Contacts of the strand formed by residues 477 - 488 (chain Z) in PDB entry 5WTI
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 LEU 477 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467Z THR* 3.3 7.1 - - - +
468Z TYR* 2.7 45.7 + - + +
475Z PHE* 3.6 35.9 - - + +
476Z PRO* 1.3 75.0 - - - +
478Z LYS* 1.3 64.7 + - - +
516Z ILE* 3.9 20.6 - - + -
517Z GLU 3.9 9.6 - - - +
519Z THR* 3.9 23.8 - - + +
865Z ILE* 3.6 43.1 - - + +
866Z TYR* 4.2 7.6 - - + -
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Residues in contact with LYS 478 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466Z PHE* 3.8 7.2 - - - +
467Z THR* 4.0 25.0 + - - +
476Z PRO* 4.6 14.4 - - - +
477Z LEU* 1.3 80.3 - - - +
479Z GLY* 1.3 59.7 + - - +
516Z ILE* 3.8 3.2 - - - +
517Z GLU* 2.8 51.3 + - + +
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Residues in contact with GLY 479 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465Z ALA* 3.2 6.4 - - - +
466Z PHE* 2.7 51.9 + - - +
478Z LYS* 1.3 76.9 - - - +
480Z THR* 1.3 61.2 + - - +
515Z ASN 3.1 14.6 - - - -
516Z ILE* 4.3 0.4 - - - -
517Z GLU* 4.4 6.9 + - - -
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Residues in contact with THR 480 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463Z LYS* 3.3 44.4 + - + +
464Z HIS 3.3 7.6 - - - -
465Z ALA* 3.9 16.6 - - + -
466Z PHE* 3.3 8.7 - - - -
479Z GLY* 1.3 78.6 - - - +
481Z LEU* 1.3 65.8 + - - +
515Z ASN* 3.0 36.7 + - - +
517Z GLU* 5.1 7.7 + - - +
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Residues in contact with LEU 481 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393Z GLU* 3.7 19.3 - - + +
402Z TYR* 3.8 18.4 - - + +
404Z ILE* 3.7 27.8 - - + +
450Z PHE* 5.1 7.4 - - + -
454Z ILE* 5.5 0.7 - - + -
456Z LEU* 3.8 21.1 - - + -
463Z LYS* 3.9 13.9 - - - +
464Z HIS* 2.9 47.9 + - + +
466Z PHE* 4.5 1.8 - - + -
480Z THR* 1.3 76.8 + - - +
482Z GLY* 1.3 59.4 + - - +
512Z MET* 4.2 18.4 - - + -
513Z THR 4.3 2.7 - - - +
514Z VAL* 4.3 15.7 - - + -
515Z ASN* 4.3 1.1 + - - -
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Residues in contact with GLY 482 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E G 3.7 9.0 - - - -
393Z GLU* 3.6 10.8 - - - +
402Z TYR* 2.5 33.3 + - - -
463Z LYS* 5.9 0.4 - - - -
480Z THR 3.8 1.2 + - - -
481Z LEU* 1.3 75.2 - - - +
483Z GLY* 1.3 62.8 + - - +
513Z THR* 2.8 21.7 + - - -
514Z VAL* 4.1 0.4 - - - +
515Z ASN* 4.1 10.8 - - - -
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Residues in contact with GLY 483 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E G 3.7 19.1 + - - +
20E G 2.9 20.6 + - - -
391Z PHE 3.2 12.8 - - - -
392Z GLU* 4.3 0.4 - - - -
393Z GLU 4.3 4.2 - - - +
402Z TYR* 4.1 1.1 - - - -
482Z GLY* 1.3 71.9 - - - -
484Z ALA* 1.3 59.6 + - - -
513Z THR* 2.9 32.0 + - - -
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Residues in contact with ALA 484 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390Z ARG* 3.3 6.9 - - - +
391Z PHE* 2.7 31.3 + - + +
402Z TYR* 3.5 14.1 - - + -
483Z GLY* 1.3 75.5 - - - +
485Z ARG* 1.3 64.9 + - - +
510Z PHE* 3.4 37.7 - - + -
511Z ASN 3.2 12.3 - - - +
512Z MET* 3.8 7.0 - - + -
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Residues in contact with ARG 485 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B G 3.9 21.4 + - - +
105B G 3.6 25.5 + - - +
18E C 4.3 4.6 + - - -
19E G 3.0 35.9 + - - -
388Z TRP* 4.0 20.6 - - + -
389Z VAL 3.1 15.5 - - - +
390Z ARG* 3.7 33.4 - - + +
391Z PHE* 4.8 0.9 - - - +
484Z ALA* 1.3 79.1 - - - +
486Z VAL* 1.3 64.0 + - - +
487Z GLN* 3.5 20.6 + - + -
510Z PHE* 3.8 3.5 - - - -
511Z ASN* 2.9 47.2 + - + +
513Z THR* 5.4 2.8 + - - -
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Residues in contact with VAL 486 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z ILE* 4.4 3.4 - - + -
20Z LEU* 4.1 27.1 - - + +
24Z HIS* 4.7 0.7 - - - -
388Z TRP* 3.4 22.7 - - - +
389Z VAL* 3.0 18.1 + - + +
391Z PHE* 3.8 27.8 - - + -
422Z LEU* 5.4 0.9 - - + -
425Z LEU* 6.0 0.9 - - + -
442Z ILE* 5.9 0.2 - - + -
485Z ARG* 1.3 71.6 - - - +
487Z GLN* 1.3 59.8 + - - +
488Z PHE* 4.2 14.9 - - + -
508Z ILE* 3.7 29.2 - - + -
509Z TYR 3.5 5.8 - - - +
510Z PHE* 4.4 14.1 - - + +
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Residues in contact with GLN 487 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B G 3.6 4.4 + - - -
105B G 3.7 27.0 - - - +
7Z ILE* 5.1 6.3 - - - +
388Z TRP* 3.7 34.0 - - + +
485Z ARG* 3.5 21.0 + - + -
486Z VAL* 1.3 74.3 - - - +
488Z PHE* 1.3 67.5 + - - +
508Z ILE* 3.8 1.9 - - - +
509Z TYR* 2.8 46.3 + - + +
511Z ASN* 2.5 35.0 + - + +
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Residues in contact with PHE 488 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Z LEU* 3.7 9.2 - - + -
21Z TRP* 3.5 37.7 - + + -
24Z HIS* 3.5 40.4 - + + -
388Z TRP* 3.3 24.2 - + + -
486Z VAL* 4.2 14.4 - - + -
487Z GLN* 1.3 79.8 + - - +
489Z ASP* 1.3 60.7 + - - +
490Z ARG* 3.2 7.3 + - - +
493Z LEU* 4.2 16.6 - - + -
505Z VAL* 3.4 36.1 - - + +
507Z ARG 4.1 3.8 - - - -
508Z ILE* 3.6 27.4 - - + -
509Z TYR* 4.8 3.8 - - - -
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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