Contacts of the helix formed by residues 539 - 553 (chain A) in PDB entry 6V3O
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 ALA 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A GLU* 3.2 33.4 - - + +
537A ALA* 5.6 0.9 - - - +
538A THR* 1.3 82.6 - - - +
540A PRO* 1.3 74.4 - - + +
541A SER* 3.1 1.6 - - - +
542A ASP* 2.9 25.2 + - - +
543A VAL* 4.0 4.0 + - - +
565A PHE* 5.2 1.5 - - - -
577A SER* 4.4 5.4 - - - -
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Residues in contact with PRO 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLU* 3.5 8.3 - - + +
487A GLN* 3.6 20.9 - - - +
539A ALA* 1.3 88.0 - - + +
541A SER* 1.3 61.7 + - - +
543A VAL* 3.1 14.8 + - + +
544A LEU* 3.2 19.2 + - + +
577A SER* 3.7 30.3 - - - +
580A ARG* 3.7 20.4 - - + -
581A LEU* 3.7 28.9 - - + +
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Residues in contact with SER 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A THR* 5.7 0.2 + - - -
478A TYR* 2.7 24.3 + - - -
483A GLU* 2.9 33.3 + - - -
486A ARG* 3.7 23.9 + - - -
487A GLN* 4.4 5.8 - - - +
490A LEU* 3.8 10.5 - - - +
539A ALA* 3.1 1.1 + - - -
540A PRO* 1.3 77.0 - - - +
542A ASP* 1.3 65.8 + - - +
544A LEU* 4.8 0.9 - - - -
545A ALA* 2.9 27.2 + - - +
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Residues in contact with ASP 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A SER* 3.7 31.0 + - - +
460A GLU* 5.4 1.4 - - - +
462A HIS* 4.9 1.5 + - - +
463A THR* 4.9 8.0 + - - -
486A ARG* 5.0 5.0 + - - -
534A ILE* 3.3 13.6 - - + +
537A ALA* 4.7 4.7 - - + -
538A THR* 2.8 39.4 + - - +
539A ALA* 2.9 19.1 + - - +
541A SER* 1.3 83.1 + - - +
543A VAL* 1.3 60.1 + - + +
545A ALA* 3.8 5.3 + - - +
546A VAL* 3.3 24.8 + - - +
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ILE* 3.7 15.5 - - + -
539A ALA 4.8 6.1 - - - +
540A PRO* 3.1 9.0 + - + +
542A ASP* 1.3 77.2 - - + +
544A LEU* 1.3 66.4 + - - +
546A VAL* 3.1 14.9 + - - +
547A GLU* 3.2 12.3 + - + +
561A VAL* 3.6 19.2 - - + +
563A PRO* 4.2 25.6 - - + -
581A LEU* 4.0 22.2 - - + -
587A TYR* 3.8 35.7 - - + +
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLN* 4.8 11.7 - - + -
490A LEU* 3.9 16.7 - - + +
491A LEU* 3.4 31.9 - - + -
494A LEU* 4.1 24.7 - - + +
540A PRO* 3.2 20.2 + - + +
541A SER 5.0 0.2 - - - +
543A VAL* 1.3 75.7 - - - +
545A ALA* 1.3 62.9 + - - +
547A GLU* 3.4 6.3 + - + +
548A LEU* 3.1 22.9 + - - +
581A LEU* 3.8 15.5 - - + -
584A VAL* 5.4 5.6 - - + -
586A TRP* 4.6 5.8 - - + -
587A TYR* 4.0 33.0 - - + -
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Residues in contact with ALA 545 (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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462A HIS* 4.7 13.9 - - + -
463A THR* 5.7 1.8 - - - +
466A ILE* 3.6 26.4 - - + +
478A TYR* 4.3 9.9 - - + +
490A LEU* 3.8 6.2 - - - +
541A SER 2.9 19.7 + - - +
542A ASP* 3.9 7.6 - - - +
543A VAL 3.1 0.2 - - - -
544A LEU* 1.3 77.4 - - - +
546A VAL* 1.3 57.3 + - - +
548A LEU* 3.3 3.6 + - - +
549A LEU* 3.0 32.4 + - - +
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A HIS* 3.4 31.4 - - + +
518A PHE* 3.6 27.6 - - + -
532A TYR* 3.6 25.6 - - + -
534A ILE* 3.6 13.9 - - + -
542A ASP 3.3 19.1 - - - +
543A VAL 3.1 5.4 + - - +
545A ALA* 1.3 74.0 - - - +
547A GLU* 1.3 60.2 + - - +
549A LEU* 4.3 5.2 - - - -
550A GLN* 2.8 35.2 + - - +
561A VAL* 4.6 8.3 - - + -
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Residues in contact with GLU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LEU* 4.4 4.4 - - + +
543A VAL 3.2 16.2 + - - +
544A LEU* 3.6 13.0 - - - +
545A ALA 3.3 0.2 - - - -
546A VAL* 1.3 77.0 - - - +
548A LEU* 1.3 60.4 + - - +
550A GLN* 3.4 15.9 + - - +
551A ARG* 3.3 21.1 + - - +
559A LEU 4.2 0.5 - - - +
560A PRO* 5.7 0.3 - - - +
561A VAL* 3.4 20.3 + - + +
586A TRP* 4.0 22.7 - - + -
587A TYR* 3.4 26.9 + - + -
590A ARG* 2.5 46.2 + - - +
591A ILE* 5.0 1.7 - - - +
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Residues in contact with LEU 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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466A ILE* 4.6 8.5 - - + -
469A ILE* 6.0 0.4 - - + -
489A TRP* 4.1 8.3 - - + -
490A LEU* 3.8 25.6 - - + +
493A GLU* 3.9 21.3 - - + -
494A LEU* 3.9 23.5 - - + +
500A LEU* 3.8 23.8 - - + -
544A LEU 3.1 13.4 + - - +
545A ALA 3.6 6.1 - - - +
546A VAL 3.2 0.2 - - - -
547A GLU* 1.3 75.0 - - - +
549A LEU* 1.3 63.1 + - + +
551A ARG* 3.1 19.6 + - - +
552A GLU* 2.8 47.1 + - + +
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A HIS* 4.0 46.2 - - + +
465A VAL* 3.7 29.2 - - + -
466A ILE* 4.1 16.2 - - + -
469A ILE* 5.3 8.3 - - + -
501A LEU* 6.1 3.6 - - + -
515A ILE* 6.1 0.4 - - + -
518A PHE* 3.9 20.7 - - + -
545A ALA 3.0 21.7 + - - +
546A VAL* 3.9 3.4 - - - +
548A LEU* 1.3 79.0 - - + +
550A GLN* 1.3 62.3 + - - +
552A GLU* 4.4 7.2 - - + +
553A CYS* 3.1 36.4 + - - +
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Residues in contact with GLN 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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518A PHE* 4.2 19.0 - - + -
521A LEU* 5.1 1.4 - - - +
532A TYR* 5.3 3.7 - - - +
546A VAL* 2.8 22.6 + - - +
547A GLU* 3.4 22.5 + - - +
548A LEU 3.2 0.2 - - - -
549A LEU* 1.3 74.7 - - - +
551A ARG* 1.3 60.2 + - - +
553A CYS 3.6 0.2 + - - -
554A GLY 3.4 2.6 + - - -
555A VAL* 3.1 49.1 + - + +
558A PRO* 3.4 13.5 - - + +
559A LEU* 2.5 62.9 + - - +
561A VAL* 4.2 6.1 - - - +
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Residues in contact with ARG 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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493A GLU 3.0 26.7 + - - -
494A LEU* 2.9 37.8 + - + +
496A GLY 3.9 9.9 + - - -
497A LYS* 5.7 2.4 - - - +
498A ARG 5.1 5.3 + - - -
547A GLU 3.3 9.0 + - - +
548A LEU* 3.1 14.2 + - - +
550A GLN* 1.3 79.6 - - - +
552A GLU* 1.3 79.1 + - - +
554A GLY* 2.9 20.1 + - - -
555A VAL 4.7 6.7 - - - +
556A ARG* 3.7 20.2 + - - +
558A PRO* 6.1 0.4 - - - +
586A TRP* 4.4 8.5 - - - +
590A ARG* 5.0 11.6 - - - +
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Residues in contact with GLU 552 (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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498A ARG 4.7 1.1 - - - +
499A PRO* 3.5 14.9 - - - +
500A LEU* 2.8 46.1 + - + -
501A LEU* 3.5 33.1 + - + +
519A HIS* 5.3 0.2 - - - -
548A LEU* 2.8 37.0 + - + +
549A LEU* 4.4 8.1 - - + +
551A ARG* 1.3 101.1 + - - +
553A CYS* 1.3 60.4 + - - +
554A GLY 3.3 0.4 - - - -
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Residues in contact with CYS 553 (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 LEU* 4.2 9.9 - - - -
515A ILE* 4.2 27.4 - - - -
518A PHE* 3.5 37.5 - - + +
519A HIS* 3.1 31.4 + - - +
522A ALA* 4.1 7.1 - - - +
549A LEU* 3.1 28.5 + - - +
550A GLN 4.2 1.8 - - - +
551A ARG 3.2 0.2 - - - -
552A GLU* 1.3 78.3 - - - +
554A GLY* 1.3 60.7 + - - +
555A VAL* 3.6 1.6 - - - -
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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