Contacts of the strand formed by residues 357 - 362 (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 ASP 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A THR* 5.2 1.0 - - - +
285A ILE* 3.9 5.5 - - - +
346A PRO* 4.1 1.9 - - - +
347A LEU* 3.1 25.9 + - + -
348A GLY 2.6 14.5 + - - +
349A ASP* 3.5 1.9 - - - +
350A LEU* 3.1 27.6 + - + +
351A ASP* 2.4 29.1 - - - +
353A ASP* 4.2 2.1 - - - +
355A PHE 3.2 7.8 - - - +
356A ASN* 1.3 79.8 - - - +
358A ILE* 1.3 64.6 + - - +
375A ILE* 5.4 0.7 - - + -
376A PHE 3.2 12.8 - - - +
377A ASN* 3.2 14.5 + - - +
378A GLY 2.9 21.8 + - - +
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Residues in contact with ILE 358 (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* 4.7 0.2 - - + -
283A THR* 4.0 13.0 - - + -
285A ILE* 4.3 3.1 - - + -
294A PHE* 3.7 35.9 - - + -
344A ILE* 3.7 22.9 - - + -
345A ALA 3.5 11.9 - - - +
346A PRO* 4.0 7.9 - - + -
347A LEU* 3.5 11.2 - - - +
357A ASP* 1.3 75.7 - - - +
359A ALA* 1.3 65.5 + - - +
360A ILE* 4.7 9.6 - - + -
375A ILE 3.8 0.5 - - - -
376A PHE* 2.8 40.3 + - + +
383A LEU* 3.7 35.7 - - + -
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 3.5 6.6 - - - +
345A ALA* 3.1 31.6 + - + +
347A LEU* 3.6 26.2 - - + +
358A ILE* 1.3 72.5 - - - +
360A ILE* 1.3 65.8 + - - +
373A VAL* 4.0 5.6 - - + -
374A TYR 3.3 10.8 - - - +
375A ILE* 3.9 11.0 - - + -
409A MET* 3.3 18.5 - - + +
423A LEU* 4.6 2.0 - - + -
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Residues in contact with ILE 360 (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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294A PHE* 5.8 1.6 - - + -
315A VAL* 4.0 25.8 - - + -
331A LEU* 4.2 7.9 - - + -
340A PHE* 3.6 25.1 - - + -
341A GLY* 3.6 32.3 - - - +
343A ALA 3.5 6.1 - - - +
344A ILE* 4.4 13.9 - - + -
358A ILE* 4.7 9.6 - - + -
359A ALA* 1.3 78.3 - - - +
361A ALA* 1.3 63.1 + - - +
373A VAL* 4.6 0.2 - - - -
374A TYR* 2.9 36.7 + - - +
376A PHE* 3.9 25.5 - - + -
383A LEU* 5.1 3.6 - - + -
409A MET* 3.8 2.0 - - - -
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Residues in contact with ALA 361 (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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340A PHE* 4.5 0.9 - - - -
341A GLY 3.1 22.3 + - - -
342A SER 3.5 9.9 + - - -
343A ALA* 3.0 12.5 + - + +
360A ILE* 1.3 74.1 - - - +
362A ALA* 1.3 59.7 + - - +
363A PRO* 3.6 3.4 - - + +
372A ILE 3.6 7.9 - - - +
373A VAL* 4.0 4.0 - - + +
406A GLY* 3.1 40.4 - - - +
409A MET* 3.5 13.4 - - + +
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Residues in contact with ALA 362 (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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335A GLU* 5.9 0.2 - - + -
338A ALA* 3.4 27.8 - - + +
339A ARG 3.9 1.6 - - - -
340A PHE* 3.9 13.5 - - + -
360A ILE 4.2 0.4 + - - -
361A ALA* 1.3 72.5 - - - +
363A PRO* 1.3 62.4 - - - +
364A TYR 2.8 12.6 + - - -
365A GLY* 2.9 11.3 + - - +
372A ILE* 2.8 25.3 + - + +
374A TYR* 4.2 20.4 - - + +
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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