Contacts of the strand formed by residues 369 - 377 (chain C) in PDB entry 5DX1
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 ARG 369 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365C GLY 4.7 0.6 + - - -
366C ASP 3.8 8.5 + - - +
368C HIS* 1.3 84.2 - - + +
370C ILE* 1.3 61.3 + - - +
371C GLU* 3.4 26.9 + - + +
439C LEU* 3.5 35.1 - - + +
440C LEU 3.4 4.9 - - - +
441C ILE* 4.6 17.8 - - + +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C PHE* 3.5 41.5 - - + -
355C TYR* 3.7 35.7 - - + +
366C ASP 4.0 15.0 - - - +
367C LEU* 4.0 13.9 - - + +
369C ARG* 1.3 73.1 - - - +
371C GLU* 1.3 61.6 + - - +
372C ILE* 4.0 15.9 - - + -
438C CYS 3.5 2.6 - - - +
439C LEU* 3.4 6.0 - - - +
440C LEU* 2.8 47.3 + - + +
448C TYR* 3.8 24.9 - - + +
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Residues in contact with GLU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C TYR* 3.6 17.2 + - - -
369C ARG* 3.4 27.1 + - + +
370C ILE* 1.3 73.2 - - - +
372C ILE* 1.3 62.5 + - - +
373C PRO* 3.4 16.0 - - + +
437C THR* 3.7 24.4 + - + +
438C CYS 3.9 1.8 - - - -
439C LEU* 3.8 9.2 - - + +
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Residues in contact with ILE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C PHE* 5.0 7.6 - - + -
292C VAL* 5.0 8.7 - - + -
294C LEU* 3.9 30.5 - - + -
353C VAL* 5.0 6.3 - - + -
355C TYR* 3.6 46.0 - - + -
370C ILE* 4.0 11.2 - - + -
371C GLU* 1.3 76.9 - - - +
373C PRO* 1.4 71.7 - - + +
374C PHE* 3.8 3.1 - - - -
389C PHE* 5.6 1.3 - - + -
437C THR* 3.5 2.3 - - - -
438C CYS* 2.9 42.3 + - + +
440C LEU* 4.0 22.4 - - + -
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Residues in contact with PRO 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C VAL* 4.1 8.8 - - - +
355C TYR* 5.4 4.3 - - + -
371C GLU* 3.4 17.9 - - + +
372C ILE* 1.4 94.9 - - + +
374C PHE* 1.3 61.6 + - - +
436C GLY 3.5 8.3 - - - +
437C THR* 4.2 9.8 - - + +
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Residues in contact with PHE 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C LEU* 4.0 20.4 - - + -
353C VAL* 4.1 8.3 - - + -
372C ILE 3.8 10.5 - - - -
373C PRO* 1.3 75.9 - - - +
375C LYS* 1.3 61.5 + - - +
376C PHE* 3.1 39.3 - + + -
387C LEU* 3.9 21.5 - - + -
434C LEU* 3.8 6.7 - - + -
435C SER* 3.2 10.4 - - - -
436C GLY 2.8 50.0 + - - +
437C THR 3.5 23.8 - - - -
438C CYS* 3.8 4.0 - - + -
452C ILE* 4.3 2.2 - - + -
453C VAL 3.5 17.9 - - - -
454C ALA* 3.8 16.6 - - + -
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Residues in contact with LYS 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C VAL* 4.2 12.8 - - - +
374C PHE* 1.3 76.3 - - - +
376C PHE* 1.3 64.8 + - - +
377C HIS 3.9 1.6 + - - -
433C THR* 4.4 28.0 - - + -
434C LEU 3.4 3.6 - - - -
435C SER* 4.2 14.1 - - - +
457C ASP* 5.0 4.5 - - - +
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Residues in contact with PHE 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C LEU* 3.0 50.5 - - + -
295C ALA* 3.7 9.0 - - - -
296C PRO* 3.6 13.2 - - + -
350C ALA* 3.9 12.3 - - + -
351C LYS 3.4 21.8 - - - -
353C VAL* 3.6 17.5 - - + -
374C PHE* 3.1 44.0 - + + -
375C LYS* 1.3 72.4 - - - +
377C HIS* 1.3 59.8 + - - +
378C MET* 3.6 11.0 + - - -
387C LEU* 4.2 11.7 - - + -
433C THR* 3.0 9.1 - - - -
434C LEU* 2.7 50.2 + - + +
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Residues in contact with HIS 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ALA* 3.6 11.8 - - - +
351C LYS* 4.9 1.4 + - - +
375C LYS 3.9 2.2 + - - -
376C PHE* 1.3 69.1 - - - +
378C MET* 1.3 63.8 + - - +
379C LEU* 3.3 26.2 + - + +
431C GLY* 3.5 37.0 + - - -
432C ASP 3.6 3.2 + - - -
433C THR* 4.4 11.6 - - + +
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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