Contacts of the helix formed by residues 545 - 561 (chain R) in PDB entry 6CNB
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 GLN 545 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486R ILE* 4.2 4.0 - - - -
543R ALA* 3.4 3.7 - - - +
544R LYS* 1.3 82.6 + - + +
546R ARG* 1.3 62.6 + - - +
547R GLU* 2.7 34.3 - - + +
548R GLU* 3.7 34.4 - - + +
549R ILE* 3.2 23.2 + - - +
587R THR* 5.7 0.2 - - - -
588R THR* 3.1 27.4 + - - -
589R ASP* 6.4 0.2 - - - -
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Residues in contact with ARG 546 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393R LEU* 3.4 35.8 - - + +
454R SER* 4.1 7.7 + - - -
455R GLU* 2.6 39.9 + - - +
486R ILE* 4.2 5.7 - - + +
545R GLN* 1.3 75.6 + - - +
547R GLU* 1.3 72.4 + - - +
549R ILE* 3.1 26.6 - - + +
550R TYR* 3.5 31.3 + - + -
585R LEU* 4.4 18.0 - - - +
586R PRO 3.5 14.4 + - - -
587R THR 5.1 0.9 - - - -
588R THR* 3.7 16.7 + - - +
591R TYR* 3.1 33.4 + - - -
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Residues in contact with GLU 547 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545R GLN* 2.7 31.7 - - + +
546R ARG* 1.3 77.4 + - - +
548R GLU* 1.3 66.7 + - + +
549R ILE 3.1 0.5 + - - -
550R TYR* 3.1 8.4 + - - +
551R GLN* 2.9 38.2 + - + +
583R HIS* 4.0 24.5 + - + +
587R THR* 3.2 42.9 - - + +
588R THR* 4.2 0.2 + - - -
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Residues in contact with GLU 548 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526R PRO* 3.6 28.1 - - + +
528R ILE* 3.9 17.9 - - + +
543R ALA* 4.7 1.3 - - + +
544R LYS* 4.7 5.5 + - - +
545R GLN* 3.7 33.7 + - + +
546R ARG 3.4 0.4 - - - -
547R GLU* 1.3 76.6 - - + +
549R ILE* 1.3 62.9 + - - +
551R GLN* 3.3 19.1 - - - +
552R ALA* 2.9 25.6 + - - +
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Residues in contact with ILE 549 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391R PRO* 4.7 8.7 - - + -
393R LEU* 3.9 14.6 - - + -
486R ILE* 3.8 29.4 - - + -
487R VAL 5.4 0.4 - - - +
488R GLY* 5.6 4.9 - - - -
528R ILE* 5.8 0.4 - - - -
540R LEU* 3.5 44.3 - - + +
543R ALA* 4.1 5.8 - - + +
545R GLN 3.2 17.9 - - - +
546R ARG* 3.1 19.7 - - - +
547R GLU 3.1 0.4 - - - -
548R GLU* 1.3 79.5 - - - +
550R TYR* 1.3 79.0 + - + +
552R ALA* 3.1 4.0 + - - +
553R PHE* 2.9 24.6 + - - +
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Residues in contact with TYR 550 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390R VAL* 3.6 18.2 - - + +
391R PRO* 2.8 58.0 + - + -
393R LEU* 3.8 20.1 - - + +
546R ARG* 3.7 36.8 - - + +
547R GLU* 3.1 7.1 + - - +
549R ILE* 1.3 84.6 - - + +
551R GLN* 1.3 61.4 + - - +
553R PHE* 3.6 5.9 - - + +
554R GLU* 2.9 32.4 + - - +
582R LEU* 4.6 16.6 - - - +
583R HIS* 6.3 3.8 - + - -
585R LEU* 5.3 11.6 - - + +
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Residues in contact with GLN 551 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526R PRO* 4.2 13.8 - - + +
547R GLU* 2.9 30.3 + - + +
548R GLU* 3.3 26.8 - - - +
550R TYR* 1.3 76.9 - - - +
552R ALA* 1.3 57.1 + - - +
554R GLU* 3.8 1.9 - - - +
555R ALA* 2.9 31.0 + - - +
582R LEU* 5.6 6.0 + - + +
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Residues in contact with ALA 552 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523R MET* 3.5 30.4 - - + +
526R PRO* 4.9 4.4 - - + +
528R ILE* 5.2 5.4 - - + -
530R LEU* 4.8 8.1 - - + -
540R LEU* 4.4 12.6 - - + -
548R GLU 2.9 13.8 + - - +
549R ILE 3.4 8.5 - - - +
551R GLN* 1.3 76.1 - - - +
553R PHE* 1.3 58.1 + - - +
555R ALA* 3.4 6.5 - - - +
556R ILE* 2.9 34.3 + - - +
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Residues in contact with PHE 553 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387R SER* 3.7 28.3 - - - -
389R ILE 3.6 25.4 - - - -
390R VAL* 5.0 0.4 - - - -
391R PRO* 3.3 29.4 - - + -
490R CYS* 3.4 29.4 - - + -
491R ASP 6.1 0.9 - - - -
492R VAL* 4.9 13.7 - - + -
530R LEU* 5.4 4.7 - - + -
538R ILE* 5.8 2.5 - - + -
540R LEU* 5.0 4.9 - - + +
549R ILE 2.9 14.8 + - - +
550R TYR* 3.7 8.1 - - + +
551R GLN 3.2 0.4 - - - -
552R ALA* 1.3 77.9 - - - +
554R GLU* 1.3 63.8 + - + +
556R ILE* 3.8 8.4 - - + +
557R TYR* 2.9 42.8 + + + +
560R LEU* 5.2 5.4 - - + -
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Residues in contact with GLU 554 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387R SER* 2.7 41.7 + - - -
550R TYR 2.9 17.1 + - - +
551R GLN* 4.4 1.8 - - - +
553R PHE* 1.3 81.7 - - + +
555R ALA* 1.3 57.2 + - - +
557R TYR* 4.2 4.7 - - - +
558R PRO* 3.1 25.1 - - - +
579R PRO* 3.2 32.8 - - + +
582R LEU* 4.2 21.1 - - + -
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Residues in contact with ALA 555 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523R MET* 4.5 9.9 - - + -
525R LYS 5.7 2.0 - - - +
551R GLN 2.9 20.3 + - - +
552R ALA* 3.4 9.0 - - - +
553R PHE 3.1 0.2 - - - -
554R GLU* 1.3 78.9 - - - +
556R ILE* 1.3 58.3 + - - +
558R PRO* 3.2 17.5 - - - +
559R VAL* 4.5 4.7 + - - +
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Residues in contact with ILE 556 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501R LEU* 6.4 2.0 - - + -
521R TYR* 3.6 47.6 - - + -
523R MET* 4.3 8.3 - - + -
530R LEU* 4.2 22.2 - - + -
532R ILE* 5.6 7.2 - - + -
538R ILE* 6.1 1.6 - - + -
552R ALA 2.9 19.7 + - - +
553R PHE* 3.8 8.7 - - + +
555R ALA* 1.3 73.9 - - - +
557R TYR* 1.3 62.6 + - - +
558R PRO 3.3 1.1 - - - -
559R VAL* 2.8 42.7 + - + -
560R LEU* 3.0 24.8 + - + +
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Residues in contact with TYR 557 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387R SER* 3.1 31.9 - - - +
492R VAL* 4.6 12.3 - - + -
494R PHE* 5.1 8.4 - + - -
553R PHE* 2.9 30.5 + + + +
554R GLU* 4.2 9.2 - - - +
556R ILE* 1.3 78.0 - - - +
558R PRO* 1.3 69.1 - - + +
560R LEU* 3.0 19.6 + - + +
561R SER* 2.9 51.7 + - - -
564R ARG* 5.6 1.7 + - - -
576R SER* 2.7 32.3 + - - -
577R GLY* 3.5 10.1 - - - -
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Residues in contact with PRO 558 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554R GLU* 3.1 24.0 - - - +
555R ALA 3.2 12.6 - - - +
557R TYR* 1.3 98.1 - - + +
559R VAL* 1.3 50.5 + - + +
561R SER* 4.6 4.3 - - - -
562R GLU* 2.4 39.9 + - - +
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Residues in contact with VAL 559 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501R LEU* 4.5 12.7 - - + +
505R HIS* 3.4 39.7 - - + +
555R ALA 4.6 4.3 - - - +
556R ILE* 2.8 46.0 + - + +
558R PRO* 1.3 72.5 - - + +
560R LEU* 1.3 57.7 + - + +
562R GLU* 3.1 14.7 - - - +
563R PHE* 2.9 33.9 + - + +
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Residues in contact with LEU 560 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492R VAL* 3.7 27.4 - - + -
494R PHE* 4.2 16.0 - - + -
496R ILE* 4.5 28.9 - - + -
501R LEU* 5.1 11.7 - - + -
532R ILE* 5.3 7.2 - - + -
538R ILE* 4.4 22.0 - - + -
553R PHE* 5.2 6.3 - - + -
556R ILE* 3.0 24.6 + - + +
557R TYR* 3.0 21.5 + - + +
559R VAL* 1.3 76.1 - - + +
561R SER* 1.3 57.9 + - - +
563R PHE* 2.7 35.9 + - - +
564R ARG* 3.6 1.2 - - - +
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Residues in contact with SER 561 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494R PHE* 4.2 4.2 - - - -
557R TYR* 2.9 49.4 + - - -
558R PRO* 4.6 4.9 - - - -
560R LEU* 1.3 73.4 - - - +
562R GLU* 1.3 61.9 + - - +
563R PHE 3.4 0.3 + - - -
564R ARG* 3.5 38.0 + - - +
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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