Contacts of the helix formed by residues 541 - 559 (chain A) in PDB entry 2ADS
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 541 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A PHE 4.3 0.2 + - - -
540A GLY* 1.3 66.3 - - - -
542A LYS* 1.3 63.3 + - + +
543A LEU* 3.0 4.6 + - - -
544A THR* 3.1 18.2 + - - +
545A GLU* 3.3 20.8 + - + +
577A ASP* 3.3 25.4 - - + +
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Residues in contact with LYS 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A PHE* 4.0 36.0 + - + +
540A GLY 3.0 1.2 - - - -
541A GLU* 1.3 75.4 - - + +
543A LEU* 1.3 65.3 + - - +
545A GLU* 3.9 10.1 - - + -
546A LYS* 2.8 45.1 + - + +
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Residues in contact with LEU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 6.0 2.2 - - + +
505A ARG* 4.1 23.1 - - - +
512A THR* 3.8 31.9 - - + +
515A ALA* 4.2 12.6 - - + +
536A TYR* 3.1 32.9 - - + +
537A PRO 3.1 28.9 - - - +
538A ALA* 4.0 4.3 - - - -
539A PHE 4.5 3.8 - - - +
540A GLY* 3.2 20.1 + - - +
541A GLU* 4.5 0.4 - - - +
542A LYS* 1.3 78.8 - - - +
544A THR* 1.3 59.3 + - - +
546A LYS* 4.4 0.7 - - - +
547A ALA* 3.1 26.7 + - - +
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Residues in contact with THR 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 4.9 5.4 - - + -
505A ARG* 2.9 29.0 + - - +
541A GLU* 3.1 10.3 + - - -
543A LEU* 1.3 73.5 - - - +
545A GLU* 1.3 68.5 + - - +
547A ALA* 4.5 2.5 - - - -
548A ILE* 3.0 41.1 + - + +
577A ASP* 4.1 18.7 - - - +
578A GLU* 4.1 10.3 - - + -
581A ALA* 3.3 31.9 - - + -
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Residues in contact with GLU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLU* 3.3 23.6 + - + +
542A LYS* 4.2 7.0 - - + +
544A THR* 1.3 77.7 - - - +
546A LYS* 1.3 57.1 + - - +
549A GLY* 2.9 22.9 + - - -
581A ALA* 3.2 31.5 - - - +
584A LYS* 5.2 10.3 + - - +
585A TYR* 2.8 38.5 + - - +
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Residues in contact with LYS 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A TYR* 4.1 19.5 - - + -
537A PRO* 6.3 1.0 - - - +
539A PHE* 5.6 8.5 - - - -
542A LYS* 2.8 36.1 + - + +
543A LEU 4.4 0.4 - - - +
545A GLU* 1.3 73.2 - - - +
547A ALA* 1.3 63.4 + - - +
549A GLY* 3.1 2.1 + - - -
550A ASP* 2.9 42.9 + - - +
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Residues in contact with ALA 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A ILE* 5.4 3.8 - - + -
517A ALA* 3.8 17.0 - - + -
536A TYR* 3.4 36.7 + - + +
543A LEU 3.1 19.6 + - - +
544A THR* 3.8 4.0 - - - +
546A LYS* 1.3 80.3 - - - +
548A ILE* 1.3 65.9 + - + +
550A ASP* 3.2 10.2 + - - +
551A VAL* 3.3 18.9 + - - +
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Residues in contact with ILE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ILE* 5.5 1.8 - - + -
503A ILE* 4.4 9.2 - - + -
544A THR* 3.0 36.8 + - + +
547A ALA* 1.3 72.0 - - + +
549A GLY* 1.3 65.9 + - - +
551A VAL* 3.1 8.3 + - + +
552A PHE* 2.9 47.2 + - + -
581A ALA* 3.6 15.3 - - + -
582A PHE* 3.5 45.1 - - + -
585A TYR* 3.4 23.3 - - + -
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Residues in contact with GLY 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A GLU 2.9 19.9 + - - -
546A LYS* 3.5 1.8 - - - -
548A ILE* 1.3 77.2 - - - +
550A ASP* 1.3 56.9 + - - +
552A PHE* 3.4 1.3 + - - -
553A SER* 2.9 32.4 + - - -
585A TYR* 4.2 17.0 - - - -
589A TYR* 3.8 6.2 + - - -
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Residues in contact with ASP 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A TYR* 3.1 37.7 + - + +
536A TYR* 3.2 19.1 + - - -
546A LYS* 2.9 30.9 + - - +
547A ALA 3.2 6.0 + - - +
549A GLY* 1.3 75.4 - - - +
551A VAL* 1.3 57.4 + - - +
553A SER* 2.8 20.2 + - - -
554A LEU* 2.9 19.8 + - - +
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A VAL* 3.8 28.3 - - + -
501A ILE* 4.3 11.2 - - + -
517A ALA* 5.9 2.0 - - + +
519A THR* 3.3 32.3 - - + +
521A ILE* 4.5 2.2 - - + +
532A TYR* 4.4 11.2 - - + -
547A ALA 3.4 15.3 - - - +
548A ILE* 3.1 10.0 + - - +
550A ASP* 1.3 76.2 - - - +
552A PHE* 1.3 65.2 + - + +
554A LEU* 3.3 7.7 + - - +
555A LEU* 2.9 43.7 + - + +
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Residues in contact with PHE 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A VAL* 6.2 1.3 - - + -
501A ILE* 5.2 1.8 - - + -
548A ILE* 2.9 38.8 + - + +
549A GLY* 4.0 1.8 - - - +
551A VAL* 1.3 85.9 - - + +
553A SER* 1.3 60.1 + - - +
555A LEU* 3.5 6.1 + - + +
556A GLU 3.0 10.7 + - - -
566A ILE* 6.6 0.2 - - + -
568A VAL* 5.5 5.2 - - + -
582A PHE* 4.2 11.7 - + - -
585A TYR* 3.6 42.6 - - + -
586A GLY* 3.7 5.4 - - - -
589A TYR* 3.4 23.7 - + + -
591A TYR* 3.0 56.1 + + + -
593A LEU* 3.9 26.5 - - + -
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Residues in contact with SER 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLY 2.9 16.1 + - - -
550A ASP* 2.8 26.3 + - - -
552A PHE* 1.3 74.9 - - - +
554A LEU* 1.3 62.7 + - - +
556A GLU* 3.2 4.8 + - - +
557A LYS* 3.0 45.9 + - - +
589A TYR* 3.5 19.2 + - - -
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Residues in contact with LEU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A THR* 6.5 0.2 - - + -
521A ILE* 3.6 23.8 - - + -
530A ARG* 4.6 18.6 - - + +
532A TYR* 4.4 20.0 - - + -
550A ASP 2.9 19.7 + - - +
551A VAL* 3.5 5.6 - - - +
553A SER* 1.3 77.6 + - - +
555A LEU* 1.3 61.9 + - - +
557A LYS* 3.2 14.6 + - + +
558A LEU* 3.0 33.4 + - + +
699A GLU* 3.5 32.1 - - - +
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Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A ALA* 4.5 4.7 - - + -
499A VAL* 4.8 4.7 - - + -
521A ILE* 3.6 38.4 - - + -
551A VAL* 2.9 38.8 + - + +
552A PHE* 3.5 15.0 - - + +
554A LEU* 1.3 75.5 - - - +
556A GLU* 1.3 61.7 + - - +
558A LEU* 3.3 15.3 + - - +
559A GLY 3.4 0.2 + - - -
560A PHE* 3.3 35.1 + - + +
566A ILE* 3.7 36.8 - - + -
591A TYR* 3.9 12.1 - - + +
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Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A PHE 3.0 9.0 + - - +
553A SER* 3.4 10.5 - - - +
555A LEU* 1.3 75.7 - - - +
557A LYS* 1.3 66.1 + - - +
559A GLY* 3.2 11.3 + - - -
560A PHE 3.9 5.2 - - - -
561A LYS* 3.6 32.6 - - + +
562A LYS* 5.5 3.3 + - - +
589A TYR* 3.5 27.2 - - + +
591A TYR* 3.1 16.6 + - + +
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Residues in contact with LYS 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A SER* 3.0 37.9 + - - +
554A LEU* 3.6 15.5 - - + +
556A GLU* 1.3 77.6 - - + +
558A LEU* 1.3 68.2 + - - +
559A GLY* 3.3 1.2 + - - -
561A LYS* 5.4 1.9 - - - -
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Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ILE* 3.9 26.0 - - + -
529A VAL* 3.7 27.6 - - + -
530A ARG* 4.4 20.9 - - + +
554A LEU* 3.0 30.8 + - + +
555A LEU* 3.4 7.2 - - - +
556A GLU 3.2 0.2 - - - -
557A LYS* 1.3 77.2 - - - +
559A GLY* 1.3 55.5 + - - +
560A PHE* 3.8 26.9 - - + -
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Residues in contact with GLY 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A GLU 3.2 9.7 + - - -
557A LYS 4.3 0.7 - - - -
558A LEU* 1.3 78.5 - - - +
560A PHE* 1.3 58.7 + - - +
561A LYS* 2.8 34.3 + - - +
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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
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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