -
329A ILE* 3.8 25.8 - - - +
343A TYR* 2.8 20.1 + - - -
345A ASP* 1.3 81.2 + - - +
347A TYR* 1.3 72.2 + - - +
353A LEU* 5.1 0.2 - - - -
354A TRP 3.1 13.0 - - - -
355A VAL* 4.2 5.4 - - - -
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Residues in contact with TYR 347 (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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274A VAL* 4.0 6.5 - - - -
275A SER* 3.8 16.2 - - - -
276A VAL 3.7 15.5 - - - -
277A GLY 3.5 20.0 - - - +
279A PRO* 3.7 40.4 - - + -
282A LYS* 3.5 31.4 + - + +
283A TYR* 4.0 11.6 + + - -
345A ASP* 3.4 27.2 + - + -
346A SER* 1.3 78.9 - - - +
348A LEU* 1.3 61.4 + - - +
349A VAL 4.3 0.2 - - - -
352A GLU 4.0 0.3 - - - +
353A LEU* 3.4 7.7 - - - +
354A TRP* 2.9 34.5 + - + -
356A VAL* 4.0 24.0 - - + -
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Residues in contact with LEU 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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267A LEU* 4.3 15.5 - - + +
270A LEU* 4.4 5.8 - - + -
271A ARG* 3.3 55.6 + - - +
274A VAL* 3.8 19.6 - - + +
275A SER 4.6 1.8 + - - +
277A GLY 4.5 5.9 + - - +
316A LEU* 3.8 12.6 - - + -
347A TYR* 1.3 73.5 - - - +
349A VAL* 1.3 65.7 + - - +
350A GLY 3.3 25.6 - - - +
352A GLU 3.1 23.3 - - - +
353A LEU* 3.9 14.4 - - + +
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Residues in contact with VAL 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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277A GLY 4.5 1.3 - - - +
278A ASP* 3.6 29.8 - - + +
279A PRO* 3.8 20.6 - - + -
280A LYS* 5.3 9.2 - - - -
347A TYR* 5.4 0.4 - - + -
348A LEU* 1.3 76.1 - - - +
350A GLY* 1.3 59.1 + - - +
351A ASP 2.8 11.1 + - - -
352A GLU* 2.9 42.2 + - + +
354A TRP* 4.6 11.0 - - + +
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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