Contacts of the helix formed by residues 716 - 731 (chain K) in PDB entry 1SOJ
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 PRO 716 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714K LYS 3.2 11.2 - - - +
715K ILE* 1.3 81.1 - - - +
717K THR* 1.3 68.0 + - - +
718K GLN* 3.1 2.0 + - + +
719K GLN* 3.3 35.8 + - - +
720K PHE* 3.3 17.7 + - - +
870K PHE* 3.8 12.3 - - - +
872K LEU* 3.7 27.4 - - + -
873K HIS* 4.4 4.5 - - + +
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Residues in contact with THR 717 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701K TYR* 4.0 38.2 + - + +
710K LEU* 4.8 7.1 - - - +
715K ILE 3.2 7.3 + - - -
716K PRO* 1.3 71.2 - - - +
718K GLN* 1.3 63.8 + - - +
720K PHE* 3.5 6.3 - - - +
721K MET* 3.1 30.6 + - + +
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Residues in contact with GLN 718 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716K PRO* 3.1 1.2 + - + -
717K THR* 1.3 77.3 - - - +
719K GLN* 1.3 69.6 + - - +
721K MET* 3.2 4.1 + - - +
722K ASN* 2.7 64.9 + - - +
725K ARG* 5.1 7.7 - - - +
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Residues in contact with GLN 719 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716K PRO* 3.3 32.7 + - - +
718K GLN* 1.3 86.7 - - - +
720K PHE* 1.3 65.1 + - - +
722K ASN* 2.9 3.8 + - - +
723K TYR* 2.9 25.8 + - - +
866K PRO 4.2 2.8 - - - +
867K GLU* 3.2 35.4 - - - +
868K TYR 3.7 5.1 - - - +
869K ASN 3.8 8.7 - - - +
870K PHE* 3.7 19.5 - - + -
872K LEU* 4.0 14.4 - - - +
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Residues in contact with PHE 720 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697K SER 4.9 0.2 - - - -
700K MET* 3.8 10.3 - - + -
701K TYR* 3.7 36.1 - + + -
704K PHE* 3.4 48.7 - + + -
710K LEU* 4.3 4.5 - - + -
715K ILE* 3.8 21.5 - - + -
716K PRO 3.3 12.4 + - - +
717K THR* 3.5 10.5 - - - +
719K GLN* 1.3 80.7 - - - +
721K MET* 1.3 78.0 - - + +
723K TYR* 3.3 0.9 + - - +
724K PHE* 3.1 58.2 + + + -
870K PHE* 3.5 16.6 - + - +
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Residues in contact with MET 721 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697K SER* 4.1 20.6 - - - +
698K GLN* 3.5 28.7 - - - +
701K TYR* 3.8 32.5 - - + -
717K THR* 3.1 28.9 + - + +
718K GLN* 3.8 4.7 - - - +
720K PHE* 1.3 91.6 - - + +
722K ASN* 1.3 58.2 + - - +
724K PHE* 4.7 1.6 - - - +
725K ARG* 2.9 74.9 + - - +
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Residues in contact with ASN 722 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718K GLN* 2.7 63.7 + - - +
719K GLN* 2.9 6.8 + - - +
721K MET* 1.3 77.2 - - - +
723K TYR* 1.3 62.0 + - - +
725K ARG* 3.9 7.3 + - - +
726K ALA* 3.2 22.2 + - - +
867K GLU* 3.1 33.3 + - + +
868K TYR* 3.5 14.1 - - + -
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Residues in contact with TYR 723 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719K GLN 2.9 13.8 + - - +
720K PHE 3.8 2.2 - - - +
722K ASN* 1.3 74.2 - - - +
724K PHE* 1.3 79.4 + + - +
726K ALA* 2.9 5.9 + - - +
727K LEU* 2.6 51.1 + - + +
820K MET* 3.2 26.7 - - + +
858K ALA 2.9 21.4 + - - -
861K LEU* 4.0 14.4 - - + -
862K TYR* 3.5 45.0 - + + +
868K TYR* 3.6 29.8 - + + +
870K PHE* 3.6 22.4 - + + -
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Residues in contact with PHE 724 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696K LEU* 5.2 3.1 - - + +
697K SER* 4.0 20.9 - - - -
700K MET* 4.1 27.4 - - + -
720K PHE* 3.1 62.4 + + + +
721K MET* 4.6 1.6 - - - +
723K TYR* 1.3 92.8 - + - +
725K ARG* 1.3 65.0 + - - +
727K LEU* 3.6 24.0 - - + +
728K GLU* 3.0 28.4 + - - +
816K VAL* 4.2 19.3 - - + -
819K ALA* 4.2 6.7 - - + -
870K PHE* 3.6 28.9 - + - -
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Residues in contact with ARG 725 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694K ARG* 2.9 54.7 - - - +
697K SER* 3.9 14.3 + - - +
698K GLN* 4.5 4.6 - - - +
718K GLN* 5.1 5.5 - - - +
721K MET* 2.9 75.2 + - + +
722K ASN* 3.9 11.0 + - - +
724K PHE* 1.3 78.0 - - - +
726K ALA* 1.3 59.8 + - - +
728K GLU* 3.5 14.3 - - - +
729K ASN* 2.9 28.3 + - - +
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Residues in contact with ALA 726 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722K ASN 3.2 12.0 + - - +
723K TYR 2.9 8.7 + - - +
725K ARG* 1.3 78.1 - - - +
727K LEU* 1.3 67.8 + - - +
728K GLU 3.1 0.2 - - - -
729K ASN* 3.1 22.5 + - - +
730K GLY* 3.4 6.4 + - - -
823K TYR* 4.8 0.5 + - - -
861K LEU* 4.1 17.6 - - + +
868K TYR* 3.7 25.6 - - + +
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Residues in contact with LEU 727 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696K LEU* 4.9 3.1 - - + -
723K TYR* 2.6 45.0 + - + +
724K PHE* 3.6 36.3 - - + +
726K ALA* 1.3 72.7 - - - +
728K GLU* 1.3 64.9 + - - +
730K GLY* 2.8 12.5 + - - -
731K TYR* 3.7 5.4 - - + -
819K ALA* 3.8 16.6 - - + +
820K MET* 3.7 20.6 - - + -
823K TYR* 3.2 39.9 - - + -
858K ALA* 3.9 13.5 - - + -
861K LEU* 3.9 10.5 - - + +
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Residues in contact with GLU 728 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693K GLY 3.2 14.8 - - - +
694K ARG* 2.7 37.4 - - - +
695K ILE* 3.2 0.7 + - - +
696K LEU* 2.9 28.3 + - + +
697K SER* 2.8 29.4 + - - +
724K PHE 3.0 19.1 + - - +
725K ARG* 3.5 18.3 - - - +
727K LEU* 1.3 77.1 - - - +
729K ASN* 1.3 60.2 + - - +
731K TYR* 2.9 21.5 + - - +
739K ARG* 2.7 32.8 + - - +
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Residues in contact with ASN 729 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693K GLY 4.9 3.6 - - - +
725K ARG* 2.9 25.2 + - - +
726K ALA* 3.1 12.6 + - - +
728K GLU* 1.3 77.3 - - - +
730K GLY* 1.3 61.2 + - - +
731K TYR 3.2 6.5 + - - +
739K ARG* 3.1 14.5 + - - +
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Residues in contact with GLY 730 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726K ALA 3.4 3.8 + - - -
727K LEU 2.8 6.3 + - - -
729K ASN* 1.3 79.1 - - - +
731K TYR* 1.3 59.5 + - - +
732K ARG* 3.3 3.5 + - - +
823K TYR* 3.0 35.9 - - - -
824K ASP* 3.3 28.7 - - - +
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Residues in contact with TYR 731 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696K LEU* 4.1 8.5 - - + -
727K LEU* 3.7 16.6 - - + -
728K GLU* 2.9 15.4 + - - +
729K ASN 3.8 3.7 - - - +
730K GLY* 1.3 76.8 - - - +
732K ARG* 1.3 64.4 + - - +
737K HIS 4.0 3.8 - - - -
738K ASN* 3.5 21.3 - - - -
739K ARG* 3.4 44.0 + - + +
742K ALA* 3.5 18.1 - - + +
819K ALA 2.9 29.5 + - - -
820K MET 3.4 2.4 - - - -
821K HIS 3.7 0.2 + - - -
822K ASP* 3.1 52.6 + - + -
823K TYR* 3.2 18.5 + + + -
824K ASP 4.4 2.5 - - - +
825K HIS 5.4 0.4 - - - +
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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
------------------------------------------------------------
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