Contacts of the helix formed by residues 493 - 507 (chain N) in PDB entry 6LTJ
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 ASP 493 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184M GLU* 3.6 14.4 + - - +
186M LEU* 3.6 24.2 - - + +
205M THR 3.7 5.8 - - - +
206M TRP 4.1 0.2 - - - -
207M ASN* 3.1 38.3 + - + +
457N LYS* 4.3 3.4 + - - -
465N TYR* 5.0 0.6 + - - -
492N GLY* 1.3 68.6 - - - -
494N VAL* 1.3 63.6 + - - +
495N CYS* 2.8 29.7 + - - +
496N ALA* 3.1 27.3 + - + +
497N ILE* 3.2 23.7 + - - +
499N ARG* 4.2 4.5 + - - -
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Residues in contact with VAL 494 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M PHE* 3.6 39.0 - - + -
205M THR 3.0 20.0 + - - +
206M TRP* 3.8 15.9 - - + -
218M PHE* 3.7 15.7 - - + -
487N ARG* 3.7 31.6 - - + +
492N GLY 4.0 5.2 - - - +
493N ASP* 1.3 73.6 + - - +
495N CYS* 1.3 60.9 + - - +
497N ILE* 3.8 8.2 - - + +
498N MET* 2.9 36.6 + - - +
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Residues in contact with CYS 495 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M TRP* 3.9 36.8 - - - -
207M ASN 4.6 0.4 - - - -
210M GLU* 3.6 40.6 - - - -
213M MET* 3.8 19.8 - - + +
493N ASP* 2.8 22.1 + - - +
494N VAL* 1.3 75.4 - - - +
496N ALA* 1.3 60.0 + - - +
498N MET* 3.4 1.4 + - - -
499N ARG* 2.9 35.8 + - - +
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Residues in contact with ALA 496 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448N GLU* 3.8 20.2 - - - +
449N PHE* 4.1 14.0 - - + -
457N LYS* 4.5 12.8 - - + -
465N TYR* 5.1 3.4 - - + -
493N ASP* 3.1 26.5 + - + +
495N CYS* 1.3 75.0 - - - +
497N ILE* 1.3 58.3 + - + +
499N ARG* 3.2 11.3 + - - +
500N VAL* 2.9 34.6 + - - +
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Residues in contact with ILE 497 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465N TYR* 3.7 22.9 - - + -
469N MET* 3.3 31.4 - - + +
483N SER 5.4 0.7 - - - +
486N CYS* 5.0 0.2 - - + -
487N ARG* 3.7 30.5 - - + +
490N LEU* 3.3 42.6 - - + +
491N ALA 4.3 1.8 - - - -
492N GLY 3.9 15.7 - - - +
493N ASP 3.2 18.3 + - - +
494N VAL* 3.9 8.3 - - + +
495N CYS 3.3 0.2 - - - -
496N ALA* 1.3 77.3 - - - +
498N MET* 1.3 56.4 + - - +
500N VAL* 3.2 1.8 + - - -
501N HIS* 2.9 24.4 + - + +
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Residues in contact with MET 498 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213M MET* 3.9 19.1 - - + +
218M PHE* 3.4 42.6 - - + +
221M ILE* 3.7 47.8 - - + -
222M LEU 5.5 0.2 - - - +
483N SER* 3.1 25.6 + - - +
484N THR* 5.7 3.8 - - + -
487N ARG* 4.7 12.3 - - + -
494N VAL 2.9 21.2 + - - +
495N CYS 3.9 3.1 - - - +
497N ILE* 1.3 76.8 - - - +
499N ARG* 1.3 57.6 + - - +
501N HIS* 3.4 2.8 + - - +
502N ALA* 2.9 28.8 + - - +
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Residues in contact with ARG 499 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M ILE* 6.1 4.7 - - - -
179M ASN* 4.0 13.0 + - - +
207M ASN* 5.6 0.8 - - - +
210M GLU* 2.7 41.1 + - - -
212M LEU* 4.7 14.7 - - - +
213M MET* 4.4 10.3 - - + +
445N ALA 5.9 0.4 - - - -
446N LEU* 3.8 19.6 - - + +
448N GLU* 2.3 36.2 + - - +
457N LYS* 5.1 4.4 - - - +
493N ASP* 4.2 3.8 + - - -
495N CYS* 2.9 30.5 + - - +
496N ALA* 3.5 11.9 - - - +
497N ILE 3.1 0.2 - - - -
498N MET* 1.3 75.4 - - - +
500N VAL* 1.3 60.3 + - - +
502N ALA* 3.3 6.5 + - + +
503N PHE* 2.9 28.9 + - - +
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Residues in contact with VAL 500 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446N LEU* 3.8 13.7 - - + -
449N PHE* 3.6 31.0 - - + -
462N TYR* 4.0 22.0 - - + -
465N TYR* 4.4 8.5 - - + -
466N ARG* 4.2 22.0 - - + +
469N MET* 4.0 16.6 - - + -
496N ALA 2.9 16.4 + - - +
497N ILE 3.2 5.8 + - - +
499N ARG* 1.3 75.3 - - - +
501N HIS* 1.3 62.8 + - - +
503N PHE* 3.3 2.3 + - - +
504N LEU* 3.0 27.8 + - + +
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Residues in contact with HIS 501 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469N MET* 3.6 16.3 - - + -
480N TYR* 4.2 9.0 - - - -
481N LEU* 2.7 34.6 + - + -
483N SER* 3.7 34.0 + - - +
486N CYS* 4.1 19.1 - - + -
497N ILE* 2.9 13.8 + - + +
498N MET* 3.6 11.8 + - - +
500N VAL* 1.3 77.5 - - - +
502N ALA* 1.3 58.4 + - - +
504N LEU* 3.3 4.7 + - - +
505N GLU* 2.9 60.9 + - + +
510N ILE* 4.3 5.5 - - + +
511N ASN* 3.9 0.8 + - - -
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Residues in contact with ALA 502 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498N MET 2.9 17.3 + - - +
499N ARG* 3.8 8.1 - - + +
501N HIS* 1.3 78.4 + - - +
503N PHE* 1.3 56.9 + - - +
505N GLU* 3.2 10.7 + - - +
506N GLN* 2.9 30.1 + - - +
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Residues in contact with PHE 503 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432N TRP* 3.9 14.4 - + - -
441N ILE* 4.2 4.9 - - + -
442N GLU* 3.7 25.1 - - + -
445N ALA* 3.4 33.0 - - + -
446N LEU* 4.0 18.2 - - + -
462N TYR* 3.7 20.2 - + - -
499N ARG 2.9 17.4 + - - +
500N VAL 3.5 4.5 - - - +
502N ALA* 1.3 75.0 - - - +
504N LEU* 1.3 84.4 + - + +
506N GLN* 3.1 10.6 + - - +
507N TRP* 3.1 59.7 + + - -
509N LEU* 4.8 1.6 - - + -
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Residues in contact with LEU 504 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466N ARG* 3.9 26.9 - - + +
469N MET* 3.9 23.8 - - + -
470N ILE* 3.8 17.7 - - + -
500N VAL* 3.0 21.6 + - + +
501N HIS* 3.8 3.1 - - - +
503N PHE* 1.3 94.8 - - + +
505N GLU* 1.3 61.7 + - - +
507N TRP 3.8 0.2 + - - -
508N GLY 3.2 1.9 + - - -
509N LEU* 3.0 52.1 + - + -
510N ILE* 3.2 34.1 + - + +
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Residues in contact with GLU 505 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480N TYR* 3.8 18.4 + - - -
501N HIS* 2.9 37.7 + - + +
502N ALA* 3.3 11.2 - - - +
504N LEU* 1.3 77.6 - - - +
506N GLN* 1.3 64.5 + - - +
508N GLY* 3.1 13.9 + - - -
510N ILE* 3.5 17.3 - - + +
511N ASN* 2.4 42.2 + - - +
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Residues in contact with GLN 506 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1674L MET* 3.3 33.2 - - + +
1677L LYS* 3.8 23.2 + - - +
429N TYR* 4.0 7.6 + - - -
445N ALA* 5.9 1.2 - - - +
502N ALA 2.9 16.5 + - - +
503N PHE* 3.6 9.9 - - - +
505N GLU* 1.3 78.2 - - - +
507N TRP* 1.3 71.8 + - - +
508N GLY* 3.0 5.0 + - - -
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Residues in contact with TRP 507 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1674L MET* 3.6 18.4 - - + -
1677L LYS* 3.6 22.6 - - + +
1678L SER* 3.5 32.5 - - - -
427N PRO* 3.2 8.3 - - - +
429N TYR* 3.2 46.6 - + - -
430N ALA* 3.2 22.3 - - + +
432N TRP* 3.4 21.5 - + + -
441N ILE* 3.5 22.6 - - + +
445N ALA* 5.3 1.4 - - - +
503N PHE* 3.1 50.8 + + - +
504N LEU 4.5 0.2 - - - +
506N GLN* 1.3 87.0 + - - +
508N GLY* 1.3 61.4 + - - +
509N LEU* 3.2 20.9 + - + -
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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