Contacts of the helix formed by residues 721 - 739 (chain D) in PDB entry 5ON2
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 THR 721 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651D PRO* 4.8 15.0 - - + -
653D ASP* 5.9 0.7 - - - +
715D ASP* 3.0 13.8 + - - +
719D ARG* 3.4 48.3 + - + +
720D GLN* 1.3 77.0 - - - +
722D PHE* 1.3 61.8 + - - +
723D ASN* 3.3 13.5 - - - +
724D THR* 2.7 40.7 + - + -
725D ALA 3.4 4.5 + - - -
14E A 5.7 1.6 - - - +
15E A 5.9 0.2 - - - +
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Residues in contact with PHE 722 (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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58D ILE* 3.9 28.5 - - + -
61D VAL* 3.4 24.7 - - + -
62D ILE* 4.1 21.3 - - + -
647D MET* 3.8 39.7 - - + +
650D SER 5.7 0.7 - - - +
651D PRO* 5.2 2.4 - - - +
652D ALA* 4.5 10.5 - - + -
716D ILE* 4.1 29.4 - - + -
720D GLN* 3.5 23.3 + - + -
721D THR* 1.3 70.1 - - - +
723D ASN* 1.3 61.9 + - - +
725D ALA* 3.3 5.4 + - - +
726D ILE* 3.0 34.4 + - - +
764D PHE* 3.7 22.7 - + + -
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Residues in contact with ASN 723 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D MET 3.3 15.0 + - - +
648D PHE* 3.4 35.2 - - + +
650D SER 4.3 3.5 + - - -
651D PRO* 3.5 23.0 - - - +
721D THR* 3.6 14.6 - - - -
722D PHE* 1.3 73.0 + - - +
724D THR* 1.3 61.9 + - - +
726D ILE 3.6 0.2 + - - -
727D ALA* 3.1 28.4 + - - +
13E G 3.1 32.8 + - - +
14E A 3.2 20.6 + - - -
22E A 5.2 2.9 - - - +
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Residues in contact with THR 724 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711D LYS* 3.9 12.6 - - - +
715D ASP* 2.7 21.4 + - - +
719D ARG* 4.1 1.3 + - - +
721D THR* 2.7 35.2 + - + +
723D ASN* 1.3 79.8 + - - +
725D ALA* 1.3 59.0 + - - +
727D ALA* 4.0 5.8 - - - +
728D ALA* 3.1 27.7 + - - +
14E A 3.4 44.2 - - - +
15E A 3.9 8.7 - - - +
22E A 5.5 2.7 - - + -
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Residues in contact with ALA 725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712D VAL* 3.4 22.1 - - + +
715D ASP* 3.8 24.5 - - + -
716D ILE* 4.3 18.6 - - + -
721D THR 3.4 2.6 + - - +
722D PHE* 3.3 10.9 + - - +
724D THR* 1.3 80.1 + - - +
726D ILE* 1.3 61.6 + - - +
728D ALA* 3.5 1.3 + - - -
729D ILE* 3.3 28.7 + - - +
764D PHE* 4.5 5.6 - - + -
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Residues in contact with ILE 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D LEU* 3.8 36.6 - - + +
647D MET* 3.7 15.9 - - + -
648D PHE* 3.6 47.3 - - + +
669D PHE* 5.4 3.1 - - + -
722D PHE 3.0 21.5 + - - +
725D ALA* 1.3 72.2 - - - +
727D ALA* 1.3 60.0 + - - +
729D ILE* 3.3 10.5 + - + +
730D MET* 3.0 42.2 + - + +
761D LEU* 5.5 2.0 - - + -
764D PHE* 3.9 21.3 - - + -
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Residues in contact with ALA 727 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D PHE* 4.1 8.2 - - + -
723D ASN 3.1 19.1 + - - +
724D THR 4.0 4.7 - - - +
725D ALA 3.4 0.2 - - - -
726D ILE* 1.3 77.0 - - - +
728D ALA* 1.3 55.3 + - - +
730D MET* 3.4 4.0 + - - +
731D GLU* 3.0 34.9 + - - +
22E A 3.7 28.9 - - + +
23E C 3.9 22.5 - - - +
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Residues in contact with ALA 728 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708D THR* 3.4 24.3 + - + +
711D LYS* 4.0 26.2 - - + -
712D VAL* 4.4 5.8 - - + -
724D THR 3.1 19.2 + - - +
725D ALA 3.7 6.7 - - - +
726D ILE 3.3 0.2 - - - -
727D ALA* 1.3 76.0 - - - +
729D ILE* 1.3 61.0 + - - +
731D GLU* 3.6 14.3 + - - +
732D LEU* 3.3 15.1 + - - +
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Residues in contact with ILE 729 (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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669D PHE* 4.3 8.7 - - + -
708D THR* 4.1 5.4 - - + -
712D VAL* 3.8 17.5 - - + -
725D ALA 3.3 17.9 + - - +
726D ILE* 3.3 10.2 + - - +
727D ALA 3.3 0.2 - - - -
728D ALA* 1.3 73.2 - - - +
730D MET* 1.3 60.9 + - - +
732D LEU* 3.1 3.3 + - - +
733D MET* 2.8 28.3 + - + +
757D VAL* 3.9 19.7 - - + -
760D MET* 3.8 40.2 - - + +
761D LEU* 3.5 38.8 - - + -
764D PHE* 4.9 4.3 - - + -
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Residues in contact with MET 730 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D LEU* 5.0 5.2 - - + -
648D PHE* 3.9 26.0 - - + -
665D GLY 4.6 9.0 - - - +
666D ALA* 5.2 0.7 - - - -
669D PHE* 3.6 51.8 - - + -
672D ARG* 5.7 1.1 - - - +
726D ILE* 3.0 28.9 + - + +
727D ALA 3.5 8.3 - - - +
729D ILE* 1.3 77.1 - - - +
731D GLU* 1.3 59.4 + - - +
733D MET* 3.5 1.2 + - - +
734D ASN* 3.1 32.7 + - - +
23E C 3.1 30.5 - - - +
24E A 3.9 18.2 - - - +
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Residues in contact with GLU 731 (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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727D ALA* 3.0 18.9 + - - +
728D ALA* 3.6 13.8 - - - +
729D ILE 3.2 0.2 - - - -
730D MET* 1.3 76.6 - - - +
732D LEU* 1.3 61.0 + - - +
734D ASN* 3.5 10.7 + - - +
735D LYS* 3.2 42.3 + - - +
22E A 3.4 23.7 + - - +
23E C 3.3 33.6 - - - +
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Residues in contact with LEU 732 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701D LEU* 4.8 2.0 - - + +
704D ASP* 3.6 28.5 - - + +
705D VAL* 3.7 34.5 - - + +
708D THR* 3.9 24.9 - - + +
728D ALA 3.3 10.5 + - - +
729D ILE* 3.1 9.2 + - - +
731D GLU* 1.3 75.8 - - - +
733D MET* 1.3 54.5 + - - +
735D LYS* 3.1 12.6 + - + +
736D LEU* 2.8 50.5 + - + +
753D ALA 5.4 0.4 - - - +
757D VAL* 3.7 24.9 - - + -
760D MET* 4.4 6.1 - - + -
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Residues in contact with MET 733 (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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669D PHE* 3.9 25.6 - - + -
672D ARG* 3.8 14.4 - - + +
673D VAL* 3.7 35.4 - - + +
676D LEU* 3.5 32.3 - - + -
729D ILE* 2.8 21.5 + - + +
730D MET 3.9 5.2 - - - +
732D LEU* 1.3 72.8 - - - +
734D ASN* 1.3 59.7 + - - +
736D LEU* 3.9 10.5 - - + +
737D ALA* 3.0 28.6 + - + +
754D LEU* 4.9 4.7 - - + -
757D VAL* 4.0 25.8 - - + -
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Residues in contact with ASN 734 (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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669D PHE* 6.0 0.3 - - - -
672D ARG* 4.8 12.5 + - - -
730D MET 3.1 16.0 + - - +
731D GLU* 3.6 10.6 - - - +
733D MET* 1.3 78.6 - - - +
735D LYS* 1.3 61.5 + - + +
737D ALA* 3.5 13.0 + - - +
738D LYS* 3.5 24.1 + - - +
23E C 3.9 10.1 + - - -
24E A 2.8 33.9 + - - -
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Residues in contact with LYS 735 (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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701D LEU* 4.0 19.7 - - + +
704D ASP* 3.5 38.6 - - + +
731D GLU* 3.2 30.1 + - - +
732D LEU* 3.1 12.8 + - + +
734D ASN* 1.3 78.7 - - + +
736D LEU* 1.3 61.1 + - - +
738D LYS* 3.7 5.4 + - - +
739D ALA* 3.4 22.0 + - - +
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Residues in contact with LEU 736 (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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676D LEU* 4.0 21.8 - - + +
701D LEU* 4.3 21.3 - - + -
705D VAL* 4.7 3.4 - - + -
732D LEU* 2.8 43.3 + - + +
733D MET* 3.9 14.1 - - - +
735D LYS* 1.3 71.6 - - - +
737D ALA* 1.3 64.0 + - - +
739D ALA* 3.8 10.2 + - - +
741D THR* 5.1 0.5 + - - -
750D MET* 3.5 36.0 - - + +
753D ALA* 3.5 29.2 - - + -
754D LEU* 5.1 3.4 - - + -
757D VAL* 3.9 20.6 - - + -
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Residues in contact with ALA 737 (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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672D ARG* 6.5 1.6 - - - -
676D LEU* 4.8 11.5 - - + +
733D MET* 3.0 18.6 + - + +
734D ASN* 3.7 8.3 - - - +
735D LYS 3.3 0.2 - - - -
736D LEU* 1.3 79.2 - - - +
738D LYS* 1.3 63.2 + - + +
739D ALA 3.5 5.7 + - - +
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Residues in contact with LYS 738 (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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734D ASN* 3.5 19.6 + - - +
735D LYS* 4.4 4.5 - - - +
736D LEU 3.5 0.2 - - - -
737D ALA* 1.3 77.2 - - + +
739D ALA* 1.3 64.1 + - - +
740D PRO* 3.9 1.4 - - - +
41E C 4.6 16.1 + - - +
42E C 5.4 6.5 + - - -
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Residues in contact with ALA 739 (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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701D LEU* 3.9 25.8 - - + -
735D LYS 3.4 16.6 + - - +
736D LEU* 3.9 11.3 - - - +
737D ALA 3.3 8.5 - - - +
738D LYS* 1.3 81.6 - - - +
740D PRO* 1.4 76.2 - - + +
741D THR* 3.5 9.1 + - - -
750D MET* 4.5 6.1 - - + -
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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
------------------------------------------------------------
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