Contacts of the strand formed by residues 344 - 348 (chain A) in PDB entry 5FFO
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A SER* 3.4 30.5 + - - +
280A VAL 4.5 4.4 - - - +
281A ALA* 3.8 23.5 - - + +
294A PHE* 4.0 16.6 - - + +
295A ILE 4.2 2.0 - - - -
296A GLY* 3.7 25.1 - - - +
315A VAL* 4.2 14.1 - - + -
341A GLY 4.4 2.9 - - - +
343A ALA* 1.3 80.1 - - - +
345A ALA* 1.3 60.4 + - - +
346A PRO* 3.8 2.3 - - - +
358A ILE* 3.7 26.7 - - + -
359A ALA 3.5 8.3 - - - +
360A ILE* 4.4 14.1 - - + -
409A MET* 4.5 3.1 - - - +
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Residues in contact with ALA 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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344A ILE* 1.3 72.2 - - - +
346A PRO* 1.3 66.8 - - - +
347A LEU* 3.4 8.7 + - + +
358A ILE* 4.0 3.1 - - - -
359A ALA 3.1 29.7 + - - -
409A MET* 3.5 49.9 - - + +
410A LYS* 3.9 11.0 - - - +
411A GLY 4.2 3.4 - - - +
423A LEU* 4.6 0.4 - - + -
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Residues in contact with PRO 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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281A ALA* 4.0 19.1 - - + -
282A ALA 4.5 6.7 - - - +
283A THR* 3.6 35.2 - - + +
344A ILE 3.8 7.2 - - - +
345A ALA* 1.3 80.9 - - + +
347A LEU* 1.3 59.8 + - - +
348A GLY 3.5 3.6 - - - +
357A ASP 4.2 1.6 - - - +
358A ILE* 4.0 9.6 - - + -
410A LYS* 5.0 16.1 - - + -
411A GLY* 3.3 27.2 + - - +
412A ALA* 3.5 5.3 + - + +
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Residues in contact with LEU 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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345A ALA 3.4 17.9 - - - +
346A PRO* 1.3 74.1 - - - +
348A GLY* 1.3 63.3 + - - +
350A LEU* 4.0 36.0 + - + +
357A ASP* 3.1 14.3 + - + +
358A ILE* 3.5 25.1 - - - +
359A ALA* 3.6 16.4 - - + +
375A ILE* 4.1 11.2 - - + -
411A GLY* 4.3 4.0 - - - -
412A ALA* 3.3 21.2 + - - +
421A PRO* 3.4 16.6 - - - +
422A ASP 5.2 0.8 - - - +
423A LEU* 3.7 37.0 - - + -
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Residues in contact with GLY 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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283A THR* 5.6 1.0 + - - -
346A PRO* 3.5 5.1 - - - +
347A LEU* 1.3 81.3 - - - +
349A ASP* 1.3 54.1 + - - -
350A LEU 3.4 1.9 + - - -
356A ASN* 3.2 18.4 - - - +
357A ASP* 2.6 33.7 + - - +
412A ALA* 3.5 16.3 - - - +
421A PRO* 4.5 1.3 - - - -
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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