Contacts of the strand formed by residues 368 - 379 (chain C) in PDB entry 3D8F
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 LYS 368 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366C GLY* 2.9 26.8 + - - +
367C ILE* 1.3 78.0 - - - +
369C CYS* 1.3 66.3 + - - +
370C PHE* 3.9 16.4 - - + -
425C GLN* 4.1 1.0 - - - +
426C LEU* 3.3 33.3 + - + +
494C SER* 3.3 31.4 + - - +
497C GLU* 3.6 19.8 + - - +
498C ILE* 4.3 20.8 - - - +
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Residues in contact with CYS 369 (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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367C ILE* 3.7 17.0 - - + +
368C LYS* 1.3 78.9 - - - +
370C PHE* 1.3 71.8 + - - +
371C ALA 4.4 0.2 + - - -
423C LEU* 3.8 38.1 - - - -
424C LEU 3.4 8.7 - - - -
425C GLN* 3.9 13.5 - - + +
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Residues in contact with PHE 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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368C LYS* 3.9 20.0 - - + -
369C CYS* 1.3 88.2 - - - +
371C ALA* 1.3 68.8 + - - +
372C VAL* 3.2 5.9 + - + +
422C LEU 3.4 2.1 - - - +
423C LEU* 3.5 5.2 - - - -
424C LEU* 2.8 48.7 + - + +
426C LEU* 3.7 17.9 - - + -
484C CYS* 5.5 1.8 - - + -
486C ALA* 5.3 12.1 - - + -
490C ASN* 4.1 20.4 - - + -
491C ILE* 3.6 61.2 - - + -
494C SER* 4.2 8.1 - - - -
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Residues in contact with ALA 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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369C CYS 4.4 0.4 + - - -
370C PHE* 1.3 71.7 - - - +
372C VAL* 1.3 60.1 + - - +
421C ASP* 6.0 4.3 - - + -
422C LEU 3.6 5.6 - - - -
423C LEU* 5.1 6.4 - - + +
484C CYS* 3.5 1.4 - - - +
485C GLU* 2.9 63.2 + - + +
486C ALA* 4.5 2.7 + - - +
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Residues in contact with VAL 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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370C PHE* 3.9 8.5 - - + +
371C ALA* 1.3 79.3 - - - +
373C ARG* 1.3 63.0 + - - +
421C ASP* 3.5 7.8 - - - +
422C LEU* 2.8 59.6 + - + +
424C LEU* 3.8 31.0 - - + +
433C LEU* 4.9 2.0 - - + -
482C PHE* 4.3 25.1 - - + -
483C ARG 3.2 7.0 - - - +
484C CYS* 3.8 28.7 - - + -
485C GLU 4.8 0.2 - - - +
491C ILE* 4.6 2.5 - - + -
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Residues in contact with ARG 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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372C VAL* 1.3 78.7 - - - +
374C SER* 1.3 65.6 + - - +
375C LEU* 3.3 13.4 + - + +
420C LYS* 3.8 40.5 + - - +
421C ASP* 3.9 20.0 + - - +
422C LEU 5.1 0.2 - - - +
482C PHE* 3.4 7.2 - - - -
483C ARG* 2.8 44.5 + - + +
373D ARG* 4.8 15.0 - - - +
421D ASP* 5.5 1.0 + - - -
485D GLU* 3.2 29.1 + - - +
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Residues in contact with SER 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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372C VAL* 4.3 0.4 - - - +
373C ARG* 1.3 71.6 - - - +
375C LEU* 1.3 62.6 + - - +
376C GLY* 3.7 12.1 + - - -
420C LYS 5.0 2.8 + - - -
422C LEU* 4.4 21.7 - - - +
433C LEU* 6.0 1.4 - - - +
481C VAL 4.7 0.2 + - - -
482C PHE* 3.9 23.2 - - - -
371D ALA* 3.5 14.9 - - - +
423D LEU* 5.7 3.1 - - - +
485D GLU* 4.8 2.4 - - - +
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Residues in contact with LEU 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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373C ARG* 3.3 14.6 + - + +
374C SER* 1.3 75.3 - - - +
376C GLY* 1.3 56.9 + - - +
401C LEU* 3.3 31.2 - - + +
402C SER* 3.1 36.6 - - - -
464C ASP* 4.3 2.9 - - - +
481C VAL* 3.2 22.5 + - + +
482C PHE 4.1 2.5 - - - -
483C ARG* 3.9 30.7 - - + +
369D CYS 3.8 2.8 - - - +
370D PHE* 4.0 1.7 - - - -
371D ALA* 3.1 27.3 + - - +
485D GLU* 3.9 30.5 - - + +
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Residues in contact with GLY 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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374C SER* 3.4 12.5 + - - -
375C LEU* 1.3 81.3 - - - +
377C TRP* 1.3 69.3 + - - +
401C LEU* 3.8 4.7 - - - -
480C HIS* 3.4 5.8 + - - +
481C VAL 3.1 22.6 + - - +
482C PHE* 5.8 0.2 - - - -
369D CYS* 3.3 12.8 - - - -
371D ALA 4.7 1.8 - - - -
423D LEU* 5.0 6.3 - - - -
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Residues in contact with TRP 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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376C GLY* 1.3 77.7 - - - +
378C VAL* 1.3 87.1 + - - +
379C GLU* 3.3 24.0 - - + -
401C LEU* 3.7 3.4 - - - +
476C MET* 4.0 9.9 - - + -
478C LYS* 3.4 45.1 - - + +
479C CYS 3.4 12.6 - - - +
480C HIS* 3.4 32.1 - + + +
367D ILE* 3.4 32.5 - - + -
369D CYS* 2.8 58.2 + - + +
423D LEU* 5.7 2.3 - - + +
425D GLN* 3.9 23.8 - - - +
439D GLN* 5.7 2.4 + - - -
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Residues in contact with VAL 378 (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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377C TRP* 1.3 87.7 - - - +
379C GLU* 1.3 75.2 + - - +
380C MET* 3.5 0.3 + - - +
397C CYS* 3.7 27.6 - - - +
400C GLN* 4.5 19.5 - - + +
401C LEU* 3.7 27.8 - - + -
479C CYS* 3.0 28.2 + - - +
367D ILE 3.8 8.1 - - - +
368D LYS* 4.0 21.1 - - + -
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Residues in contact with GLU 379 (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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377C TRP* 3.3 11.2 - - + -
378C VAL* 1.3 83.8 - - - +
380C MET* 1.3 68.3 + - - +
381C THR* 5.2 8.6 - - + +
384C GLU* 4.5 1.4 - - - +
476C MET* 3.4 33.3 - - + +
477C LEU 3.3 7.4 - - - +
366D GLY* 3.4 18.4 + - - -
367D ILE* 2.9 51.7 + - - +
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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