Contacts of the strand formed by residues 469 - 478 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398D THR 3.9 0.2 - - - +
399D PHE* 3.3 6.4 - - - -
400D ASP* 2.9 34.0 + - - -
401D SER 2.7 24.6 + - - -
402D LEU* 3.7 15.2 + - - +
404D SER* 4.0 1.4 + - - -
405D GLY* 4.2 7.3 + - - +
422D ASN* 3.5 27.5 + - + +
424D MET* 4.9 4.7 - - - -
468D PHE* 1.3 73.3 - - - +
470D ILE* 1.3 64.1 + - - +
471D ARG* 4.0 37.2 - - + +
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Residues in contact with ILE 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D VAL* 4.5 13.5 - - + -
398D THR 4.1 1.3 - - - -
399D PHE* 4.2 6.3 - - + -
421D LYS 4.9 2.5 - - - +
422D ASN 2.9 13.7 + - - +
423D PHE* 3.5 14.1 - - + -
424D MET* 3.0 26.2 + - - +
462D ILE* 4.1 23.1 - - + -
466D PHE* 3.8 35.0 - - + -
468D PHE 3.7 8.3 - - - +
469D THR* 1.3 78.4 - - - +
471D ARG* 1.3 63.0 + - - +
472D VAL* 4.5 2.7 - - + -
495D LEU* 3.7 26.9 - - + -
500D VAL* 4.0 18.6 - - + -
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Residues in contact with ARG 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 3.9 12.6 - - - -
115B ASN* 5.6 3.8 - - - +
116B TYR* 3.3 49.2 + - + -
396D THR 3.7 0.7 - - - +
397D VAL* 3.5 2.9 - - - +
398D THR* 2.9 48.9 + - - +
400D ASP* 2.7 29.0 + - + +
404D SER* 2.8 35.3 + - - -
405D GLY* 4.7 1.6 - - - -
424D MET* 2.6 49.0 - - + +
469D THR* 4.0 12.5 - - + +
470D ILE* 1.3 78.5 - - - +
472D VAL* 1.3 64.9 + - - +
473D THR* 5.1 4.3 + - - +
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Residues in contact with VAL 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D CYS* 4.7 3.8 - - + -
396D THR 3.4 9.4 - - - +
397D VAL* 4.5 6.5 - - + -
423D PHE* 3.7 29.8 - - + -
424D MET 2.8 9.5 + - - +
425D LEU* 3.1 30.5 - - + +
426D HIS* 2.7 33.4 + - - +
458D LEU* 5.1 0.4 - - + -
470D ILE* 4.5 0.9 - - + -
471D ARG* 1.3 78.5 - - - +
473D THR* 1.3 60.5 + - - +
474D SER* 4.0 7.2 - - - +
491D GLY* 4.3 16.2 - - - -
495D LEU* 3.9 23.6 - - + -
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Residues in contact with THR 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LYS* 5.0 4.7 - - + -
115B ASN* 2.8 35.8 + - - +
394D LEU 3.6 1.0 - - - +
395D CYS* 3.1 5.4 - - - +
396D THR* 2.8 51.0 + - + +
398D THR* 5.4 2.8 + - - -
426D HIS* 3.3 13.8 + - + +
428D GLU* 5.8 0.4 - - - +
471D ARG* 4.1 5.0 + - - +
472D VAL* 1.3 74.5 + - - +
474D SER* 1.3 63.6 + - - +
475D GLU* 3.8 32.1 - - + +
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Residues in contact with SER 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D VAL* 4.1 0.7 - - - -
394D LEU 3.4 4.5 - - - -
395D CYS* 3.5 16.6 - - - -
425D LEU* 3.5 26.0 - - - +
426D HIS 2.9 7.4 + - - +
427D TYR* 3.3 5.2 - - - -
428D GLU 2.9 25.5 + - - +
472D VAL* 4.0 0.9 - - - +
473D THR* 1.3 73.1 - - - +
475D GLU* 1.3 64.8 + - - +
476D VAL 4.2 0.7 - - - -
487D SER* 3.3 36.7 - - - -
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Residues in contact with GLU 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS* 2.8 42.9 + - - +
115B ASN* 5.6 0.3 + - - -
155B ASN* 3.2 16.3 + - - +
393D VAL* 3.4 3.4 - - - +
394D LEU* 2.8 49.1 + - + +
396D THR* 4.8 1.6 - - - +
428D GLU* 3.5 29.0 - - + +
430D PRO* 5.2 4.3 - - + -
473D THR* 3.8 19.7 - - + +
474D SER* 1.3 79.4 - - - +
476D VAL* 1.3 64.1 + - - +
477D LEU* 3.3 18.5 + - + +
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Residues in contact with VAL 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D GLN 3.6 5.2 - - - +
393D VAL* 4.3 9.4 - - + -
427D TYR* 3.6 22.2 - - + +
428D GLU 3.0 17.5 + - - +
429D PHE* 4.2 12.1 - - + -
430D PRO* 3.2 21.0 - - - +
433D ALA* 3.2 11.7 - - + +
475D GLU* 1.3 71.6 - - - +
477D LEU* 1.3 57.1 + - - +
478D GLU 3.5 25.4 - - - +
479D SER* 4.1 13.2 - - - -
483D SER* 3.5 34.3 - - - -
487D SER* 5.0 0.4 - - - +
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Residues in contact with LEU 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 4.0 22.4 - - + -
64B ALA* 3.4 21.6 - - + +
66B PHE 5.3 0.5 + - - -
81B MET* 4.3 9.4 - - + -
155B ASN* 4.4 4.9 - - - +
157B LEU* 5.3 1.1 - - + -
385D LEU* 4.6 2.7 - - + -
392D GLN* 2.8 36.6 + - - +
394D LEU* 3.8 26.2 - - + -
430D PRO* 4.9 0.4 - - + -
432D TYR* 3.7 28.3 - - + +
433D ALA* 3.4 15.7 - - - -
475D GLU* 3.7 28.3 - - + +
476D VAL* 1.3 76.7 - - - +
478D GLU* 1.3 65.9 + - - +
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Residues in contact with GLU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA* 3.3 5.6 + - - -
65B ARG* 2.7 70.2 + - - +
66B PHE* 3.8 12.5 - - + -
387D GLN* 3.1 14.2 + - - -
390D GLN* 3.4 15.1 - - - +
391D THR* 3.3 2.6 - - - +
392D GLN* 2.8 44.2 + - + +
433D ALA 3.7 6.7 - - - -
476D VAL* 3.5 11.3 - - - +
477D LEU* 1.3 82.5 - - - +
479D SER* 1.3 61.9 + - - +
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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