Contacts of the strand formed by residues 469 - 478 (chain C) in PDB entry 3U1K
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 THR 469 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398C THR 3.8 0.5 - - - +
399C PHE* 3.4 5.5 - - - -
400C ASP* 2.8 35.1 + - - -
401C SER 2.8 24.8 + - - -
402C LEU* 3.6 14.9 + - - +
404C SER* 3.8 1.4 + - - -
405C GLY* 4.1 7.5 + - - +
422C ASN* 3.5 27.3 - - + +
424C MET* 5.7 2.0 - - + +
468C PHE* 1.3 70.7 - - - +
470C ILE* 1.3 62.7 + - - +
471C ARG* 3.9 39.7 - - + +
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Residues in contact with ILE 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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397C VAL* 4.4 12.6 - - + -
398C THR 4.1 1.6 - - - -
399C PHE* 4.1 6.7 - - + -
421C LYS 4.8 5.8 - - - +
422C ASN 2.8 11.7 + - - +
423C PHE* 3.5 15.0 - - + -
424C MET 3.0 25.8 + - - +
462C ILE* 4.1 25.4 - - + -
463C PRO* 5.0 0.4 - - + -
466C PHE* 3.6 37.5 - - + -
468C PHE 3.6 11.0 - - - +
469C THR* 1.3 73.1 - - - +
471C ARG* 1.3 64.7 + - - +
495C LEU* 3.7 27.4 - - + -
500C VAL* 4.2 14.1 - - + -
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Residues in contact with ARG 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C THR 3.5 1.0 - - - +
397C VAL* 3.4 2.6 - - - +
398C THR* 2.7 53.5 + - - +
400C ASP* 2.7 25.2 + - + +
404C SER* 3.1 40.2 + - - -
405C GLY* 4.8 1.6 - - - -
424C MET* 2.8 46.9 - - + +
469C THR* 3.9 16.2 - - + +
470C ILE* 1.3 77.1 - - - +
472C VAL* 1.3 61.5 + - - +
473C THR* 4.1 4.6 + - + +
113D PRO* 3.9 19.5 - - - -
115D ASN* 5.7 0.9 - - - -
116D TYR* 3.4 36.9 + - - -
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Residues in contact with VAL 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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395C CYS* 4.6 4.5 - - + -
396C THR 3.2 8.5 - - - +
397C VAL* 4.2 9.2 - - + -
423C PHE* 4.0 24.7 - - + -
424C MET* 3.0 11.1 + - - +
425C LEU* 3.2 28.5 - - + -
426C HIS 2.9 24.1 + - - -
458C LEU* 5.0 0.2 - - + -
471C ARG* 1.3 75.4 - - - +
473C THR* 1.3 67.0 + - - +
474C SER* 3.9 10.1 - - - +
491C GLY* 4.2 16.6 - - - +
495C LEU* 4.0 26.0 - - + -
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Residues in contact with THR 473 (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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394C LEU 3.6 1.0 - - - +
395C CYS* 3.2 5.4 - - - +
396C THR* 2.8 48.6 + - + +
398C THR* 5.1 7.2 - - - +
424C MET* 5.2 2.5 - - + -
426C HIS* 3.3 13.5 - - + -
471C ARG* 4.9 6.7 - - + +
472C VAL* 1.3 78.2 - - - +
474C SER* 1.3 62.5 + - - +
475C GLU* 3.8 21.1 + - - +
105D LYS* 5.0 4.9 - - + +
115D ASN* 3.1 36.0 + - - +
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Residues in contact with SER 474 (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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393C VAL* 4.1 0.4 - - - -
394C LEU 3.5 4.3 - - - -
395C CYS* 3.5 18.6 - - - -
425C LEU* 3.8 22.6 - - - +
426C HIS* 2.8 12.4 + - - +
427C TYR* 3.3 5.5 - - - +
428C GLU 2.8 27.1 + - - +
472C VAL* 3.9 0.5 - - - +
473C THR* 1.3 72.8 - - - +
475C GLU* 1.3 63.6 + - - +
487C SER* 3.4 34.2 - - - -
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Residues in contact with GLU 475 (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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393C VAL* 3.4 3.0 - - - +
394C LEU* 2.8 46.7 + - + +
396C THR* 4.9 1.6 + - - -
426C HIS* 6.3 0.2 - - + -
428C GLU* 3.4 29.4 - - + +
430C PRO* 5.1 4.3 - - + -
473C THR* 3.8 17.9 + - - +
474C SER* 1.3 80.5 - - - +
476C VAL* 1.3 61.9 + - - +
477C LEU* 3.5 16.3 + - + +
103D ARG* 5.8 0.5 + - - -
105D LYS* 2.7 36.8 + - - +
115D ASN* 6.0 1.3 - - - -
155D ASN* 2.9 23.2 + - - +
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Residues in contact with VAL 476 (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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391C THR* 5.7 0.2 - - + -
392C GLN 3.5 4.0 - - - -
393C VAL* 4.0 15.5 - - + -
427C TYR* 3.7 27.6 - - + +
428C GLU 3.0 19.9 + - - +
429C PHE* 3.6 17.3 - - + -
430C PRO* 3.2 24.1 - - - +
433C ALA* 3.3 18.1 - - + +
475C GLU* 1.3 71.6 - - - +
477C LEU* 1.3 59.8 + - - +
478C GLU 3.6 18.4 - - - +
479C SER* 4.0 11.7 - - - -
483C SER* 3.9 11.0 - - - -
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Residues in contact with LEU 477 (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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385C LEU* 4.7 0.7 - - + -
392C GLN* 2.7 34.7 + - - +
394C LEU* 3.9 24.0 - - + +
430C PRO* 4.9 0.2 - - + -
432C TYR* 3.6 29.5 - - + +
433C ALA* 3.3 16.0 - - - -
475C GLU* 3.7 28.0 - - + +
476C VAL* 1.3 77.4 - - - +
478C GLU* 1.3 65.2 + - - +
63D LEU* 4.2 26.9 - - + -
64D ALA* 3.4 20.9 - - + +
66D PHE 5.3 0.3 + - - -
81D MET* 4.3 10.1 - - + -
155D ASN* 4.4 5.2 - - - +
157D LEU* 5.4 0.9 - - + -
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Residues in contact with GLU 478 (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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387C GLN* 3.1 13.5 + - - -
390C GLN* 3.4 15.6 - - - +
391C THR* 3.4 2.3 - - - +
392C GLN* 2.8 45.2 + - + +
433C ALA 3.6 6.7 - - - -
476C VAL* 3.6 8.2 - - - +
477C LEU* 1.3 84.2 - - - +
479C SER* 1.3 59.1 + - - +
64D ALA 3.4 5.0 + - - -
65D ARG* 2.7 72.3 + - - +
66D PHE* 3.9 12.3 - - + -
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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