Contacts of the helix formed by residues 539 - 553 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483H GLU* 3.3 34.3 - - + +
537H ALA* 5.5 0.9 - - - +
538H THR* 1.3 85.8 - - - +
540H PRO* 1.3 76.6 - - + +
541H SER* 3.1 2.4 + - - +
542H ASP* 2.9 22.1 + - - +
543H VAL* 4.1 4.9 + - - +
565H PHE* 4.9 2.7 - - - -
577H SER* 3.7 4.9 - - - -
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Residues in contact with PRO 540 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483H GLU* 3.8 5.8 - - + +
487H GLN* 3.7 23.6 - - + +
539H ALA* 1.3 88.4 - - + +
541H SER* 1.3 61.9 + - - +
543H VAL* 3.0 16.6 + - + +
544H LEU* 3.1 17.2 + - + +
577H SER* 3.3 36.8 - - - +
580H ARG* 4.2 14.4 - - + -
581H LEU* 3.9 26.8 - - + +
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Residues in contact with SER 541 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478H TYR* 3.8 7.6 + - - -
483H GLU* 2.6 37.2 + - - -
486H ARG* 3.9 21.6 + - - -
487H GLN* 4.5 6.2 - - - +
490H LEU* 3.8 22.5 - - - +
539H ALA* 3.1 1.8 + - - +
540H PRO* 1.3 76.1 - - - +
542H ASP* 1.3 58.0 + - - +
544H LEU* 4.4 2.9 - - - +
545H ALA* 2.7 38.1 + - - +
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Residues in contact with ASP 542 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459H SER* 3.6 30.8 + - - +
460H GLU* 5.4 1.6 - - - +
462H HIS* 5.0 1.6 + - - +
463H THR* 4.9 6.4 + - - -
486H ARG* 5.1 5.9 + - - -
534H ILE* 3.4 17.1 - - + +
536H MET 4.5 0.2 - - - +
537H ALA* 4.5 11.7 - - + -
538H THR* 2.7 36.9 + - - -
539H ALA* 2.9 16.9 + - - +
541H SER* 1.3 82.3 + - - +
543H VAL* 1.3 63.2 + - + +
545H ALA* 3.8 6.1 + - - +
546H VAL* 3.6 13.5 + - - +
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Residues in contact with VAL 543 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534H ILE* 3.9 11.2 - - + -
537H ALA* 5.7 0.2 - - + -
539H ALA 4.5 7.0 - - - +
540H PRO* 3.0 10.2 + - + +
542H ASP* 1.3 78.4 - - + +
544H LEU* 1.3 65.7 + - - +
546H VAL* 3.1 14.0 + - - +
547H GLU* 3.1 12.7 + - + +
561H VAL* 3.5 23.7 - - + +
563H PRO* 4.3 26.7 - - + -
565H PHE* 6.2 0.9 - - + -
581H LEU* 4.0 20.0 - - + -
587H TYR* 3.8 33.4 - - + +
595H GLN* 5.7 0.2 - - - +
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Residues in contact with LEU 544 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487H GLN* 4.9 11.9 - - + -
490H LEU* 4.0 20.3 - - + +
491H LEU* 3.7 31.6 - - + -
494H LEU* 3.9 26.0 - - + +
540H PRO* 3.1 17.3 + - + +
541H SER* 4.0 3.8 - - - +
543H VAL* 1.3 76.8 - - - +
545H ALA* 1.3 62.3 + - - +
547H GLU* 3.2 7.2 + - + +
548H LEU* 3.0 23.4 + - - +
581H LEU* 3.9 14.6 - - + -
584H VAL* 5.4 4.9 - - + -
586H TRP* 4.9 2.5 - - + -
587H TYR* 4.0 31.9 - - + -
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Residues in contact with ALA 545 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462H HIS* 4.8 13.9 - - + -
463H THR* 5.8 0.7 - - - +
466H ILE* 3.6 26.1 - - + +
478H TYR* 4.1 10.5 - - + +
490H LEU* 4.0 6.4 - - - +
541H SER 2.7 23.7 + - - +
542H ASP* 3.9 7.2 - - - +
544H LEU* 1.3 72.8 - - - +
546H VAL* 1.3 62.2 + - - +
548H LEU* 3.3 3.8 + - - +
549H LEU* 3.0 28.7 + - - +
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Residues in contact with VAL 546 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462H HIS* 3.6 41.5 - - + +
518H PHE* 4.4 7.8 - - + -
532H TYR* 3.8 26.0 - - + -
534H ILE* 3.7 13.9 - - + -
542H ASP 3.6 11.4 + - - +
543H VAL 3.1 9.6 + - - +
545H ALA* 1.3 76.7 - - - +
547H GLU* 1.3 56.8 + - - +
549H LEU* 3.2 6.5 + - - +
550H GLN* 2.8 34.8 + - - +
561H VAL* 3.9 17.7 - - + -
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Residues in contact with GLU 547 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494H LEU* 4.4 4.6 - - + +
543H VAL 3.1 16.5 + - - +
544H LEU* 3.2 12.1 + - - +
546H VAL* 1.3 77.1 - - - +
548H LEU* 1.3 64.0 + - - +
550H GLN* 3.4 21.8 + - - +
551H ARG* 3.3 20.1 + - - +
558H PRO* 4.6 3.6 - - - +
561H VAL* 3.5 14.2 - - + +
586H TRP* 4.1 26.2 - - + -
587H TYR* 3.6 24.4 - - + -
590H ARG* 2.9 40.2 + - - +
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Residues in contact with LEU 548 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466H ILE* 4.5 9.2 - - + -
489H TRP* 4.0 12.3 - - + -
490H LEU* 3.9 22.7 - - + -
493H GLU* 4.1 18.2 - - + +
494H LEU* 3.9 24.3 - - + +
500H LEU* 3.9 23.1 - - + -
544H LEU 3.0 12.9 + - - +
545H ALA* 3.6 8.3 - - - +
547H GLU* 1.3 76.5 - - - +
549H LEU* 1.3 61.3 + - + +
551H ARG* 3.1 23.0 + - - +
552H GLU* 2.9 45.7 + - + +
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Residues in contact with LEU 549 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462H HIS* 4.1 33.0 - - + +
465H VAL* 3.8 28.3 - - + -
466H ILE* 4.2 22.2 - - + -
469H ILE* 4.4 11.0 - - + -
500H LEU* 6.2 0.7 - - + -
501H LEU* 6.3 2.5 - - + -
514H VAL* 5.0 0.9 - - + -
515H ILE* 6.1 0.4 - - + -
518H PHE* 3.8 27.1 - - + -
545H ALA 3.0 21.7 + - - +
546H VAL* 3.7 4.3 - - - +
548H LEU* 1.3 81.5 - - + +
550H GLN* 1.3 62.1 + - - +
552H GLU* 4.5 6.1 - - + +
553H CYS* 3.0 37.4 + - - -
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Residues in contact with GLN 550 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518H PHE* 3.7 29.8 - - + -
521H LEU* 5.0 2.6 - - + +
532H TYR* 5.2 4.0 - - - +
546H VAL* 2.8 16.8 + - + +
547H GLU* 3.4 22.1 + - - +
549H LEU* 1.3 78.3 - - - +
551H ARG* 1.3 59.5 + - - +
553H CYS 3.6 0.2 + - - -
554H GLY 3.4 2.8 + - - -
555H VAL* 3.1 40.7 + - + +
558H PRO* 3.4 15.8 - - + +
559H LEU* 2.6 59.3 + - - +
561H VAL* 3.7 10.3 - - - +
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Residues in contact with ARG 551 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503E PRO* 5.8 10.6 - - + +
493H GLU* 2.9 27.3 + - - +
494H LEU* 2.8 37.7 + - + +
496H GLY 4.0 9.1 + - - -
497H LYS 5.9 0.4 - - - -
498H ARG 4.8 7.7 + - - +
547H GLU 3.3 9.2 + - - +
548H LEU* 3.1 16.4 + - - +
550H GLN* 1.3 80.5 - - - +
552H GLU* 1.3 78.1 + - - +
554H GLY* 3.0 18.7 + - - -
555H VAL 4.7 7.2 - - - +
556H ARG* 5.1 7.1 + - - +
558H PRO* 5.8 4.0 - - + +
586H TRP* 4.2 14.9 - - + +
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Residues in contact with GLU 552 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503E PRO* 6.2 0.3 - - - +
469H ILE* 6.5 0.9 - - + -
498H ARG 4.8 0.4 - - - +
499H PRO* 3.3 14.4 - - - +
500H LEU* 2.6 46.6 + - + +
501H LEU* 3.6 30.2 + - + +
519H HIS* 5.3 0.2 - - - -
548H LEU* 2.9 35.4 + - + +
549H LEU* 4.2 8.1 - - + +
551H ARG* 1.3 105.4 + - - +
553H CYS* 1.3 61.2 + - - +
554H GLY 3.3 0.4 + - - -
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Residues in contact with CYS 553 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501H LEU* 4.4 9.4 - - - -
515H ILE* 4.3 23.6 - - - -
518H PHE* 3.5 40.6 - - + -
519H HIS* 3.1 30.8 + - + -
522H ALA* 4.2 6.2 - - - +
549H LEU* 3.0 33.0 + - - +
550H GLN 4.1 2.5 - - - +
551H ARG 3.2 0.4 - - - -
552H GLU* 1.3 78.8 - - - +
554H GLY* 1.3 60.8 + - - +
555H VAL* 3.6 0.9 - - + -
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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) + - + + + + + -
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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