Contacts of the helix formed by residues 539 - 553 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483D GLU* 3.2 35.0 - - + +
537D ALA* 5.6 0.9 - - - +
538D THR* 1.3 82.8 + - - +
540D PRO* 1.3 76.1 - - + +
541D SER* 3.1 2.4 + - - +
542D ASP* 2.8 23.6 + - - +
543D VAL* 4.1 4.5 + - - +
565D PHE* 5.1 2.2 - - - -
577D SER* 4.2 6.1 - - - -
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Residues in contact with PRO 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D GLU* 3.6 7.2 - - + +
487D GLN* 3.6 21.3 - - + +
539D ALA* 1.3 89.1 - - + +
541D SER* 1.3 60.5 + - - +
542D ASP 3.3 0.2 - - - -
543D VAL* 3.2 7.1 + - + +
544D LEU* 3.1 27.8 + - + +
577D SER* 3.6 31.6 - - - +
580D ARG* 3.7 17.7 - - + -
581D LEU* 3.7 28.2 - - + +
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Residues in contact with SER 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D TYR* 3.4 18.8 + - - -
483D GLU* 3.0 32.2 + - - -
486D ARG* 3.8 19.0 + - - -
487D GLN* 4.5 5.6 - - - +
490D LEU* 3.7 14.2 - - - +
539D ALA 3.1 0.4 + - - -
540D PRO* 1.3 73.6 - - - +
542D ASP* 1.3 69.1 + - - +
544D LEU* 4.5 1.6 - - - +
545D ALA* 2.8 34.8 + - - +
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Residues in contact with ASP 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D SER* 4.3 17.1 - - - +
460D GLU* 5.2 2.6 - - - +
462D HIS* 5.1 2.1 + - - +
463D THR* 4.8 8.7 + - - -
486D ARG* 5.0 4.2 + - - -
534D ILE* 3.1 33.6 - - + +
537D ALA* 4.5 6.5 - - + -
538D THR* 2.9 25.1 + - - +
539D ALA* 2.8 33.7 + - - +
541D SER* 1.3 83.1 + - - +
543D VAL* 1.3 62.8 + - + +
545D ALA* 3.8 5.6 + - - +
546D VAL* 3.6 12.6 + - - +
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Residues in contact with VAL 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D ILE* 3.7 12.6 - - + -
539D ALA 4.8 5.4 - - - +
540D PRO 3.2 8.1 + - - +
541D SER 3.1 0.6 - - - -
542D ASP* 1.3 76.9 - - + +
544D LEU* 1.3 67.1 + - - +
546D VAL* 3.0 15.4 + - - +
547D GLU* 3.1 11.6 + - + +
561D VAL* 3.6 17.7 - - + +
563D PRO* 4.0 31.2 - - + -
581D LEU* 4.1 21.1 - - + -
587D TYR* 3.7 36.8 - - + +
595D GLN* 6.0 0.4 - - - +
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Residues in contact with LEU 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D GLN* 4.9 10.5 - - + -
490D LEU* 4.0 25.0 - - + +
491D LEU* 4.2 35.0 - - + -
494D LEU* 4.0 19.3 - - + +
540D PRO* 3.1 20.6 + - + +
543D VAL* 1.3 77.0 - - - +
545D ALA* 1.3 61.6 + - - +
547D GLU* 3.2 5.5 + - + +
548D LEU* 3.0 23.9 + - - +
581D LEU* 4.0 13.5 - - + -
584D VAL* 5.5 4.9 - - + -
586D TRP* 4.8 3.8 - - + -
587D TYR* 4.0 33.2 - - + -
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Residues in contact with ALA 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D HIS* 4.9 8.3 - - + -
463D THR* 5.8 1.1 - - - +
466D ILE* 4.1 20.9 - - + +
478D TYR* 4.1 15.0 - - + +
490D LEU* 3.9 13.3 - - + +
541D SER 2.8 18.5 + - - +
542D ASP* 3.9 7.2 - - - +
543D VAL 3.1 0.2 - - - -
544D LEU* 1.3 77.9 - - - +
546D VAL* 1.3 57.9 + - - +
548D LEU* 3.4 3.3 + - - +
549D LEU* 3.0 33.7 + - - +
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Residues in contact with VAL 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462D HIS* 3.5 42.8 - - + +
518D PHE* 4.3 9.6 - - + -
532D TYR* 3.6 29.2 - - + -
534D ILE* 3.6 21.8 - - + -
542D ASP 3.6 2.4 + - - +
543D VAL 3.0 9.2 + - - +
545D ALA* 1.3 73.2 - - - +
547D GLU* 1.3 61.7 + - - +
549D LEU* 3.8 5.7 - - - +
550D GLN* 2.8 32.0 + - + +
561D VAL* 4.1 15.0 - - + -
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Residues in contact with GLU 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D LEU* 4.4 5.2 - - + +
543D VAL 3.1 13.7 + - - +
544D LEU* 3.2 12.1 + - - +
546D VAL* 1.3 77.8 - - - +
548D LEU* 1.3 59.0 + - - +
550D GLN* 3.2 23.1 + - - +
551D ARG* 3.3 21.7 + - - +
558D PRO* 4.5 2.1 - - - +
559D LEU 4.2 2.3 - - - +
560D PRO* 5.7 0.5 - - - +
561D VAL* 3.4 20.1 + - + +
586D TRP* 4.0 21.1 - - + -
587D TYR* 3.6 25.9 - - + -
590D ARG* 3.5 35.4 + - - +
591D ILE* 4.8 1.6 - - - +
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Residues in contact with LEU 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D ILE* 5.0 10.1 - - + -
489D TRP* 4.0 16.8 - - + -
490D LEU* 3.8 24.7 - - + +
493D GLU* 3.9 21.8 - - + -
494D LEU* 3.6 27.1 - - + +
500D LEU* 4.0 16.2 - - + -
544D LEU 3.0 12.5 + - - +
545D ALA* 3.6 8.1 - - - +
547D GLU* 1.3 76.6 - - - +
549D LEU* 1.3 61.6 + - + +
551D ARG* 3.1 16.3 + - - +
552D GLU* 2.9 46.0 + - + +
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Residues in contact with LEU 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D HIS* 4.1 23.3 - - + -
465D VAL* 3.7 29.4 - - + -
466D ILE* 3.5 31.4 - - + -
469D ILE* 4.5 9.4 - - + -
500D LEU* 6.5 0.4 - - + -
501D LEU* 5.7 1.3 - - + -
514D VAL* 4.8 1.1 - - + -
515D ILE* 5.2 7.4 - - + -
518D PHE* 3.9 28.5 - - + -
545D ALA 3.0 18.9 + - - +
546D VAL* 3.9 3.4 - - - +
548D LEU* 1.3 78.7 - - + +
550D GLN* 1.3 63.4 + - - +
552D GLU* 4.4 7.0 - - + +
553D CYS* 2.9 32.4 + - - +
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Residues in contact with GLN 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D PHE* 3.8 27.3 - - + -
521D LEU* 5.1 1.3 - - + +
532D TYR* 5.4 3.6 - - + -
546D VAL* 2.8 20.1 + - + +
547D GLU* 3.2 23.2 + - - +
548D LEU 3.2 0.2 - - - -
549D LEU* 1.3 78.2 - - - +
551D ARG* 1.3 62.5 + - - +
553D CYS 3.5 0.5 + - - -
554D GLY 3.3 3.1 + - - -
555D VAL* 3.1 37.9 + - + +
558D PRO* 3.3 16.3 - - + +
559D LEU* 2.6 60.4 + - - +
561D VAL* 4.0 8.1 - - - +
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Residues in contact with ARG 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B PRO* 6.1 6.1 - - + -
493D GLU* 2.9 25.3 + - - +
494D LEU* 2.9 45.5 + - + +
496D GLY 4.1 8.6 + - - -
497D LYS 6.1 0.4 - - - -
498D ARG 5.0 5.7 + - - -
547D GLU 3.3 9.5 + - - +
548D LEU* 3.1 12.5 + - - +
550D GLN* 1.3 79.3 - - - +
552D GLU* 1.3 81.0 + - - +
554D GLY* 2.9 20.1 + - - -
555D VAL 4.3 7.4 + - - +
558D PRO* 5.9 3.3 - - + +
586D TRP* 4.3 12.2 - - + +
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Residues in contact with GLU 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D ILE* 6.4 0.9 - - + -
498D ARG 4.9 1.0 - - - +
499D PRO* 3.4 14.1 - - - +
500D LEU* 2.7 42.9 + - + -
501D LEU* 3.7 28.1 + - + +
548D LEU* 2.9 35.9 + - + +
549D LEU* 4.1 8.1 - - + +
551D ARG* 1.3 106.2 + - - +
553D CYS* 1.3 61.4 + - - +
554D GLY 3.4 0.6 + - - -
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Residues in contact with CYS 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D LEU* 4.0 9.2 - - - -
515D ILE* 4.0 33.2 - - - -
518D PHE* 3.6 34.1 - - + -
519D HIS* 3.4 28.8 - - + -
522D ALA* 4.0 7.8 - - - +
549D LEU* 2.9 25.4 + - - +
550D GLN 3.8 1.3 - - - +
551D ARG 3.2 0.2 - - - -
552D GLU* 1.3 78.2 - - - +
554D GLY* 1.3 60.7 + - - +
555D VAL* 3.6 2.4 + - + +
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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