Contacts of the helix formed by residues 523 - 544 (chain E) in PDB entry 6T8B
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 GLU 523 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518E VAL* 3.4 19.3 - - + +
519E THR 5.2 1.7 + - - -
520E ASP* 3.3 40.6 + - + +
521E MET 3.2 0.8 - - - -
522E LYS* 1.3 78.1 - - + +
524E ALA* 1.3 59.1 + - - +
525E ALA 3.6 0.4 - - - -
526E ASN* 3.7 16.3 - - - +
527E ALA* 3.8 4.5 + - - +
721E LEU 3.4 28.9 - - - +
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Residues in contact with ALA 524 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497E ILE* 4.8 9.9 - - + +
518E VAL* 3.6 18.2 - - + +
520E ASP 4.2 2.2 - - - +
521E MET* 3.3 18.3 + - + +
522E LYS 3.2 1.0 - - - -
523E GLU* 1.3 76.4 - - - +
525E ALA* 1.3 62.3 + - - +
526E ASN 3.1 1.7 + - - -
527E ALA* 3.2 4.7 + - - +
528E LEU* 2.9 33.6 + - - +
600E MET* 4.1 28.0 - - + -
604E VAL* 4.9 0.7 - - + -
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Residues in contact with ALA 525 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521E MET 4.2 2.8 + - - -
522E LYS* 4.4 8.5 + - - +
523E GLU 3.6 0.2 - - - -
524E ALA* 1.3 76.3 - - - +
526E ASN* 1.3 58.7 + - - +
528E LEU* 3.7 12.4 - - + +
529E ARG* 2.9 52.1 + - + +
604E VAL* 4.6 21.4 - - + +
607E LYS* 5.5 8.3 - - + +
611E LEU* 5.7 0.7 - - + -
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Residues in contact with ASN 526 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522E LYS 3.8 17.3 + - - -
523E GLU* 3.7 9.3 + - - +
524E ALA 3.1 0.8 - - - -
525E ALA* 1.3 76.3 - - - +
527E ALA* 1.3 60.9 + - - +
529E ARG* 3.3 12.8 + - - +
530E TRP* 2.9 28.6 + - - +
719E ASP 5.2 1.3 - - - +
720E ILE 3.2 19.5 - - - +
721E LEU* 3.4 44.9 + - + +
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Residues in contact with ALA 527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495E ILE* 4.0 29.1 - - + +
497E ILE* 5.5 5.4 - - + -
518E VAL* 4.1 19.5 - - + -
523E GLU 3.8 2.5 + - - +
524E ALA* 3.2 8.1 + - - +
526E ASN* 1.3 78.2 - - - +
528E LEU* 1.3 57.8 + - + +
530E TRP* 3.3 7.1 + - - +
531E SER* 2.9 28.1 + - - -
592E VAL* 5.9 2.1 - - + +
720E ILE* 3.6 19.3 + - + -
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Residues in contact with LEU 528 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497E ILE* 4.3 20.0 - - + -
524E ALA 2.9 24.0 + - - +
525E ALA* 3.7 9.4 - - - +
527E ALA* 1.3 78.1 - - - +
529E ARG* 1.3 56.9 + - - +
531E SER* 2.4 24.8 + - - +
532E VAL* 2.9 15.9 + - - +
592E VAL* 4.8 10.5 - - + -
594E VAL* 5.4 1.8 - - + -
600E MET* 4.1 11.9 - - + -
607E LYS 5.1 0.2 - - - +
608E VAL* 3.6 34.8 - - + -
611E LEU* 3.4 28.7 - - + -
612E ILE* 4.7 11.2 - - + -
615E ILE* 4.4 11.0 - - + -
626E LEU* 5.7 0.4 - - + -
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Residues in contact with ARG 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525E ALA* 2.9 33.0 + - - +
526E ASN* 3.8 11.4 + - - +
528E LEU* 1.3 75.5 - - - +
530E TRP* 1.3 58.1 + - - +
532E VAL* 3.3 9.3 + - - +
533E ALA* 2.9 27.9 + - - +
607E LYS* 4.2 31.1 - - - +
611E LEU* 4.1 15.5 - - + +
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Residues in contact with TRP 530 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495E ILE* 3.6 15.5 - - + -
514E LEU* 3.5 33.9 - - + -
526E ASN 2.9 18.2 + - - +
527E ALA* 3.6 4.9 - - - +
528E LEU 3.2 0.2 - - - -
529E ARG* 1.3 78.5 - - - +
531E SER* 1.3 62.8 + - - +
533E ALA* 3.3 8.6 + - + -
534E GLU* 2.8 55.9 + - + +
537E ARG* 6.1 0.8 - - - +
590E ILE* 3.9 17.7 - - + -
624E ILE* 5.6 0.9 - - + -
717E ILE* 4.5 14.7 - - + +
719E ASP* 3.6 32.9 + - - +
720E ILE* 3.4 30.3 - - + -
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Residues in contact with SER 531 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495E ILE* 5.7 0.4 - - - -
527E ALA 2.9 13.3 + - - -
528E LEU* 2.4 29.9 + - - +
530E TRP* 1.3 87.7 - - - +
532E VAL* 1.3 55.1 + - - +
534E GLU* 3.3 4.5 + - - +
535E MET* 2.9 31.4 + - - +
592E VAL* 4.3 22.2 - - - -
615E ILE* 3.2 23.2 - - - +
624E ILE* 4.5 13.4 - - - +
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Residues in contact with VAL 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528E LEU 2.9 14.5 + - - +
529E ARG* 3.6 9.9 - - - +
530E TRP 3.3 0.2 - - - -
531E SER* 1.3 81.9 + - - +
533E ALA* 1.3 62.5 + - - +
535E MET* 3.1 19.9 - - + +
536E GLU* 3.0 34.4 + - - +
611E LEU* 3.6 18.2 - - + +
614E ARG* 3.7 33.9 - - - +
615E ILE* 3.6 22.0 - - + -
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Residues in contact with ALA 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529E ARG 2.9 17.8 + - - +
530E TRP* 3.7 12.3 - - + +
532E VAL* 1.3 77.3 - - - +
534E GLU* 1.3 58.1 + - - +
536E GLU* 3.4 6.0 + - - +
537E ARG* 2.9 36.8 + - - +
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Residues in contact with GLU 534 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530E TRP* 2.8 55.4 + - + +
531E SER* 3.6 6.5 - - - +
533E ALA* 1.3 75.1 - - - +
535E MET* 1.3 60.5 + - - +
537E ARG* 3.1 34.5 + - - +
538E ARG* 2.9 65.3 + - - +
587E LEU* 4.9 3.3 - - - +
590E ILE* 4.5 1.3 - - + -
624E ILE* 4.4 14.1 - - + -
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Residues in contact with MET 535 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531E SER 2.9 13.0 + - - +
532E VAL* 3.1 34.3 - - + +
534E GLU* 1.3 76.2 - - - +
536E GLU* 1.3 66.2 + - + +
538E ARG* 3.8 1.8 - - - +
539E TYR* 2.9 30.7 + - - +
614E ARG* 3.2 29.4 - - + +
615E ILE* 3.4 38.8 - - - +
618E LYS* 4.8 15.2 - - + +
619E ALA* 4.3 13.0 - - - +
622E ALA* 4.2 10.9 - - + +
624E ILE* 4.0 20.8 - - + +
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Residues in contact with GLU 536 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532E VAL* 3.0 30.2 + - - +
533E ALA* 3.7 5.0 - - - +
535E MET* 1.3 85.4 - - + +
537E ARG* 1.3 57.6 + - - +
539E TYR* 4.0 8.2 - - + +
540E ARG* 3.4 30.5 + - + +
614E ARG* 5.8 0.7 - - - -
618E LYS* 5.3 13.1 + - - +
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Residues in contact with ARG 537 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530E TRP* 6.1 1.1 - - - +
533E ALA* 2.9 22.9 + - - +
534E GLU* 3.1 43.1 + - - +
536E GLU* 1.3 76.5 - - - +
538E ARG* 1.3 62.2 + - - +
539E TYR 3.2 1.1 - - - -
540E ARG* 3.3 29.0 + - - +
541E LEU* 2.9 34.9 + - - +
569E ASP* 5.6 4.8 + - - -
587E LEU* 5.3 7.9 - - - +
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Residues in contact with ARG 538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534E GLU* 2.9 45.0 + - - +
535E MET* 5.2 0.2 - - - +
537E ARG* 1.3 80.1 - - + +
539E TYR* 1.3 56.9 + - - +
541E LEU* 3.2 9.1 + - + +
542E MET* 2.9 40.8 + - + +
550E LEU* 3.9 6.1 - - - +
587E LEU* 3.9 31.1 - - + +
588E PRO* 2.5 44.9 + - - +
589E THR* 4.3 0.2 - - - +
590E ILE* 3.4 26.0 - - - +
622E ALA* 2.4 53.8 + - + -
623E GLY* 3.8 7.5 - - - -
624E ILE* 4.5 2.4 - - - +
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Residues in contact with TYR 539 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535E MET 2.9 19.9 + - - +
536E GLU* 4.2 10.8 - - + +
537E ARG 3.2 0.2 - - - -
538E ARG* 1.3 76.2 - - - +
540E ARG* 1.3 63.7 + - + +
542E MET* 3.8 19.8 - - + +
543E ALA* 3.8 7.8 + - - +
548E ARG* 5.0 20.6 + - - -
618E LYS* 3.3 60.9 - - + +
621E ALA* 5.1 11.0 - - + -
622E ALA* 4.7 4.7 - - + +
501F MET* 5.8 3.1 - - - +
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Residues in contact with ARG 540 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536E GLU* 3.4 21.1 + - + +
537E ARG* 3.3 29.5 + - - +
538E ARG 3.2 0.4 - - - -
539E TYR* 1.3 79.2 - - + +
541E LEU* 1.3 65.6 + - - +
542E MET 3.1 2.6 + - - -
543E ALA* 3.2 8.2 + - - +
544E ALA* 3.1 20.0 + - - +
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Residues in contact with LEU 541 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E ARG* 2.9 24.8 + - - +
538E ARG* 3.2 7.4 + - + +
540E ARG* 1.3 75.4 - - - +
542E MET* 1.3 65.0 + - + +
544E ALA* 3.4 15.1 - - + +
545E MET* 3.6 4.2 + - - +
553E PHE* 3.5 40.4 - - + -
569E ASP* 4.3 9.2 - - - +
570E PRO* 3.5 36.8 - - + -
587E LEU* 3.7 22.9 - - + -
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Residues in contact with MET 542 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538E ARG* 2.9 34.6 + - + +
539E TYR* 3.8 13.7 - - + +
540E ARG 3.1 0.2 - - - -
541E LEU* 1.3 74.4 - - + +
543E ALA* 1.3 61.3 + - - +
545E MET* 2.8 20.4 + - - -
546E GLY 2.8 9.2 + - - -
547E VAL* 3.2 32.9 + - - +
548E ARG* 3.8 12.8 - - - +
549E ASN 3.7 7.6 - - - +
550E LEU* 3.6 43.1 - - + +
553E PHE* 3.5 26.7 - - + -
587E LEU* 5.1 2.0 - - + -
621E ALA 4.1 8.5 - - - +
622E ALA* 4.7 1.6 - - + -
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Residues in contact with ALA 543 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539E TYR 3.8 7.7 + - - +
540E ARG* 3.2 10.3 + - - +
542E MET* 1.3 79.2 - - - +
544E ALA* 1.3 60.9 + - - +
545E MET 3.2 0.5 + - - -
546E GLY* 3.2 15.3 + - - +
547E VAL 4.1 1.8 + - - -
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Residues in contact with ALA 544 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540E ARG 3.1 11.7 + - - +
541E LEU* 3.4 16.8 - - + +
542E MET 3.0 0.6 - - - -
543E ALA* 1.3 76.8 - - - +
545E MET* 1.3 66.6 + - - +
570E PRO* 3.6 33.0 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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