Contacts of the helix formed by residues 470 - 493 (chain S) in PDB entry 5LN3
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 ARG 470 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469S THR* 1.3 76.7 + - - +
471S GLU* 1.3 70.5 + - - +
472S PRO 3.3 1.1 - - - -
473S GLN* 2.8 23.6 + - - +
474S LEU* 3.2 39.6 + - + +
327T ASP* 3.8 26.9 + - + +
328T THR* 3.3 27.1 - - - +
329T THR* 3.3 29.1 + - + +
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Residues in contact with GLU 471 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467S TYR 6.1 0.2 - - - +
469S THR* 3.1 11.5 + - + +
470S ARG* 1.3 89.5 + - - +
472S PRO* 1.3 70.4 - - + +
474S LEU* 3.5 23.8 + - - +
475S ALA* 3.3 16.1 + - - +
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Residues in contact with PRO 472 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370R ILE* 6.2 0.9 - - + -
467S TYR* 4.1 47.8 - - + +
469S THR 3.2 18.8 - - - +
471S GLU* 1.3 94.7 - - + +
473S GLN* 1.3 62.2 + - - +
475S ALA* 3.1 10.4 + - + +
476S PHE* 3.0 48.4 + - + -
258U VAL* 4.4 13.2 - - + -
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Residues in contact with GLN 473 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470S ARG* 2.8 30.3 + - - +
472S PRO* 1.3 73.9 - - - +
474S LEU* 1.4 58.4 + - - +
476S PHE* 3.2 18.6 + - - +
477S HIS* 3.3 14.1 + - - +
328T THR* 3.8 21.1 - - - +
329T THR* 4.0 10.1 - - + -
334T GLU* 3.2 26.2 + - - +
337T LYS* 4.3 15.1 - - - +
338T GLN* 3.5 22.2 + - - +
341T GLU* 5.1 0.8 + - - -
258U VAL* 5.3 3.7 - - + +
261U TYR* 3.2 27.0 - - - -
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Residues in contact with LEU 474 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470S ARG* 3.2 39.4 + - - +
471S GLU* 3.8 25.4 - - - +
473S GLN* 1.4 75.6 - - - +
475S ALA* 1.3 66.1 + - - +
477S HIS* 3.4 6.7 + - - +
478S GLN* 3.1 22.5 + - - +
328T THR* 4.3 19.5 - - + +
337T LYS* 4.5 12.8 - - - +
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Residues in contact with ALA 475 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370R ILE* 5.9 9.2 - - + -
471S GLU 3.3 7.0 + - - +
472S PRO* 3.1 16.9 + - + +
474S LEU* 1.3 78.1 - - - +
476S PHE* 1.4 70.5 + - + +
478S GLN* 3.3 5.6 + - - +
479S ARG* 3.0 38.1 + - + +
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Residues in contact with PHE 476 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370R ILE* 4.2 12.6 - - + -
467S TYR* 6.4 0.4 - + - -
472S PRO* 3.0 35.2 + - + -
473S GLN* 3.2 22.4 + - - +
475S ALA* 1.4 79.9 - - + +
477S HIS* 1.3 54.3 + - - +
479S ARG* 3.5 4.3 + - - +
480S ILE* 2.9 42.9 + - + +
258U VAL* 3.3 49.6 - - + -
261U TYR* 3.7 20.4 - + + +
262U LEU* 3.9 35.4 - - + -
265U LEU* 4.3 14.9 - - + +
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Residues in contact with HIS 477 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473S GLN* 3.3 11.6 + - - +
474S LEU* 3.6 8.7 - - - +
475S ALA 3.2 0.4 - - - -
476S PHE* 1.3 78.1 - - - +
478S GLN* 1.4 59.3 + - - +
480S ILE* 3.2 20.8 - - - +
481S SER* 2.9 22.6 + - - -
337T LYS* 3.7 28.6 - - - +
340T ILE* 5.0 6.3 - - + +
341T GLU* 2.8 43.6 + - + +
344T ARG* 3.7 18.9 + - - -
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Residues in contact with GLN 478 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474S LEU 3.1 15.8 + - - +
475S ALA* 3.6 7.6 - - - +
477S HIS* 1.4 74.4 - - - +
479S ARG* 1.3 67.0 + - + +
481S SER* 3.3 24.5 + - - -
482S PHE* 3.5 40.6 - - + -
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Residues in contact with ARG 479 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370R ILE* 3.6 19.5 + - - +
373R GLY* 3.2 25.9 + - - -
374R ASP* 3.2 41.9 + - - +
377R LEU* 3.9 28.2 - - + +
475S ALA* 3.0 26.2 + - - +
476S PHE* 4.0 0.4 - - - +
478S GLN* 1.3 81.4 - - + +
480S ILE* 1.4 64.4 + - - +
482S PHE* 3.4 32.9 + - + +
483S CYS* 3.8 12.1 + - - -
265U LEU* 3.4 40.2 - - + +
269U VAL* 5.6 4.9 - - - +
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Residues in contact with ILE 480 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476S PHE* 2.9 24.5 + - + +
477S HIS* 3.2 26.0 - - - +
479S ARG* 1.4 68.7 - - - +
481S SER* 1.3 61.2 + - - +
482S PHE 3.3 0.2 + - - -
483S CYS* 3.4 7.6 + - - +
484S LEU* 3.0 32.3 + - + +
341T GLU* 4.3 25.1 - - + +
344T ARG* 5.0 6.5 - - - +
261U TYR 5.8 0.2 - - - +
264U SER* 5.4 3.8 - - - -
265U LEU* 3.8 31.0 - - + +
268U SER* 4.6 13.1 - - - +
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Residues in contact with SER 481 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477S HIS* 2.9 21.8 + - - -
478S GLN* 3.3 15.7 + - - -
480S ILE* 1.3 77.0 - - - +
482S PHE* 1.3 67.6 + - - +
484S LEU* 3.2 3.8 + - - +
485S ASP* 2.9 33.1 + - - +
344T ARG* 3.4 27.1 + - - +
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Residues in contact with PHE 482 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377R LEU* 4.1 27.8 - - + -
381R GLN* 5.2 12.1 - - - +
478S GLN* 3.5 51.6 - - + -
479S ARG* 3.4 18.8 + - + +
480S ILE 3.3 0.6 - - - -
481S SER* 1.3 81.0 - - - +
483S CYS* 1.3 66.1 + - - +
485S ASP* 3.5 14.4 + - - +
486S ILE* 3.5 13.7 + - - +
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Residues in contact with CYS 483 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377R LEU* 4.2 18.2 - - - -
380R VAL* 5.9 2.7 - - - -
479S ARG 3.8 13.5 - - - -
480S ILE* 3.7 6.7 - - - +
481S SER 3.4 0.2 - - - -
482S PHE* 1.3 81.4 - - - +
484S LEU* 1.4 58.5 + - - +
486S ILE* 3.0 26.9 - - - +
487S HIS* 3.0 15.3 + - - +
265U LEU* 5.3 3.4 - - - -
268U SER* 4.8 16.4 - - - -
269U VAL* 3.9 33.2 - - - +
272U LEU* 3.9 14.7 - - + +
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Residues in contact with LEU 484 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480S ILE* 3.0 21.5 + - + +
481S SER* 3.2 5.3 + - - +
483S CYS* 1.4 58.5 - - - +
485S ASP* 1.4 61.7 + - - +
487S HIS* 3.2 24.5 + - + +
488S ASN* 2.7 44.8 + - - +
341T GLU 5.7 0.4 - - - +
344T ARG* 4.3 31.4 - - + +
345T GLN* 4.5 33.0 - - + +
268U SER* 6.6 0.2 - - - -
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Residues in contact with ASP 485 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481S SER* 2.9 24.5 + - - +
482S PHE* 4.0 9.4 - - - +
483S CYS 3.4 0.4 - - - -
484S LEU* 1.4 73.7 - - - +
486S ILE* 1.4 58.7 + - - +
488S ASN* 3.3 11.3 - - - +
489S MET* 2.9 27.4 + - - +
344T ARG* 5.9 0.7 + - - -
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Residues in contact with ILE 486 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380R VAL* 5.4 3.1 - - + -
381R GLN* 5.4 5.6 - - - +
384R SER* 4.0 20.2 - - - +
388R ASN* 3.6 28.5 - - - +
482S PHE 3.5 11.6 + - - +
483S CYS* 3.0 19.3 - - - +
485S ASP* 1.4 80.0 - - - +
487S HIS* 1.4 53.2 + - - +
489S MET* 2.9 20.9 + - + -
490S SER* 2.9 36.3 + - - +
272U LEU* 3.5 28.9 - - + -
276U ILE* 5.5 6.7 - - + -
279U LYS* 5.8 0.9 - - - -
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Residues in contact with HIS 487 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483S CYS 3.0 15.4 + - - +
484S LEU* 3.2 28.1 + - + +
486S ILE* 1.4 74.2 - - - +
488S ASN* 1.3 61.9 + - - +
490S SER* 3.1 18.2 + - - -
491S VAL* 3.4 15.7 - - + +
268U SER* 4.7 4.5 - - - -
271U ALA* 4.1 15.7 - - + +
272U LEU* 3.7 31.6 - - + -
275U LEU* 3.4 27.7 - - + +
292V MET* 5.2 6.3 - - - +
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Residues in contact with ASN 488 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484S LEU* 2.7 36.0 - - - +
485S ASP* 3.3 13.2 - - - +
487S HIS* 1.3 77.7 + - - +
489S MET* 1.4 61.4 + - - +
491S VAL* 3.3 21.2 - - - +
492S LYS* 3.4 28.0 + - - +
344T ARG 5.6 4.2 + - - -
347T GLU* 6.2 2.2 - - - +
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Residues in contact with MET 489 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388R ASN* 3.8 40.0 + - + +
485S ASP 2.9 12.2 + - - +
486S ILE* 2.9 20.4 + - + +
488S ASN* 1.4 78.7 - - - +
490S SER* 1.3 63.5 + - - +
492S LYS* 3.0 30.6 + - + +
493S ALA* 4.0 2.3 + - - +
279U LYS* 5.3 0.2 - - - +
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Residues in contact with SER 490 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388R ASN* 5.0 2.0 - - - +
486S ILE* 2.9 20.4 + - - +
487S HIS* 3.1 16.2 + - - -
489S MET* 1.3 72.3 - - - +
491S VAL* 1.4 60.9 + - - +
492S LYS 3.5 0.3 + - - -
493S ALA* 3.6 12.3 - - - +
272U LEU* 5.3 3.1 - - - -
275U LEU* 3.5 33.7 - - - +
276U ILE* 5.2 4.0 - - - -
279U LYS* 3.5 39.5 - - - +
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Residues in contact with VAL 491 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487S HIS* 3.4 19.7 - - + +
488S ASN* 3.3 13.0 - - - +
490S SER* 1.4 80.0 - - - +
492S LYS* 1.3 63.8 + - - +
493S ALA* 3.3 4.7 + - - +
275U LEU* 4.7 9.9 - - + -
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Residues in contact with LYS 492 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488S ASN* 3.5 29.7 + - - +
489S MET* 3.0 25.8 + - + +
491S VAL* 1.3 78.2 - - - +
493S ALA* 1.4 63.1 + - - +
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Residues in contact with ALA 493 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489S MET 4.0 1.7 + - - +
490S SER 3.6 16.1 + - - +
491S VAL 3.3 4.4 + - - -
492S LYS* 1.4 83.0 - - - +
279U LYS* 4.7 16.8 - - + +
283U ARG* 5.9 4.9 - - + -
293U LYS* 3.1 36.6 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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