Contacts of the helix formed by residues 530 - 542 (chain D) in PDB entry 6PUO
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 CYS 530 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D LEU* 4.0 13.5 - - - -
527D ASP* 3.4 22.5 + - - +
528D PRO 4.5 1.7 - - - +
529D SER* 1.3 83.3 + - - +
531D LEU* 1.3 63.3 + - - +
532D PHE* 3.6 11.7 - - - +
533D HIS* 3.2 38.2 + - - +
534D SER* 3.7 9.2 + - - -
631D VAL 4.5 12.8 - - - +
632D GLN* 4.8 7.9 - - - +
666D GLU* 6.0 1.1 - - - -
675D MET* 6.2 2.5 - - + -
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Residues in contact with LEU 531 (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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529D SER 3.9 0.8 + - - -
530D CYS* 1.3 72.5 - - - +
532D PHE* 1.3 65.4 + - - +
534D SER* 2.4 33.8 + - - +
535D LYS* 3.0 25.1 + - + +
631D VAL 5.7 0.2 + - - -
662D LEU* 4.1 31.6 - - + +
665D GLU* 3.4 41.3 - - + +
666D GLU* 4.1 23.4 + - + +
675D MET* 6.0 4.2 - - + +
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Residues in contact with PHE 532 (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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523D TYR* 4.3 17.0 - + - -
526D LEU* 3.6 19.3 - - + -
530D CYS* 3.3 10.2 - - - -
531D LEU* 1.3 80.2 - - - +
533D HIS* 1.3 56.4 + - - +
535D LYS* 3.4 10.4 + - + +
536D LEU* 2.9 42.3 + - + +
561D VAL* 4.3 12.3 - - + -
564D VAL* 3.6 35.7 - - + -
565D LEU* 4.7 9.9 - - + -
568D LEU* 4.4 23.8 - - + -
627D ILE* 6.3 0.9 - - + -
631D VAL* 3.9 43.4 + - + +
662D LEU* 5.1 7.9 - - + +
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Residues in contact with HIS 533 (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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524D GLU 5.9 1.2 + - - -
526D LEU* 4.6 23.8 + - + -
527D ASP 4.0 6.3 - - - +
528D PRO* 3.5 35.0 + - + +
530D CYS* 3.2 26.4 - - - +
531D LEU 3.2 0.8 - - - -
532D PHE* 1.3 77.2 - - - +
534D SER* 1.3 57.8 + - - +
536D LEU* 3.3 10.7 + - + +
537D GLN* 2.9 60.0 + - + +
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Residues in contact with SER 534 (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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530D CYS 3.7 5.6 + - - -
531D LEU* 2.4 39.0 + - - +
533D HIS* 1.3 78.0 + - - +
535D LYS* 1.3 60.1 + - - +
537D GLN* 3.3 8.6 + - - +
538D LYS* 3.0 29.2 + - - +
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Residues in contact with LYS 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531D LEU* 3.0 37.1 + - + +
532D PHE* 3.9 11.4 - - + +
534D SER* 1.3 79.0 + - - +
536D LEU* 1.3 58.4 + - - +
538D LYS* 3.3 12.9 + - - +
539D VAL* 3.0 30.3 + - - +
564D VAL* 4.2 24.4 - - + +
567D GLU* 4.2 20.2 + - - -
568D LEU* 4.6 15.3 - - - -
662D LEU* 4.8 6.1 - - + -
665D GLU* 3.4 28.8 + - - +
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Residues in contact with LEU 536 (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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523D TYR* 4.5 14.6 - - + +
526D LEU* 5.1 7.0 - - + -
532D PHE* 2.9 34.0 + - + +
533D HIS* 3.7 12.6 - - + +
535D LYS* 1.3 75.4 - - - +
537D GLN* 1.3 66.2 + - - +
539D VAL* 3.3 17.2 - - + +
540D LEU* 2.9 32.7 + - + +
556D LEU* 4.2 28.9 - - + -
560D HIS* 4.4 13.7 - - + +
561D VAL* 4.5 9.4 - - + +
564D VAL* 4.3 17.2 - - + +
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Residues in contact with GLN 537 (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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533D HIS* 2.9 50.8 + - + +
534D SER* 3.3 8.3 + - - +
536D LEU* 1.3 83.5 - - - +
538D LYS* 1.3 57.0 + - - +
540D LEU* 3.7 19.2 - - - +
541D VAL* 3.0 32.3 + - - +
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Residues in contact with LYS 538 (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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534D SER 3.0 13.8 + - - +
535D LYS* 3.6 14.7 - - - +
537D GLN* 1.3 76.0 - - - +
539D VAL* 1.3 59.1 + - - +
541D VAL* 3.3 9.4 - - + +
542D GLU* 2.9 45.6 + - + +
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Residues in contact with VAL 539 (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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535D LYS 3.0 16.2 + - - +
536D LEU* 3.3 31.4 - - + +
538D LYS* 1.3 77.4 - - - +
540D LEU* 1.3 60.6 + - - +
542D GLU* 4.0 7.0 - - + -
543D ASP* 3.4 20.3 + - - +
560D HIS* 4.4 13.1 + - + +
563D GLN* 3.5 41.3 - - + +
564D VAL* 4.3 15.9 - - + -
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Residues in contact with LEU 540 (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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536D LEU* 2.9 21.0 + - + +
537D GLN* 3.7 24.2 - - - +
539D VAL* 1.3 79.0 - - + +
541D VAL* 1.3 61.4 + - - +
542D GLU 3.5 0.3 + - - -
543D ASP* 3.5 14.8 + - + +
546D ARG* 5.1 8.9 - - + +
547D PRO* 5.5 0.9 - - - +
554D PRO* 4.3 21.7 - - + +
555D ARG 3.5 26.2 - - - +
556D LEU* 4.3 28.0 - - + +
560D HIS* 3.6 26.7 - - + +
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Residues in contact with VAL 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D GLN 3.0 17.8 + - - +
538D LYS* 3.3 19.3 - - + +
540D LEU* 1.3 77.6 - - - +
542D GLU* 1.3 72.7 + - - +
543D ASP 3.4 6.8 + - - +
547D PRO* 4.8 10.4 - - + +
554D PRO* 6.0 4.0 - - + -
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Residues in contact with GLU 542 (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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538D LYS* 2.9 31.6 + - + +
539D VAL* 4.0 8.7 - - + +
540D LEU 3.3 0.6 - - - -
541D VAL* 1.3 89.7 - - - +
543D ASP* 1.3 63.1 + - - +
544D PRO* 3.6 5.5 - - - +
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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