Contacts of the helix formed by residues 509 - 524 (chain r) in PDB entry 6FF7
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 LYS 509 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501r LEU* 6.4 1.8 - - + -
503r ALA* 5.8 9.0 - - + +
507r ALA* 3.7 3.7 - - + +
508r GLY* 1.3 77.1 - - - +
510r THR* 1.3 61.1 + - - +
512r VAL* 2.9 25.6 + - + +
513r ALA* 3.5 4.4 + - - +
651r LEU* 4.8 17.5 - - + -
652r SER 6.2 0.4 - - - +
2201r ADP 2.8 26.5 + - - +
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Residues in contact with THR 510 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509r LYS* 1.3 76.0 - - - +
511r ASN* 1.3 52.9 + - - +
513r ALA* 2.9 13.0 + - - +
514r LEU* 2.8 33.7 + - - +
2201r ADP 3.0 25.9 + - - -
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Residues in contact with ASN 511 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485r GLN* 5.5 10.3 - - + +
508r GLY 3.5 8.8 + - - +
509r LYS 3.2 0.8 - - - -
510r THR* 1.3 78.2 - - - +
512r VAL* 1.3 60.3 + - - +
514r LEU* 3.7 12.6 - - + +
515r MET* 3.6 15.4 + - - +
2201r ADP 5.1 12.1 - - + +
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Residues in contact with VAL 512 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485r GLN* 5.3 15.5 - - - +
488r LEU* 6.3 3.4 - - + -
492r ALA* 4.6 5.5 - - - +
508r GLY 4.3 2.1 + - - +
509r LYS* 2.9 16.7 + - + +
511r ASN* 1.3 75.3 - - - +
513r ALA* 1.3 66.4 + - - +
515r MET* 2.9 18.7 + - - +
516r CYS* 3.2 9.4 + - - +
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Residues in contact with ALA 513 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509r LYS 3.5 3.7 + - - +
510r THR* 2.9 11.7 + - - +
512r VAL* 1.3 79.6 - - - +
514r LEU* 1.3 63.4 + - - +
516r CYS* 2.9 22.1 + - - +
517r MET* 2.9 12.5 + - - +
613r ILE* 5.0 16.2 - - + -
649r ILE* 5.1 11.4 - - + -
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Residues in contact with LEU 514 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510r THR 2.8 19.8 + - - +
511r ASN* 3.7 14.6 - - + +
513r ALA* 1.3 71.0 - - - +
515r MET* 1.3 55.9 + - - +
517r MET* 2.9 12.2 + - - +
518r LEU* 2.8 26.4 + - - +
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Residues in contact with MET 515 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489r TYR* 5.8 5.2 - - + -
492r ALA* 4.2 18.9 - - + +
493r LEU* 5.3 6.4 - - + +
511r ASN 3.6 8.8 + - - +
512r VAL* 2.9 12.3 + - - +
514r LEU* 1.3 79.5 - - - +
516r CYS* 1.3 56.8 + - - +
518r LEU* 2.9 9.5 + - - +
519r ARG* 2.9 30.3 + - - +
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Residues in contact with CYS 516 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492r ALA* 4.4 20.5 - - + +
512r VAL 3.2 3.7 + - - +
513r ALA* 2.9 20.7 + - - +
515r MET* 1.3 76.9 - - - +
517r MET* 1.3 59.0 + - - +
519r ARG* 3.9 4.3 - - - +
520r GLU* 3.8 14.2 + - - +
611r LEU* 5.2 5.2 - - - +
649r ILE* 4.7 15.9 - - + -
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Residues in contact with MET 517 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513r ALA 2.9 8.8 + - - +
514r LEU* 2.9 13.7 + - - +
516r CYS* 1.3 75.6 - - - +
518r LEU* 1.3 57.2 + - - +
519r ARG 3.0 4.5 - - - -
520r GLU* 2.9 9.3 + - - +
521r ILE* 2.8 29.2 + - - +
538r ILE* 5.5 11.2 - - + -
585r ILE* 6.3 2.5 - - + -
611r LEU* 6.0 3.6 - - - -
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Residues in contact with LEU 518 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471r ALA* 4.2 31.0 - - + +
514r LEU 2.8 15.8 + - - +
515r MET* 2.9 11.6 + - - +
517r MET* 1.3 72.4 - - - +
519r ARG* 1.3 59.6 - - - +
521r ILE* 3.9 10.5 - - - +
522r GLY* 3.1 16.8 + - - -
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Residues in contact with ARG 519 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492r ALA 4.3 5.6 - - - +
493r LEU* 4.3 29.1 - - + +
515r MET 2.9 14.3 + - - +
516r CYS 3.9 7.6 - - - +
517r MET 3.0 0.2 - - - -
518r LEU* 1.3 75.8 - - - +
520r GLU* 1.3 60.1 + - - +
522r GLY* 2.9 4.5 + - - -
523r LYS* 2.8 25.8 + - - +
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Residues in contact with GLU 520 (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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516r CYS 3.8 8.6 + - - +
517r MET* 2.9 9.1 + - - +
519r ARG* 1.3 75.5 - - - +
521r ILE* 1.3 66.8 + - - +
523r LYS* 2.9 25.1 + - + +
524r HIS* 3.6 6.2 + - - +
536r PHE* 5.3 13.3 - - + +
610r ARG* 5.4 10.8 - - + -
611r LEU* 4.9 15.7 - - + -
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Residues in contact with ILE 521 (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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517r MET 2.8 16.3 + - - +
518r LEU* 4.0 10.5 - - - +
520r GLU* 1.3 75.5 - - - +
522r GLY* 1.3 56.2 + - - +
524r HIS* 3.2 20.1 - - - +
525r ILE* 5.0 0.9 - - - +
531r ILE* 4.2 16.8 - - + +
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Residues in contact with GLY 522 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470r TYR* 6.1 5.8 - - - -
518r LEU 3.1 11.8 + - - -
519r ARG* 2.9 9.5 + - - -
521r ILE* 1.3 77.3 - - - +
523r LYS* 1.3 63.2 + - - +
524r HIS 3.1 4.4 + - - -
525r ILE* 3.7 18.4 - - - +
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Residues in contact with LYS 523 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519r ARG 2.8 11.2 + - - +
520r GLU* 2.9 15.9 + - + +
522r GLY* 1.3 76.6 - - - +
524r HIS* 1.3 59.6 + - + +
525r ILE 3.9 1.7 + - - -
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Residues in contact with HIS 524 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520r GLU 3.6 5.9 + - - +
521r ILE 3.2 15.7 - - - +
522r GLY 3.1 0.9 - - - -
523r LYS* 1.3 78.0 - - + +
525r ILE* 1.3 60.0 + - - +
531r ILE* 3.4 15.7 - - - -
532r ASN* 4.3 12.3 - - + +
535r ASP* 4.3 24.2 - - + -
536r PHE* 5.5 6.5 - - + -
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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
------------------------------------------------------------
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