Contacts of the helix formed by residues 481 - 500 (chain C) in PDB entry 1V40
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 481 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479C GLY 3.5 0.2 - - - -
480C ASN* 1.3 84.2 - - + +
482C GLU* 1.3 60.7 + - - +
483C MET* 3.4 7.0 + - - +
484C GLU* 3.0 40.2 + - + +
485C GLN* 2.8 35.2 + - - +
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Residues in contact with GLU 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B TYR* 3.7 32.2 - - + +
273B LYS* 4.5 19.8 + - + +
274B ASN* 3.3 27.4 + - - -
481C THR* 1.3 73.6 - - - +
483C MET* 1.3 63.0 + - - +
485C GLN* 3.4 13.2 + - - +
486C CYS 3.1 15.9 + - - -
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Residues in contact with MET 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 5.0 11.2 - - - -
259B LEU* 3.3 46.0 - - + -
260B THR 5.4 0.2 - - - +
261B LEU* 3.8 24.5 - - + -
270B TYR* 3.7 28.5 - - + +
481C THR* 3.2 6.5 + - - +
482C GLU* 1.3 78.2 - - - +
484C GLU* 1.3 61.5 + - + +
486C CYS* 3.2 6.8 + - - +
487C HIS* 3.0 45.6 + - + +
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Residues in contact with GLU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLY* 4.6 0.4 - - - -
480C ASN* 3.5 29.1 + - - +
481C THR* 3.0 33.2 + - - +
483C MET* 1.3 75.9 - - + +
485C GLN* 1.3 60.3 + - - +
487C HIS* 3.1 13.4 + - + +
488C VAL* 2.9 33.7 + - - +
542C ILE* 3.6 13.3 - - + +
543C GLY* 3.5 31.9 + - - -
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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
----------------------------------------------------------
273B LYS* 2.2 47.0 + - - +
478C ALA* 3.2 37.3 - - + +
479C GLY* 3.1 21.6 + - - -
480C ASN 5.1 0.8 - - - -
481C THR 2.8 23.2 + - - +
482C GLU* 3.5 7.7 - - - +
484C GLU* 1.3 76.2 - - - +
486C CYS* 1.3 62.6 + - - +
488C VAL* 3.4 3.1 + - - +
489C ASP* 3.1 28.1 + - - +
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Residues in contact with CYS 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 4.0 30.3 - - + -
262B HIS 4.8 2.0 - - - -
266B ALA* 3.6 30.4 - - - +
267B ILE* 4.2 4.9 - - - -
270B TYR* 3.9 21.5 - - + +
482C GLU 3.1 12.5 + - - +
483C MET* 3.3 11.4 - - - +
484C GLU 3.1 0.4 - - - -
485C GLN* 1.3 74.8 - - - +
487C HIS* 1.3 60.5 + - - +
489C ASP* 3.3 8.1 + - - +
490C ALA* 2.8 29.8 + - - +
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Residues in contact with HIS 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B THR 3.5 24.2 - - - -
261B LEU* 3.5 22.0 - - + +
262B HIS* 5.0 10.7 + - - -
483C MET* 3.0 38.9 + - + +
484C GLU* 3.1 15.4 + - + +
486C CYS* 1.3 73.2 - - - +
488C VAL* 1.3 60.3 + - - +
490C ALA* 3.5 5.0 - - - +
491C ILE* 2.8 35.2 + - - +
534C TYR* 3.6 27.1 + + - +
542C ILE* 3.9 10.8 - - + -
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Residues in contact with VAL 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C ALA 3.6 17.0 - - - +
479C GLY* 4.3 0.7 - - - -
484C GLU 2.9 20.5 + - - +
485C GLN 3.5 7.6 - - - +
487C HIS* 1.3 77.8 - - - +
489C ASP* 1.3 63.4 + - - +
491C ILE* 3.3 1.6 + - - +
492C VAL* 3.0 28.9 + - + +
542C ILE* 3.9 19.5 - - + -
547C THR* 3.8 23.3 - - + +
548C TRP* 3.4 40.2 - - + +
549C ALA* 3.9 13.7 - - + +
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Residues in contact with ASP 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 3.6 17.1 - - + +
269B ARG* 3.0 31.2 + - - +
469C ARG* 2.8 39.4 + - - +
485C GLN 3.1 14.2 + - - +
486C CYS* 3.6 8.9 - - - +
488C VAL* 1.3 81.4 - - - +
490C ALA* 1.3 58.8 + - - +
492C VAL* 3.4 7.1 + - - +
493C ASP* 2.9 34.1 + - - +
548C TRP* 3.9 9.5 + - - -
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Residues in contact with ALA 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B HIS* 3.4 46.2 - - + +
263B GLN* 3.3 13.4 - - + +
266B ALA* 3.6 3.3 - - + +
486C CYS* 2.8 18.6 + - - +
487C HIS* 3.5 8.7 - - - +
489C ASP* 1.3 75.1 - - - +
491C ILE* 1.3 64.8 + - - +
493C ASP 3.4 0.3 + - - -
494C THR* 2.9 28.0 + - - -
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Residues in contact with ILE 491 (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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248B PHE* 3.6 37.0 - - + -
262B HIS* 4.4 4.3 - - + +
487C HIS 2.8 23.8 + - - +
488C VAL 3.9 3.1 - - - +
490C ALA* 1.3 72.1 - - - +
492C VAL* 1.3 63.4 + - - +
494C THR* 3.2 5.1 + - - -
495C LEU* 3.0 37.6 + - + +
531C LEU* 4.7 7.6 - - + -
534C TYR* 3.6 27.1 - - + -
541C LEU* 4.0 24.7 - - + -
542C ILE* 3.8 19.3 - - + -
549C ALA* 4.3 6.3 - - + -
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Residues in contact with VAL 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C LEU* 3.5 29.2 - - + -
469C ARG* 5.2 1.8 - - - +
488C VAL 3.0 22.9 + - - +
489C ASP* 3.6 4.5 - - - +
491C ILE* 1.3 77.2 - - - +
493C ASP* 1.3 60.0 + - - +
495C LEU* 3.3 2.2 + - - -
496C ASP* 3.0 25.8 + - - +
548C TRP* 3.8 40.4 - - + -
549C ALA* 3.9 24.9 - - + -
552C TYR* 3.6 20.2 - - + -
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Residues in contact with ASP 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLN* 3.6 26.7 - - + +
265B LEU* 4.0 26.3 - - - +
266B ALA* 4.6 5.4 + - - -
269B ARG* 5.4 3.8 + - - -
293B ASP* 5.1 4.6 - - - +
3400B GSH 6.0 0.2 - - - -
3901B MG 4.3 12.4 - - - -
465C LEU* 3.6 20.1 - - - +
469C ARG* 4.9 7.4 + - - -
489C ASP 2.9 20.0 + - - +
492C VAL* 1.3 75.1 - - - +
494C THR* 1.3 60.9 + - - +
496C ASP* 3.8 4.2 - - - +
497C ASP* 2.8 39.2 + - - +
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Residues in contact with THR 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PHE* 3.7 33.6 - - + +
262B HIS* 3.4 17.5 + - - -
263B GLN* 3.3 17.3 + - - +
490C ALA 2.9 21.9 + - - -
491C ILE* 3.2 8.5 + - - -
493C ASP* 1.3 78.4 - - - +
495C LEU* 1.3 62.3 + - + +
497C ASP* 3.5 5.0 + - - +
498C PHE* 3.4 17.3 + - - +
527C LEU* 3.9 18.0 - - + +
531C LEU* 5.2 3.6 - - + -
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Residues in contact with LEU 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C ILE* 3.0 31.3 + - + +
492C VAL 3.7 5.4 - - - +
494C THR* 1.3 75.0 - - - +
496C ASP* 1.3 59.9 + - - +
498C PHE* 3.2 7.4 + - - +
499C MET* 3.0 31.7 + - - +
527C LEU* 4.5 11.2 - - + -
528C MET* 5.6 0.2 - - + -
531C LEU* 3.7 32.5 - - + -
541C LEU* 5.5 0.2 - - + -
549C ALA 4.5 0.9 - - - +
552C TYR* 3.9 21.1 - - + +
553C TRP* 3.6 48.5 - - + +
556C CYS* 4.2 10.3 - - + -
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Residues in contact with ASP 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ASP* 5.4 1.0 - - - +
3901B MG 3.9 12.3 - - - -
414C ARG* 2.8 38.0 + - - -
465C LEU* 3.7 22.6 - - + +
492C VAL 3.0 17.9 + - - +
493C ASP* 3.8 5.2 - - - +
495C LEU* 1.3 73.6 - - - +
497C ASP* 1.3 61.9 + - - +
499C MET* 3.3 3.1 + - - -
500C SER* 2.9 37.8 + - - -
552C TYR* 2.8 22.6 + - - +
3600C GSH 4.9 5.4 + - - -
3601C O16 3.5 2.4 - - - -
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Residues in contact with ASP 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLN* 3.1 16.7 + - - -
296B ASP* 5.4 1.0 - - - +
3400B GSH 2.7 35.5 + - - +
3901B MG 4.1 15.6 - - - -
493C ASP* 2.8 24.7 + - - +
494C THR* 3.6 6.3 - - - +
496C ASP* 1.3 74.0 - - - +
498C PHE* 1.3 61.4 + - - +
500C SER* 3.5 12.0 + - - -
501C CYS* 3.5 17.5 + - - -
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Residues in contact with PHE 498 (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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494C THR 3.4 4.5 + - - +
495C LEU 3.2 8.1 + - - +
496C ASP 3.2 0.6 - - - -
497C ASP* 1.3 78.0 - - - +
499C MET* 1.3 67.5 + - - +
501C CYS* 2.9 31.1 + - + +
502C PHE* 3.4 38.3 - + - -
519C LEU* 4.0 11.9 - - + -
520C LEU* 4.7 0.2 - - + -
523C ASN* 3.9 24.0 - - + -
524C ALA* 3.7 33.9 - - + -
527C LEU* 3.7 33.2 - - + -
528C MET* 5.3 0.7 - - + -
560C LEU* 4.1 22.9 - - + -
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Residues in contact with MET 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG* 4.8 0.9 - - - -
495C LEU 3.0 20.5 + - - +
496C ASP 3.3 3.8 + - - +
498C PHE* 1.3 78.3 - - - +
500C SER* 1.3 60.8 + - - +
501C CYS 3.1 1.3 + - - -
502C PHE* 3.3 10.1 + - - -
504C TRP* 2.8 51.4 + - + -
556C CYS* 3.6 39.0 - - + +
559C THR* 4.3 5.8 - - + -
560C LEU* 3.8 36.6 - - + -
3601C O16 3.4 41.7 - - + -
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Residues in contact with SER 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ASP* 5.8 0.2 + - - -
414C ARG* 2.8 27.8 + - - +
496C ASP* 2.9 20.9 + - - -
497C ASP* 3.7 8.3 - - - -
498C PHE 3.1 0.6 - - - -
499C MET* 1.3 75.0 - - - +
501C CYS* 1.3 60.0 + - - +
502C PHE 3.3 6.6 + - - +
504C TRP* 4.7 3.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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