Contacts of the helix formed by residues 718 - 732 (chain B) 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 SER 718 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611B TYR* 4.2 10.2 + - - -
702B GLU 6.0 0.7 - - - -
716B VAL* 3.3 11.7 - - - +
717B ALA* 1.3 80.5 - - - +
719B PHE* 1.3 60.1 + - - +
720B GLU* 3.2 29.6 + - - +
721B GLN* 3.6 22.5 + - - +
722B ALA* 2.9 24.8 + - - +
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Residues in contact with PHE 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B LEU* 5.1 12.3 - - + -
580B LEU* 4.4 13.5 - - + -
583B LEU* 4.3 21.3 - - + -
584B VAL* 4.2 23.3 - - + -
587B TYR* 4.6 29.2 - + + -
611B TYR* 3.9 9.8 + - - +
697B LEU* 5.1 8.1 - - + -
700B LEU* 5.9 0.2 - - + -
702B GLU* 3.2 43.2 + - + +
717B ALA 4.4 0.2 - - - -
718B SER* 1.3 72.1 + - - +
720B GLU* 1.3 60.7 + - - +
722B ALA* 3.3 10.5 + - + +
723B LEU* 2.9 43.7 + - + +
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Residues in contact with GLU 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B TYR* 3.2 32.0 + - + +
591B GLN* 5.2 2.6 + - - +
607B LYS* 4.5 23.1 + - - -
610B ILE* 5.5 4.6 - - - +
611B TYR* 4.9 8.2 + - - +
718B SER* 3.2 16.0 + - - +
719B PHE* 1.3 81.7 - - - +
721B GLN* 1.3 58.8 + - + +
723B LEU* 3.3 8.6 + - - +
724B ASP* 2.9 40.6 + - - +
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Residues in contact with GLN 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716B VAL* 4.5 23.3 - - + +
717B ALA* 5.0 1.4 + - - +
718B SER* 3.2 26.4 + - - +
720B GLU* 1.3 81.5 - - + +
722B ALA* 1.3 59.3 + - - +
724B ASP* 3.3 9.0 + - + +
725B TRP* 2.9 29.0 + - + +
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Residues in contact with ALA 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B LEU* 6.5 0.9 - - + -
707B ILE* 5.0 15.3 - - + -
714B GLN 5.9 1.6 - - - +
716B VAL* 3.7 19.4 - - + +
718B SER 2.9 14.0 + - - +
719B PHE* 3.6 14.1 - - + +
721B GLN* 1.3 76.8 - - - +
723B LEU* 1.3 56.9 + - - +
725B TRP* 3.3 10.7 + - + +
726B LEU* 2.9 36.3 + - + +
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Residues in contact with LEU 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B VAL* 3.7 36.3 - - + -
587B TYR* 4.4 23.1 - - + -
588B ASN* 4.6 9.0 - - - +
719B PHE* 2.9 26.2 + - + +
720B GLU* 3.6 7.2 - - - +
721B GLN 3.3 0.2 - - - -
722B ALA* 1.3 77.7 - - - +
724B ASP* 1.3 66.6 + - - +
726B LEU* 3.3 11.1 + - + +
727B VAL* 2.9 49.4 + - + +
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Residues in contact with ASP 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B GLU* 2.9 29.0 + - - +
721B GLN* 3.7 8.9 - - + +
723B LEU* 1.3 85.6 - - - +
725B TRP* 1.3 57.3 + - - +
727B VAL* 3.3 7.9 + - - +
728B LYS* 2.9 29.3 + - - +
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Residues in contact with TRP 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B ILE* 4.2 18.2 - - + -
709B ARG 5.6 2.0 - - - -
712B ARG* 3.6 40.8 - - + -
713B ARG 4.3 0.4 - - - -
714B GLN* 3.6 44.6 + - + -
716B VAL* 6.1 5.2 - - + -
721B GLN* 2.9 17.6 + - + +
722B ALA* 3.3 7.8 + - + +
724B ASP* 1.3 76.0 - - - +
726B LEU* 1.3 86.2 + - + +
728B LYS* 3.3 10.6 + - + +
729B GLU* 2.9 63.0 + - + +
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Residues in contact with LEU 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B ALA* 4.6 17.7 - - + +
561B LEU* 5.4 8.7 - - + -
564B ALA* 5.3 2.5 - - + -
707B ILE* 3.8 39.7 - - + -
709B ARG* 4.3 29.9 + - + +
722B ALA* 2.9 25.4 + - + +
723B LEU* 3.3 9.2 + - + +
725B TRP* 1.3 100.1 - - + +
727B VAL* 1.3 56.9 + - + +
729B GLU* 3.3 7.1 + - + +
730B SER* 2.9 29.1 + - - -
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Residues in contact with VAL 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B ALA* 4.5 13.7 - - + -
723B LEU* 2.9 39.4 + - + +
724B ASP* 3.3 8.5 + - - +
726B LEU* 1.3 75.0 - - + +
728B LYS* 1.3 59.3 + - - +
730B SER* 2.6 22.6 + - - +
731B ARG* 2.9 52.4 + - + +
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Residues in contact with LYS 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724B ASP 2.9 17.4 + - - +
725B TRP* 3.6 13.0 - - + +
726B LEU 3.2 0.2 - - - -
727B VAL* 1.3 78.1 - - - +
729B GLU* 1.3 60.0 + - - +
731B ARG* 3.2 5.4 + - + -
732B ARG* 2.9 43.0 + - + +
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Residues in contact with GLU 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B ARG* 4.0 21.9 + - - +
712B ARG* 3.4 38.0 + - - -
725B TRP* 2.9 58.3 + - + +
726B LEU* 3.6 7.9 - - + +
728B LYS* 1.3 78.0 - - - +
730B SER* 1.3 62.3 + - - +
732B ARG* 2.9 58.0 + - - +
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Residues in contact with SER 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B LYS* 5.0 1.6 - - - -
556B GLN 5.1 0.9 + - - -
559B ILE* 4.1 12.7 - - - +
560B ALA* 3.7 30.7 - - - +
709B ARG* 3.5 19.6 + - - +
726B LEU 2.9 12.5 + - - -
727B VAL* 2.6 28.4 + - - +
729B GLU* 1.3 79.4 - - - +
731B ARG* 1.3 63.9 + - - +
732B ARG 3.3 1.4 + - - -
733B GLY 4.5 4.0 + - - -
734B LEU* 3.8 12.1 + - - +
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Residues in contact with ARG 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B GLN* 2.4 49.2 + - + +
727B VAL* 2.9 41.0 + - - +
728B LYS* 3.6 6.3 - - + +
730B SER* 1.3 79.2 + - - +
732B ARG* 1.3 67.8 + - - +
733B GLY 3.4 2.1 + - - -
734B LEU* 3.6 32.4 + - + +
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Residues in contact with ARG 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B ARG* 5.4 3.6 - - - +
712B ARG* 4.8 17.7 - - - +
728B LYS* 2.9 36.1 + - + +
729B GLU* 2.9 50.2 + - - +
730B SER 3.3 1.6 - - - -
731B ARG* 1.3 79.1 - - - +
733B GLY* 1.3 59.6 + - - +
734B LEU 4.0 1.4 + - - +
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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