Contacts of the strand formed by residues 461 - 472 (chain C) in PDB entry 5ZHU
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 GLN 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399C ILE 3.6 1.9 - - - +
400C GLY* 4.2 0.6 - - - -
401C MET* 2.9 26.4 + - - +
402C LEU* 5.9 0.4 - - - +
458C PRO* 3.3 50.7 - - + +
459C PRO 3.3 4.3 - - - +
460C GLU* 1.3 78.8 - - - +
462C VAL* 1.3 71.7 + - - +
463C THR* 3.8 4.4 + - - +
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Residues in contact with VAL 462 (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 THR* 4.4 6.1 - - + +
398C TYR* 4.2 21.1 - - + -
399C ILE 3.1 20.6 - - - +
400C GLY* 3.6 16.8 - - - +
461C GLN* 1.3 79.4 + - - +
463C THR* 1.3 64.5 + - - +
464C LYS* 4.0 1.8 + - + +
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Residues in contact with THR 463 (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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397C VAL 3.7 1.6 - - - +
398C TYR* 3.6 1.7 - - - -
399C ILE* 2.7 35.9 + - - +
455C VAL* 5.0 0.2 - - + -
456C ASN 3.6 16.5 + - - +
457C LEU* 3.6 20.7 - - + +
458C PRO* 3.3 27.3 - - + +
461C GLN* 3.8 6.4 + - - +
462C VAL* 1.3 75.8 - - - +
464C LYS* 1.3 70.5 + - - +
465C VAL* 4.1 10.6 + - + +
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Residues in contact with LYS 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C THR* 4.2 9.9 - - + -
397C VAL 3.5 3.8 - - - -
398C TYR* 3.6 42.6 - - + +
462C VAL 4.0 1.9 + - - +
463C THR* 1.3 79.8 - - - +
465C VAL* 1.3 66.0 + - - +
466C THR* 3.3 29.6 + - + +
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Residues in contact with VAL 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C VAL 4.0 0.7 - - - +
396C THR* 3.3 2.4 - - - +
397C VAL* 2.7 42.7 + - + +
399C ILE* 5.6 5.4 - - + -
422C LEU* 4.0 26.9 - - + +
453C VAL* 5.0 4.3 - - + -
455C VAL* 3.9 37.0 - - + -
457C LEU* 5.7 0.4 - - + -
463C THR* 4.5 10.1 - - + +
464C LYS* 1.3 78.6 - - - +
466C THR* 1.3 65.8 + - - +
467C VAL* 4.3 14.6 - - + -
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Residues in contact with THR 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C GLN* 4.8 12.8 - - - +
395C VAL 3.5 4.3 - - - -
396C THR* 3.2 24.5 - - + +
464C LYS* 3.3 36.2 + - - +
465C VAL* 1.3 80.3 - - - +
467C VAL* 1.3 64.5 + - - +
468C GLY 4.1 1.6 + - - -
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Residues in contact with VAL 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C PHE 4.2 0.9 - - - +
394C GLN* 3.2 5.8 - - - +
395C VAL* 2.9 48.1 + - + +
422C LEU* 4.7 7.9 - - + -
424C LEU* 3.5 29.8 - - + -
440C GLN* 5.5 0.9 - - - +
450C PHE* 3.4 35.2 - - + -
453C VAL* 4.6 8.3 - - + -
465C VAL* 4.3 15.9 - - + +
466C THR* 1.3 75.5 - - - +
468C GLY* 1.3 59.0 + - - +
470C LEU* 4.1 6.8 - - + +
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Residues in contact with GLY 468 (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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392C HIS* 5.8 0.2 - - - -
393C PHE 4.1 0.7 - - - -
394C GLN* 3.4 21.7 - - - -
440C GLN* 3.0 24.8 + - - +
466C THR 4.1 2.6 + - - -
467C VAL* 1.3 73.7 - - - +
469C ARG* 1.3 70.0 + - - -
470C LEU* 3.2 8.9 + - - +
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Residues in contact with ARG 469 (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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392C HIS* 3.3 58.0 + - - -
393C PHE 3.7 0.6 + - - -
440C GLN* 3.3 8.1 - - + +
441C SER* 2.9 56.1 + - - +
442C GLN* 5.2 9.7 + - - -
468C GLY* 1.3 73.2 - - - +
470C LEU* 1.3 57.7 + - - +
471C HIS* 3.6 1.3 - - - -
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Residues in contact with LEU 470 (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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392C HIS* 3.1 5.3 - - - +
393C PHE* 2.8 63.3 + - + +
424C LEU* 3.8 28.7 - - + -
438C ILE* 3.9 9.2 - - + -
439C GLU 3.2 13.7 - - - +
440C GLN* 3.7 16.6 - - + +
450C PHE* 3.8 28.7 - - + -
467C VAL* 4.1 12.1 - - + +
468C GLY 3.2 22.4 - - - +
469C ARG* 1.3 77.1 - - - +
471C HIS* 1.3 62.8 + - - +
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Residues in contact with HIS 471 (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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389C LYS* 3.0 24.3 + - - +
390C LYS 3.7 11.4 - - - -
391C ASN 5.3 0.9 - - - -
392C HIS* 3.4 36.0 - + + +
393C PHE* 4.0 7.9 - - - -
438C ILE* 3.6 4.1 - - - +
439C GLU* 2.8 37.8 + - + +
441C SER* 2.5 33.3 + - - -
447C LYS* 3.2 35.1 + - + +
469C ARG 3.6 4.0 - - - -
470C LEU* 1.3 76.8 - - - +
472C PHE* 1.3 66.0 + - - +
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Residues in contact with PHE 472 (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 PHE* 4.3 16.8 - + - -
387C CYS* 4.1 7.0 - - - -
389C LYS* 3.1 28.6 - - + +
393C PHE* 3.6 20.2 - + - -
426C GLY* 4.1 17.5 - - - -
436C ILE* 3.8 16.4 - - + -
437C ASN 4.2 1.6 - - - -
438C ILE* 3.6 22.2 - - + -
439C GLU* 4.7 1.0 - - - +
471C HIS* 1.3 74.7 - - - +
473C SER* 1.3 57.3 + - - +
474C GLU 3.1 17.3 - - - +
493C PHE* 4.1 21.8 - + + -
495C LEU* 4.3 25.4 - - + -
518C ILE* 4.6 6.3 - - + -
520C VAL* 3.8 29.8 - - + -
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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