Contacts of the helix formed by residues 476 - 498 (chain K) in PDB entry 6R1U
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 476 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469K GLN* 4.8 1.0 - - - +
473K ARG* 6.1 0.6 - - - +
474K ILE 3.4 4.5 + - - -
475K THR* 1.3 73.4 - - - +
477K PRO* 1.3 74.5 - - - +
478K THR* 2.8 33.3 + - - +
479K ILE* 3.1 26.2 + - + +
480K ASP* 2.8 26.7 + - - +
531K LEU* 5.8 0.2 - - - +
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Residues in contact with PRO 477 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I T 4.9 18.6 - - - -
475K THR 3.3 6.5 - - - +
476K ASP* 1.3 91.6 - - - +
478K THR* 1.3 58.7 + - + +
480K ASP* 3.4 8.5 - - + +
481K LYS* 3.0 35.9 + - - +
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Residues in contact with THR 478 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I T 5.2 2.9 - - - +
476K ASP* 2.8 29.3 + - - +
477K PRO* 1.3 74.0 - - + +
479K ILE* 1.3 64.9 + - - +
481K LYS* 3.8 6.6 - - - +
482K ARG* 2.9 45.6 + - - +
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Residues in contact with ILE 479 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475K THR* 4.0 13.2 - - + -
476K ASP* 3.1 30.2 + - + +
478K THR* 1.3 82.3 + - - +
480K ASP* 1.3 64.7 + - - +
482K ARG* 3.3 19.1 + - - +
483K MET* 3.1 26.2 + - + +
529K SER* 5.7 1.1 - - - +
531K LEU* 3.8 24.0 - - + -
532K GLU* 4.1 24.5 - - + +
535K VAL* 4.4 13.9 - - + -
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Residues in contact with ASP 480 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466K ASP* 5.5 0.3 - - - -
467K LEU* 3.9 18.8 + - - +
475K THR* 4.1 13.3 - - + +
476K ASP 2.8 16.4 + - - +
477K PRO* 3.4 11.8 - - + +
479K ILE* 1.3 78.5 - - - +
481K LYS* 1.3 63.6 + - + +
483K MET* 3.5 1.2 + - - +
484K ASP* 3.1 22.5 + - - +
535K VAL* 5.0 4.9 - - - -
539K HIS* 4.9 2.4 + - - -
8M ARG* 2.6 46.4 + - - -
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Residues in contact with LYS 481 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I A 2.2 17.4 + - - -
73I T 1.3 105.2 + - + +
477K PRO 3.0 21.0 + - - +
478K THR* 3.9 5.4 - - - +
479K ILE 3.3 0.2 - - - -
480K ASP* 1.3 76.0 - - + +
482K ARG* 1.3 64.9 + - - +
484K ASP* 3.8 5.5 - - - +
485K PHE* 3.1 24.6 + - - +
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Residues in contact with ARG 482 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478K THR* 2.9 32.4 + - - +
479K ILE* 3.7 26.4 - - - +
480K ASP 3.3 0.2 - - - -
481K LYS* 1.3 78.9 - - - +
483K MET* 1.3 61.9 + - - +
485K PHE* 3.6 6.2 - - - +
486K HIS* 3.0 50.0 + - + +
526K ILE* 5.9 2.0 - - - -
528K PHE* 5.0 4.5 - - - -
532K GLU* 2.9 32.8 + - - -
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Residues in contact with MET 483 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479K ILE* 3.1 18.6 + - + +
482K ARG* 1.3 84.9 - - - +
484K ASP* 1.3 61.6 + - - +
486K HIS* 3.9 9.0 - - + +
487K PHE* 2.8 32.1 + - - +
517K TYR* 5.2 0.4 - - + +
528K PHE* 3.9 33.9 - - + -
532K GLU* 3.2 53.6 - - + +
533K GLY* 5.1 0.4 - - - -
535K VAL* 3.8 22.9 - - + -
536K LEU* 4.2 28.3 - - + +
539K HIS* 4.5 2.4 - - - -
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Residues in contact with ASP 484 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480K ASP* 3.1 21.7 + - - +
481K LYS* 3.8 7.4 - - - +
483K MET* 1.3 77.4 - - - +
485K PHE* 1.3 65.0 + - - +
487K PHE* 3.4 1.2 + - - +
488K ASN* 2.8 50.9 + - - +
539K HIS* 3.9 27.6 + - + +
8M ARG* 4.7 7.2 + - - +
9M LYS 5.1 5.4 - - - +
11M THR* 4.9 1.4 + - - -
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Residues in contact with PHE 485 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481K LYS 3.1 16.3 + - - +
482K ARG* 3.6 7.9 - - - +
484K ASP* 1.3 85.3 + - - +
486K HIS* 1.3 77.0 + + - +
488K ASN* 3.5 3.3 + - - +
489K ALA* 2.9 40.8 + - + +
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Residues in contact with HIS 486 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482K ARG* 3.0 35.8 + - + +
483K MET* 3.9 14.9 - - + +
485K PHE* 1.3 93.7 - + - +
487K PHE* 1.3 67.4 + - - +
489K ALA* 3.1 8.6 + - + +
490K LEU* 3.0 30.7 + - + +
517K TYR* 6.2 2.0 - - + -
520K PHE* 3.9 35.3 - + - -
526K ILE* 4.3 7.5 - - + +
528K PHE* 3.6 30.0 - + + -
536K LEU* 5.8 2.5 - - + -
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Residues in contact with PHE 487 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483K MET 2.8 22.3 + - - +
484K ASP 3.6 2.2 - - - +
486K HIS* 1.3 72.0 - - - +
488K ASN* 1.3 76.3 + - - +
490K LEU* 3.1 25.9 + - + +
491K LEU* 3.3 19.4 + - + +
513K ILE* 5.0 1.8 - - + -
536K LEU* 3.7 25.9 - - + +
539K HIS* 3.6 45.8 - + + -
540K LEU* 3.8 16.4 - - + -
542K ASN* 6.4 0.2 - - + -
543K LEU* 3.4 38.4 - - + -
5M GLN* 5.9 0.2 - - - -
10M SER* 3.7 24.5 - - - -
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Residues in contact with ASN 488 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484K ASP* 2.8 50.6 + - - +
485K PHE* 4.1 2.9 - - - +
487K PHE* 1.3 82.0 - - - +
489K ALA* 1.3 61.0 + - - +
491K LEU* 3.2 7.8 + - - +
492K ASP* 3.0 31.6 + - - +
9M LYS 5.4 0.8 + - - -
10M SER* 3.6 11.7 - - - +
11M THR* 2.7 43.5 + - - +
12M GLY* 2.9 16.6 + - - +
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Residues in contact with ALA 489 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485K PHE* 2.9 32.0 + - + +
486K HIS* 3.1 13.4 + - + +
488K ASN* 1.3 73.8 - - - +
490K LEU* 1.3 64.0 + - + +
492K ASP* 3.2 19.3 + - - +
493K VAL* 3.0 22.3 + - - +
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Residues in contact with LEU 490 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486K HIS* 3.0 19.8 + - + +
487K PHE* 3.1 17.5 + - + +
489K ALA* 1.3 78.1 - - + +
491K LEU* 1.3 62.4 + - + +
493K VAL* 3.2 7.7 - - + +
494K VAL* 3.1 28.2 + - - +
513K ILE* 3.8 31.9 - - + +
516K ILE* 3.7 27.7 - - + +
517K TYR* 4.1 38.6 - - + +
520K PHE* 5.5 5.8 - - + -
536K LEU* 4.5 13.0 - - + -
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Residues in contact with LEU 491 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487K PHE* 3.3 33.8 + - + +
488K ASN* 3.2 14.2 + - - +
490K LEU* 1.3 75.7 - - - +
492K ASP* 1.3 65.0 + - - +
494K VAL* 3.3 5.5 + - + +
495K SER* 3.0 21.8 + - - -
509K LEU* 4.5 9.6 - - + -
513K ILE* 4.0 26.9 - - + -
543K LEU* 4.4 7.6 - - + -
559K TRP* 4.3 22.4 - - + +
2M ARG* 4.4 1.8 - - - +
10M SER* 4.0 18.8 - - - +
12M GLY 3.5 23.1 - - - +
13M GLY* 3.5 6.9 - - - -
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Residues in contact with ASP 492 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488K ASN* 3.0 19.6 + - - +
489K ALA* 3.2 16.2 + - - +
491K LEU* 1.3 76.1 - - - +
493K VAL* 1.3 58.6 + - - +
495K SER* 2.5 24.6 + - - -
496K GLU* 3.0 16.0 + - - +
12M GLY* 3.5 5.0 - - - -
13M GLY* 2.8 26.3 + - - +
14M LYS 4.6 0.5 + - - +
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Residues in contact with VAL 493 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489K ALA 3.0 19.1 - - - +
490K LEU* 3.2 14.1 - - + +
492K ASP* 1.3 72.1 - - - +
494K VAL* 1.3 58.4 + - - +
496K GLU* 3.1 9.3 + - + +
497K TRP* 2.8 29.7 + - + +
516K ILE* 3.3 40.6 - - + -
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Residues in contact with VAL 494 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490K LEU 3.1 16.9 + - - +
491K LEU* 3.5 10.3 - - + +
493K VAL* 1.3 76.5 - - - +
495K SER* 1.3 64.5 + - - +
497K TRP* 3.0 17.0 + - + +
498K ARG* 3.0 15.3 + - - +
509K LEU* 4.0 19.7 - - + -
512K LYS* 4.3 10.1 - - + -
513K ILE* 4.1 22.9 - - + -
516K ILE* 3.6 19.7 - - + -
556K ALA* 4.1 27.1 - - + +
559K TRP* 5.0 5.2 - - - +
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Residues in contact with SER 495 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491K LEU 3.0 12.3 + - - -
492K ASP* 2.5 22.3 + - - -
494K VAL* 1.3 76.6 - - - +
496K GLU* 1.3 63.8 + - - +
498K ARG* 3.4 37.8 + - - +
499K LYS* 3.5 17.4 - - - +
13M GLY* 3.5 30.9 + - - -
14M LYS 5.5 0.2 + - - -
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Residues in contact with GLU 496 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492K ASP 3.0 13.1 + - - +
493K VAL* 3.4 13.9 - - + +
494K VAL 3.0 0.6 - - - -
495K SER* 1.3 81.0 + - - +
497K TRP* 1.3 63.0 + - - +
498K ARG 3.3 0.7 + - - -
499K LYS* 3.0 53.1 + - - +
500K ASP* 5.2 1.6 - - - +
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Residues in contact with TRP 497 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493K VAL* 2.8 22.9 + - + +
494K VAL* 3.0 8.5 + - + +
496K GLU* 1.3 75.6 - - - +
498K ARG* 1.3 95.1 + - + +
499K LYS 3.4 1.0 + - - -
500K ASP* 3.7 3.3 - - - +
501K LYS* 3.1 66.0 + - + +
505K GLN 3.9 15.7 - - - -
506K ASP* 4.7 1.6 - - - -
507K VAL* 3.8 35.7 - - + -
512K LYS* 3.2 40.5 - - + +
516K ILE* 5.4 0.4 - - + -
556K ALA* 4.0 20.2 - - + -
557K ARG* 4.3 6.5 - - + -
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Residues in contact with ARG 498 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494K VAL* 3.0 9.4 + - - +
495K SER* 3.4 33.9 + - - +
497K TRP* 1.3 95.9 - - + +
499K LYS* 1.3 67.7 + - + +
500K ASP 3.1 3.1 - - - -
501K LYS* 3.0 21.9 + - - +
556K ALA 3.2 24.5 + - - +
557K ARG* 3.5 30.0 + - + +
559K TRP* 3.5 10.9 - - - +
560K ASP* 2.7 41.3 + - - -
13M GLY 3.8 14.3 + - - -
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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