Contacts of the strand formed by residues 475 - 487 (chain C) in PDB entry 2UX0
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 ALA 475 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395C ARG* 6.0 0.2 - - - -
470C VAL* 4.0 1.6 - - - +
471C ILE* 2.9 47.1 + - + +
472C GLY 3.2 9.8 + - - +
473C GLU 3.7 0.2 - - - -
474C ASP* 1.3 81.4 - - - +
476C ALA* 1.3 63.6 + - - +
503C VAL* 6.3 1.6 - - + -
504C TRP 3.4 9.2 - - - +
505C HIS* 5.3 4.7 - - + -
511C TRP* 3.7 3.4 - - - -
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Residues in contact with ALA 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C ARG* 5.5 0.9 - - + -
399C ILE* 3.4 39.9 - - + -
468C VAL* 4.6 2.2 - - + -
469C HIS 3.3 12.3 - - - +
470C VAL* 4.6 6.3 - - + -
471C ILE* 4.2 5.5 - - - +
475C ALA* 1.3 77.1 - - - +
477C CYS* 1.3 65.9 + - - +
503C VAL* 3.8 5.9 - - - +
504C TRP* 2.9 33.1 + - + +
511C TRP* 4.0 4.7 - - + -
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Residues in contact with CYS 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ILE* 5.0 0.2 - - - -
467C HIS 3.8 1.0 - - - +
468C VAL* 3.3 6.9 - - - +
469C HIS* 2.9 50.8 + - + +
471C ILE* 3.9 17.9 - - + -
476C ALA* 1.3 80.5 - - - +
478C ILE* 1.3 65.0 + - - +
479C ALA* 5.2 2.5 - - - -
501C THR* 4.6 15.5 - - - -
502C ARG 3.5 9.6 - - - +
503C VAL* 4.8 10.8 - - + -
504C TRP* 4.6 1.1 - - - -
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Residues in contact with ILE 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ILE* 4.1 8.7 - - + +
400C ILE* 4.2 19.3 - - + -
403C THR* 3.6 35.4 - - + +
463C ILE* 6.2 0.9 - - + -
466C PRO* 4.4 10.3 - - + -
467C HIS 3.4 11.7 - - - +
468C VAL* 3.9 18.6 - - + -
477C CYS* 1.3 76.2 - - - +
479C ALA* 1.3 65.5 + - - +
480C TYR* 4.1 18.4 - - + -
500C GLU 3.7 0.7 - - - +
501C THR* 3.3 5.2 - - - +
502C ARG* 2.8 55.1 + - + +
504C TRP* 3.6 8.5 - - - +
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Residues in contact with ALA 479 (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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465C ASN 4.0 1.6 - - - +
466C PRO* 3.4 1.2 - - - +
467C HIS* 2.9 40.7 + - + +
469C HIS* 6.1 4.2 - - + -
477C CYS* 5.2 2.9 - - - -
478C ILE* 1.3 73.4 - - - +
480C TYR* 1.3 61.7 + - - +
500C GLU 3.2 7.6 - - - +
501C THR* 4.5 10.3 - - + +
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Residues in contact with TYR 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C THR* 3.7 22.8 - - + +
407C ILE* 3.9 22.7 - - + +
463C ILE* 3.9 32.5 - - + -
464C LEU 4.1 4.5 - - - +
465C ASN 4.5 1.6 - - - -
466C PRO* 4.1 9.6 - - + -
478C ILE* 4.1 21.5 - - + -
479C ALA* 1.3 79.2 - - - +
481C ILE* 1.3 71.6 + - - +
482C ARG* 4.3 4.5 - - + -
499C GLU* 3.7 2.4 - - - +
500C GLU* 2.8 75.8 + - + +
502C ARG* 3.0 32.0 + - + -
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Residues in contact with ILE 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C THR 3.6 0.5 - - - +
463C ILE* 3.4 4.3 - - - -
464C LEU* 2.7 54.5 + - + +
465C ASN* 4.6 14.6 + - + +
480C TYR* 1.3 79.0 - - - +
482C ARG* 1.3 66.6 + - - +
483C LEU* 4.4 6.1 - - + -
497C GLN* 3.7 41.3 - - + +
498C SER 3.5 3.1 - - - +
499C GLU* 4.4 15.0 - - + -
436D ASN* 4.0 13.0 - - - +
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Residues in contact with ARG 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C ILE* 4.6 20.0 - - - +
461C THR* 3.6 33.8 + - + -
462C THR 3.5 2.9 - - - -
463C ILE* 5.3 0.7 - - + -
480C TYR* 4.1 7.1 + - + -
481C ILE* 1.3 73.0 - - - +
483C LEU* 1.3 60.7 + - - +
484C THR* 2.8 35.6 + - - +
496C SER* 3.4 7.8 + - - +
497C GLN* 3.4 0.9 - - - -
498C SER* 2.8 53.8 + - - +
500C GLU* 2.7 41.2 + - - +
502C ARG* 5.8 0.4 - - - +
516C TYR* 4.1 6.3 + - - -
518C CYS* 4.6 3.2 - - - -
1521C GLY* 6.4 0.6 - - - -
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Residues in contact with LEU 483 (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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460C HIS 3.7 1.0 - - - +
461C THR* 3.4 4.0 - - - +
462C THR* 2.8 48.4 + - - +
464C LEU* 4.3 12.1 - - + +
481C ILE* 4.1 3.7 - - + -
482C ARG* 1.3 73.4 - - - +
484C THR* 1.3 61.2 + - - +
485C GLN* 4.1 0.7 - - - -
495C THR* 3.9 15.3 - - + -
496C SER 3.3 2.0 - - - +
497C GLN* 3.6 28.0 - - + +
433D ALA* 3.8 19.5 - - - +
434D LEU* 4.3 2.2 - - + -
436D ASN* 3.5 23.1 - - - +
438D VAL* 4.3 11.9 - - + -
443D PHE* 3.7 29.6 - - + -
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Residues in contact with THR 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ILE* 4.6 15.7 - - + -
460C HIS 3.5 3.1 - - - +
461C THR* 4.3 14.1 + - - +
482C ARG* 2.8 33.8 + - - +
483C LEU* 1.3 75.9 + - - +
485C GLN* 1.3 73.3 + - - +
486C TYR* 3.6 14.1 - - + -
495C THR* 3.2 4.6 - - - -
496C SER* 2.9 40.9 + - - +
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Residues in contact with GLN 485 (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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459C ILE* 3.2 7.6 - - - +
460C HIS* 2.8 61.7 + - - +
462C THR* 4.4 1.7 + - - +
483C LEU 5.6 0.7 - - - -
484C THR* 1.3 75.9 - - - +
486C TYR* 1.3 61.0 + - - +
494C ARG 3.3 5.6 - - - +
495C THR* 4.2 9.9 - - + +
443D PHE* 2.8 58.2 + - + +
446D PHE* 3.5 29.4 - - + +
447D TYR* 3.3 22.9 - - - +
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Residues in contact with TYR 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C PRO 3.9 3.8 - - - -
459C ILE* 4.2 15.7 - - + -
484C THR* 3.6 22.4 - - + -
485C GLN* 1.3 75.5 - - - +
487C ILE* 1.3 75.6 + - - +
488C ASP* 4.3 16.2 - - + -
493C PRO* 3.2 5.7 - - - +
494C ARG* 2.8 67.8 + - + +
495C THR 4.2 2.0 + - - -
496C SER* 4.1 23.5 - - - -
446D PHE* 3.6 8.1 - - - -
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Residues in contact with ILE 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C LYS* 5.3 16.5 - - + +
458C PRO* 4.1 20.5 + - + -
459C ILE* 5.5 0.2 - - - +
486C TYR* 1.3 88.5 - - - +
488C ASP* 1.3 67.0 + - - +
491C GLY* 3.0 31.4 - - - +
492C ARG 3.5 2.0 - - - +
493C PRO* 4.2 11.4 - - + -
446D PHE* 4.0 14.8 - - + -
450D ASN* 3.9 33.7 - - + +
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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