Contacts of the helix formed by residues 533 - 548 (chain M) 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 TYR 533 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531M HIS* 4.4 12.8 - - + +
532M LYS* 1.3 78.6 - - - +
534M PHE* 1.3 65.3 + - - +
535M GLU* 3.3 11.6 + - + +
536M GLU* 3.7 6.5 + - - +
537M SER* 3.6 15.4 + - - -
564M PHE* 5.9 0.2 - - - +
568M TYR* 4.5 11.8 - - - +
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Residues in contact with PHE 534 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533M TYR* 1.3 74.4 - - - +
535M GLU* 1.3 59.5 + - - +
536M GLU 3.3 0.2 - - - -
537M SER* 3.2 9.3 + - - -
538M PHE* 2.9 30.0 + - - +
568M TYR* 4.4 14.5 - - + +
569M GLY* 5.5 5.6 - - - +
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Residues in contact with GLU 535 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533M TYR* 3.3 7.6 - - + +
534M PHE* 1.3 78.0 - - - +
536M GLU* 1.3 57.8 + - - +
538M PHE* 3.5 5.0 + - - +
539M LYS* 2.9 30.5 + - - +
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Residues in contact with GLU 536 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524M TYR* 5.4 2.5 - - - +
527M PHE* 4.0 37.7 - - + +
528M LEU* 4.6 5.8 - - + +
531M HIS* 4.8 10.5 - - + +
533M TYR* 3.7 10.9 + - - +
534M PHE 3.3 0.2 - - - -
535M GLU* 1.3 78.5 - - - +
537M SER* 1.3 58.2 + - - +
539M LYS* 4.0 5.9 - - - +
540M ALA* 2.9 29.3 + - - +
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Residues in contact with SER 537 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533M TYR 3.6 10.9 + - - -
534M PHE* 3.2 13.3 + - - -
536M GLU* 1.3 77.0 - - - +
538M PHE* 1.3 54.7 + - - +
540M ALA* 3.6 5.5 - - - +
541M TYR* 2.9 9.5 + - - +
560M TYR* 5.1 1.3 - - - -
561M LEU* 6.2 0.7 - - - -
564M PHE* 3.7 30.7 - - - -
568M TYR* 5.7 0.9 - - - -
467O GLY 2.6 24.3 - - - +
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Residues in contact with PHE 538 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534M PHE 2.9 16.6 + - - +
535M GLU* 4.0 5.2 - - - +
537M SER* 1.3 70.5 - - - +
539M LYS* 1.3 55.4 + - - +
541M TYR* 3.2 7.5 + - - +
542M GLU* 2.9 18.9 + - - +
467O GLY 2.2 18.9 - - - +
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Residues in contact with LYS 539 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535M GLU 2.9 19.2 + - - +
536M GLU* 4.0 7.0 - - - +
538M PHE* 1.3 71.1 - - - +
540M ALA 1.3 46.2 - - - +
542M GLU* 4.5 3.4 - - - +
466O ARG* 1.5 58.0 - - + +
467O GLY 1.8 10.5 - - - -
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Residues in contact with ALA 540 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524M TYR* 3.8 29.6 - - + -
536M GLU 2.9 19.0 + - - +
537M SER* 3.6 6.3 - - - +
539M LYS* 1.3 35.0 - - - +
541M TYR* 1.3 50.8 + - - +
544M GLY* 2.9 19.8 + - - -
557M TRP* 4.4 6.8 - - - +
560M TYR* 5.6 9.2 - - + -
466O ARG 2.8 0.7 - - - -
467O GLY* 0.7 230.0 + - - +
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Residues in contact with TYR 541 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537M SER 2.9 11.8 + - - +
538M PHE* 3.6 7.9 - - - +
540M ALA* 1.3 50.6 - - - +
542M GLU* 1.3 55.5 + - - +
544M GLY 3.4 0.5 + - - -
545M ILE* 2.9 29.6 + - - +
557M TRP* 4.3 21.2 - - + +
561M LEU* 5.9 4.5 - - + -
466O ARG 2.9 3.8 - - - -
467O GLY 1.2 44.1 + - - +
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Residues in contact with GLU 542 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538M PHE 2.9 12.6 + - - +
539M LYS* 4.1 5.2 - - - +
541M TYR* 1.3 68.5 - - - +
543M ARG* 1.3 59.8 + - - +
545M ILE* 3.9 4.4 - - - +
546M SER* 2.9 20.6 + - - -
465O ARG* 2.7 13.1 - - - -
466O ARG* 2.3 14.4 + - + +
467O GLY 2.8 4.4 + - - -
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Residues in contact with ARG 543 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520M ILE* 5.9 3.5 - - + +
540M ALA 4.1 0.2 - - - +
542M GLU 1.3 47.5 - - - -
544M GLY* 1.3 46.3 + - - -
547M LEU* 2.7 14.4 - - - +
464O ASP 4.2 1.3 - - - +
465O ARG* 1.1 108.8 - - - +
466O ARG* 1.2 125.1 + - - +
467O GLY 2.6 3.8 - - - +
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Residues in contact with GLY 544 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520M ILE* 5.7 4.9 - - - -
540M ALA 2.9 19.6 + - - -
541M TYR 3.8 0.9 - - - -
543M ARG* 1.3 77.0 - - - +
545M ILE* 1.3 64.0 + - - +
547M LEU* 3.5 14.7 - - - +
548M PHE 3.7 9.7 + - - +
553M VAL* 3.8 26.8 - - - +
554M SER* 3.9 7.1 + - - -
557M TRP* 4.6 3.1 - - - -
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Residues in contact with ILE 545 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541M TYR 2.9 18.3 + - - +
542M GLU* 3.9 5.6 - - - +
544M GLY* 1.3 79.9 - - - +
546M SER* 1.3 61.5 + - - +
547M LEU 3.4 0.5 + - - -
548M PHE 3.6 14.9 + - - +
549M LYS* 4.8 1.4 - - - -
554M SER* 5.1 8.3 - - - -
557M TRP* 5.1 0.8 - - - +
460O LYS* 4.6 10.8 - - + +
461O LYS* 4.2 10.5 - - - +
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Residues in contact with SER 546 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515M ILE* 3.6 7.6 - - - +
542M GLU 2.9 9.2 + - - -
545M ILE* 1.3 74.7 - - - +
547M LEU* 1.3 64.8 + - - +
548M PHE* 4.7 0.2 - - - -
460O LYS 3.2 25.5 + - - -
461O LYS* 3.8 15.9 - - - +
463O GLY* 3.6 18.5 + - - +
465O ARG* 2.4 34.6 - - - +
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Residues in contact with LEU 547 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515M ILE* 3.7 13.1 - - + +
516M ALA 4.9 1.3 - - - +
517M THR* 3.7 30.7 - - - +
520M ILE* 5.7 0.2 - - + -
543M ARG 2.7 18.8 - - - +
544M GLY* 3.5 11.0 - - - +
545M ILE 3.2 0.8 - - - -
546M SER* 1.3 76.5 - - - +
548M PHE* 1.3 62.0 + - - +
553M VAL* 4.1 3.1 - - + -
465O ARG* 1.9 18.8 - - + +
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Residues in contact with PHE 548 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517M THR* 5.9 2.0 - - - -
544M GLY 3.7 7.7 + - - +
545M ILE* 3.6 12.6 - - - +
546M SER 5.1 0.2 - - - -
547M LEU* 1.3 83.4 - - + +
549M LYS* 1.3 68.8 + - - +
550M TRP 3.5 7.3 - - - +
552M ASN* 4.3 16.6 - - + -
553M VAL* 4.7 7.3 + - + +
554M SER* 4.8 1.6 + - - -
461O LYS* 5.9 0.4 - - - -
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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