Contacts of the strand formed by residues 425 - 433 (chain C) in PDB entry 4K94
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 MET 425 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420C ARG* 4.6 0.2 - - - +
421C LEU* 2.8 50.0 + - + +
422C VAL 3.8 7.6 + - - +
423C ASN* 3.3 7.4 - - - +
424C GLY* 1.3 80.7 - - - +
426C LEU* 1.3 65.7 + - - +
458C ASP* 5.4 5.6 - - + +
477C SER* 3.5 32.1 - - - -
478C ILE 3.0 17.3 - - - +
479C ASP* 3.6 24.5 - - + +
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Residues in contact with LEU 426 (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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419C ASP 3.6 2.5 - - - +
420C ARG* 4.0 33.0 - - + +
424C GLY 4.6 3.4 - - - +
425C MET* 1.3 84.1 - - - +
427C GLN* 1.3 61.8 + - - +
440C TRP* 3.8 17.1 - - + -
477C SER* 3.2 5.6 - - - -
478C ILE* 2.8 37.4 + - + -
480C SER* 4.1 22.0 - - - +
489C VAL* 4.0 37.9 - - + -
504C PHE* 4.0 22.4 - - + -
506C PHE* 5.0 5.8 - - + -
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Residues in contact with GLN 427 (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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417C THR* 4.8 1.4 + - - -
418C TYR* 3.2 3.3 - - - +
419C ASP* 2.7 54.1 + - - +
421C LEU* 3.7 31.4 - - + +
426C LEU* 1.3 77.5 - - - +
428C CYS* 1.3 65.4 + - - +
429C VAL* 4.0 14.1 - - + +
440C TRP* 3.7 3.7 - - - -
475C GLN* 3.2 39.6 + - + +
476C SER 3.3 12.8 - - - +
477C SER* 3.3 9.2 + - - +
504C PHE* 3.8 1.6 - - - -
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Residues in contact with CYS 428 (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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415C ILE* 4.8 7.4 - - + -
417C THR 3.4 9.4 - - - +
418C TYR* 3.9 8.5 - - + -
427C GLN* 1.3 76.7 - - - +
429C VAL* 1.3 62.3 + - - +
430C ALA 4.2 0.2 - - - -
438C ILE* 3.6 25.7 - - - +
440C TRP* 3.6 4.3 - - + -
476C SER 3.1 28.9 + - - +
491C CYS* 2.0 55.0 - - + -
493C ALA* 6.0 0.4 - - - -
502C ALA* 4.8 0.9 - - + -
504C PHE* 5.0 0.2 - - + -
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Residues in contact with VAL 429 (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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415C ILE* 3.5 4.6 - - - -
416C LEU* 2.8 41.1 + - + -
417C THR* 2.8 33.7 + - + +
427C GLN* 4.0 11.4 - - - +
428C CYS* 1.3 77.1 - - - +
430C ALA* 1.3 63.4 + - - +
462C LEU* 4.3 11.7 - - + -
473C VAL* 3.8 26.2 - - + -
474C VAL 3.4 4.9 - - - +
475C GLN* 3.9 25.1 - - + +
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Residues in contact with ALA 430 (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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413C PRO* 4.7 0.9 - - + -
414C GLU 3.2 9.4 - - - +
415C ILE* 4.6 3.4 - - + -
416C LEU* 4.8 0.4 - - - -
429C VAL* 1.3 77.0 - - - +
431C ALA* 1.3 62.2 + - - +
436C PRO* 4.1 12.6 - - + +
438C ILE* 3.8 14.5 - - + +
472C LEU 3.8 1.0 - - - +
473C VAL* 3.5 2.0 - - - +
474C VAL* 2.8 38.8 + - - +
493C ALA* 3.5 33.2 - - + -
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Residues in contact with ALA 431 (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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412C LYS 4.4 0.2 - - - +
413C PRO* 3.3 1.4 - - - +
414C GLU* 2.6 41.8 + - + +
416C LEU* 3.6 29.4 - - + -
430C ALA* 1.3 75.2 - - - +
432C GLY* 1.3 58.6 + - - +
436C PRO* 3.8 4.0 - - - -
468C PRO* 4.0 19.5 - - + -
471C LYS* 4.2 4.3 - - + -
472C LEU 3.5 5.2 - - - -
473C VAL* 4.0 12.6 - - + -
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Residues in contact with GLY 432 (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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411C THR* 4.2 10.1 - - - -
412C LYS 4.7 0.4 - - - -
413C PRO* 4.4 3.6 - - - -
431C ALA* 1.3 75.7 - - - +
433C PHE* 1.3 60.4 + - - -
434C PRO 3.4 9.9 - - - +
436C PRO* 3.6 7.9 - - - +
471C LYS* 3.7 19.3 - - - +
472C LEU* 3.0 30.9 + - - +
495C ASN* 4.8 0.2 - - - -
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Residues in contact with PHE 433 (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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324C PHE* 3.3 46.2 - + + -
408C TYR* 3.7 39.7 - + + -
409C VAL 3.8 11.2 - - - +
410C ASN* 3.2 32.4 - - - -
411C THR* 2.8 40.3 + - - +
432C GLY* 1.3 73.3 - - - +
434C PRO* 1.3 81.8 + - + +
470C GLY 4.1 12.3 - - - +
471C LYS* 4.5 0.4 - - + -
472C LEU* 3.8 21.8 - - + -
495C ASN* 3.6 2.0 - - - -
497C VAL* 3.8 0.5 - - - +
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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