Contacts of the helix formed by residues 548 - 561 (chain D) in PDB entry 6RKU
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 ASP 548 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531D GLN* 5.4 3.1 - - - +
534D LEU* 4.5 6.5 - - - -
535D TYR* 4.6 0.6 - - - -
546D ILE* 3.7 3.6 - - - +
547D LYS* 1.3 115.8 - - - +
549D ASP* 1.3 61.6 + - - +
550D GLU* 3.4 4.7 - - + +
551D ALA* 3.4 16.5 + - + +
552D MET* 2.9 28.9 + - - +
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Residues in contact with ASP 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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534D LEU* 4.7 6.3 - - + +
535D TYR* 5.1 10.0 + - + -
548D ASP* 1.3 73.5 - - - +
550D GLU* 1.3 58.4 + - - +
552D MET* 3.2 8.3 + - - +
553D ASP* 2.9 42.2 + - - +
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Residues in contact with GLU 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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548D ASP* 3.4 4.1 - - + +
549D ASP* 1.3 77.9 - - - +
551D ALA* 1.3 57.6 + - - +
553D ASP* 3.3 12.2 + - + +
554D GLN* 2.9 53.9 + - + +
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Residues in contact with ALA 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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546D ILE* 4.1 12.7 - - + +
547D LYS* 5.0 4.7 - - + +
548D ASP* 3.4 25.2 + - + +
549D ASP 3.2 0.2 - - - -
550D GLU* 1.3 78.6 - - - +
552D MET* 1.3 57.3 + - - +
554D GLN* 3.3 9.7 + - - +
555D TYR* 2.9 30.0 + - - +
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Residues in contact with MET 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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535D TYR* 4.2 28.9 - - + -
537D VAL* 3.9 13.2 - - + -
546D ILE* 3.5 30.8 - - + +
548D ASP 2.9 14.8 + - - +
549D ASP* 3.5 11.9 - - - +
551D ALA* 1.3 75.0 - - - +
553D ASP* 1.3 59.8 + - - +
555D TYR* 3.3 10.3 + - + +
556D GLN* 2.9 73.1 + - + +
734D LEU* 6.5 0.2 - - + -
736D ILE* 3.7 27.1 - - + -
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Residues in contact with ASP 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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549D ASP* 2.9 37.5 + - - +
550D GLU* 3.5 12.7 - - + +
551D ALA 3.2 0.2 - - - -
552D MET* 1.3 79.3 - - - +
554D GLN* 1.3 57.3 + - + +
556D GLN* 3.3 16.2 + - - +
557D ILE* 2.9 39.9 + - + +
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Residues in contact with GLN 554 (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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550D GLU* 2.9 46.2 + - + +
551D ALA* 3.8 7.3 - - - +
553D ASP* 1.3 77.2 - - + +
555D TYR* 1.3 57.4 + - - +
557D ILE* 3.3 13.7 + - + +
558D SER* 2.9 29.8 + - - -
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Residues in contact with TYR 555 (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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537D VAL* 3.6 20.6 + - + +
539D LYS* 3.2 33.0 + - - +
542D GLN* 3.6 27.0 + - - +
544D GLN* 3.9 33.8 - - + +
546D ILE* 3.7 21.8 - - + -
551D ALA 2.9 18.1 + - - +
552D MET* 3.6 13.2 - - + +
554D GLN* 1.3 77.4 - - - +
556D GLN* 1.3 59.4 + - + +
558D SER* 3.3 7.7 + - - -
559D ILE* 2.9 49.9 + - + +
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Residues in contact with GLN 556 (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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552D MET* 2.9 54.7 + - + +
553D ASP* 3.7 13.8 - - - +
555D TYR* 1.3 77.9 - - + +
557D ILE* 1.3 59.1 + - + +
559D ILE* 3.3 6.4 + - - +
560D ALA* 2.9 30.5 + - - +
730D SER* 5.1 1.0 + - - -
731D ARG* 2.4 45.9 + - + +
734D LEU* 6.2 3.6 - - + -
736D ILE* 4.9 6.1 - - - +
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Residues in contact with ILE 557 (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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553D ASP* 2.9 29.6 + - + +
554D GLN* 3.6 12.1 - - + +
556D GLN* 1.3 77.5 - - + +
558D SER* 1.3 57.7 + - - +
560D ALA* 3.2 5.5 + - - +
561D LEU* 2.9 51.0 + - + +
581D GLU 5.8 1.6 - - - +
584D VAL* 5.2 7.6 - - + -
585D SER* 5.7 7.9 - - - +
588D ASN* 4.2 22.2 - - + +
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Residues in contact with SER 558 (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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554D GLN 2.9 17.6 + - - -
555D TYR* 3.7 8.7 - - - -
557D ILE* 1.3 77.5 - - - +
559D ILE* 1.3 62.9 + - - +
561D LEU* 3.3 16.3 + - - +
562D ASP* 2.8 18.8 + - - +
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Residues in contact with ILE 559 (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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539D LYS* 3.7 27.6 - - + +
542D GLN* 4.4 12.6 - - - +
555D TYR* 2.9 59.5 + - + +
556D GLN* 3.8 6.3 - - - +
558D SER* 1.3 79.2 - - - +
560D ALA* 1.3 57.0 + - - +
562D ASP* 2.8 17.6 - - - +
709D ARG* 2.5 40.7 + - - +
730D SER* 4.2 16.4 - - - +
734D LEU* 5.2 2.5 - - + -
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Residues in contact with ALA 560 (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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556D GLN 2.9 17.4 + - - +
557D ILE* 3.7 6.5 - - - +
559D ILE* 1.3 76.6 - - - +
561D LEU* 1.3 65.4 + - + +
562D ASP 3.4 3.1 + - - -
564D ALA* 5.3 1.4 - - - +
709D ARG* 4.0 14.9 + - - +
726D LEU* 4.6 15.7 - - + +
727D VAL* 4.5 22.7 - - + +
730D SER* 3.7 25.3 - - - +
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Residues in contact with LEU 561 (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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557D ILE* 2.9 38.4 + - + +
558D SER* 3.4 8.6 - - - +
559D ILE 3.2 0.4 - - - -
560D ALA* 1.3 82.4 - - + +
562D ASP* 1.3 51.8 + - - +
563D GLY* 2.6 17.6 + - - -
564D ALA* 4.4 10.4 + - + +
580D LEU* 4.7 16.8 - - + -
581D GLU* 3.9 49.0 - - + +
584D VAL* 4.5 26.0 - - + -
726D LEU* 5.4 11.0 - - + -
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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