Contacts of the strand formed by residues 469 - 478 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398B THR 3.8 0.3 - - - +
399B PHE* 3.4 7.1 - - - +
400B ASP* 2.9 34.3 + - - -
401B SER 2.8 25.0 + - - -
402B LEU* 3.6 16.9 + - - +
404B SER* 3.9 1.2 + - - -
405B GLY* 4.2 7.5 + - - +
422B ASN* 3.4 25.4 + - + +
423B PHE 5.9 0.2 - - - -
424B MET* 5.5 2.5 - - + +
468B PHE* 1.3 72.3 - - - +
470B ILE* 1.3 64.7 + - - +
471B ARG* 3.9 35.6 + - + +
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Residues in contact with ILE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B VAL* 4.6 10.1 - - + -
398B THR 4.2 1.6 - - - -
399B PHE* 4.1 5.8 - - + -
421B LYS 5.0 2.5 - - - +
422B ASN 2.8 14.4 + - - +
423B PHE* 3.4 13.8 - - + -
424B MET* 3.0 26.7 + - - +
462B ILE* 4.2 19.3 - - + -
466B PHE* 3.6 47.8 - - + -
468B PHE 3.9 1.1 - - - +
469B THR* 1.3 74.2 - - - +
471B ARG* 1.3 60.9 + - - +
472B VAL* 4.4 4.9 - - + -
495B LEU* 3.6 28.3 - - + -
500B VAL* 4.1 21.1 - - + -
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Residues in contact with ARG 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B THR 3.5 1.4 - - - +
397B VAL* 3.3 3.7 - - - -
398B THR* 2.9 46.8 + - - +
400B ASP* 2.7 25.6 + - + +
404B SER* 2.9 41.2 + - - -
405B GLY* 4.8 1.2 - - - -
424B MET* 3.2 41.5 - - + +
469B THR* 4.0 16.0 - - + +
470B ILE* 1.3 75.0 - - - +
472B VAL* 1.3 62.9 + - - +
473B THR* 3.9 3.8 + - - +
113C PRO* 3.8 19.5 - - - -
115C ASN* 5.5 2.0 - - - +
116C TYR* 3.3 43.6 + - - -
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Residues in contact with VAL 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B CYS* 4.7 2.7 - - + -
396B THR 3.4 11.0 - - - +
397B VAL* 4.6 5.8 - - + -
423B PHE* 3.7 30.1 - - + -
424B MET* 2.9 10.0 + - - +
425B LEU* 3.1 27.7 - - + -
426B HIS* 2.8 33.1 + - - +
458B LEU* 5.1 0.4 - - + -
470B ILE* 4.4 2.0 - - + -
471B ARG* 1.3 76.3 - - - +
473B THR* 1.3 64.3 + - - +
474B SER* 4.2 3.4 - - - +
491B GLY* 4.1 19.5 - - - -
495B LEU* 4.1 22.7 - - + -
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Residues in contact with THR 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU 3.7 0.3 - - - +
395B CYS* 3.1 6.6 - - - +
396B THR* 2.8 49.1 + - + +
398B THR* 5.4 2.6 + - - -
424B MET* 5.5 1.4 - - - +
426B HIS* 3.4 13.5 + - + +
428B GLU* 6.2 0.2 - - - -
471B ARG* 3.9 4.0 + - - +
472B VAL* 1.3 75.8 + - - +
474B SER* 1.3 63.9 + - - +
475B GLU* 3.7 32.1 - - + +
105C LYS* 5.0 3.1 - - + -
115C ASN* 2.8 35.9 + - - +
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Residues in contact with SER 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B VAL* 4.2 0.4 - - - -
394B LEU 3.6 3.8 - - - -
395B CYS* 3.3 20.7 - - - -
425B LEU* 3.9 21.8 - - - +
426B HIS 2.8 13.3 + - - +
427B TYR* 3.3 5.5 - - - +
428B GLU 2.8 26.7 + - - +
472B VAL* 4.2 0.9 - - - +
473B THR* 1.3 72.8 - - - +
475B GLU* 1.3 65.5 + - - +
476B VAL 4.2 0.4 - - - -
487B SER* 3.4 33.0 + - - -
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Residues in contact with GLU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B VAL* 3.4 3.5 - - - +
394B LEU* 2.9 51.7 + - + +
396B THR* 4.7 1.9 - - - +
428B GLU* 3.5 25.2 - - + +
430B PRO* 5.2 4.0 - - + -
473B THR* 3.7 19.9 - - + +
474B SER* 1.3 80.9 - - - +
476B VAL* 1.3 64.5 + - - +
477B LEU* 3.3 16.3 + - + +
105C LYS* 2.6 39.1 + - - +
155C ASN* 2.9 23.2 + - - +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B GLN 3.7 4.7 - - - +
393B VAL* 4.2 8.1 - - + -
427B TYR* 3.7 23.1 - - + +
428B GLU 2.9 19.0 + - - +
429B PHE* 4.0 13.0 - - + -
430B PRO* 3.2 16.3 - - - +
433B ALA* 3.2 21.0 - - + +
475B GLU* 1.3 69.4 - - - +
477B LEU* 1.3 59.6 + - - +
478B GLU 3.6 25.1 - - - +
479B SER* 4.1 7.9 - - - -
483B SER* 3.7 33.2 - - - -
487B SER* 5.0 0.7 - - - +
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LEU* 4.5 2.0 - - + -
392B GLN* 2.7 40.0 + - + +
394B LEU* 3.8 26.0 - - + +
432B TYR* 3.6 27.2 - - - +
433B ALA* 3.2 17.0 - - - -
475B GLU* 3.7 26.5 - - + +
476B VAL* 1.3 77.5 - - - +
478B GLU* 1.3 62.2 + - - +
63C LEU* 3.8 25.1 - - + -
64C ALA* 3.5 19.1 - - + +
66C PHE 5.4 0.2 + - - -
81C MET* 4.1 13.2 - - + -
155C ASN* 4.5 4.3 - - - +
157C LEU* 5.4 1.1 - - + -
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Residues in contact with GLU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B GLN* 3.2 13.5 + - - -
390B GLN* 3.4 14.8 - - - +
391B THR* 3.4 2.9 - - - +
392B GLN* 2.8 44.4 + - + +
433B ALA 3.6 7.0 - - - -
476B VAL* 3.6 8.4 - - - +
477B LEU* 1.3 81.9 - - - +
479B SER* 1.3 59.9 + - - +
42C HIS* 5.8 1.2 - - - -
64C ALA* 3.3 7.6 + - - -
65C ARG* 2.7 71.3 + - - +
66C PHE* 3.8 13.6 - - + -
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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