Contacts of the helix formed by residues 707 - 725 (chain O) in PDB entry 5A31
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 LYS 707 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701O PHE 4.8 0.2 + - - -
705O ASP* 3.3 19.0 - - - +
706O CYS* 1.3 71.3 - - - +
708O GLU* 1.3 65.3 + - + +
709O ARG 3.1 0.9 - - - -
710O ILE* 3.0 20.7 - - + +
711O ARG* 2.8 30.3 + - - +
740O LEU* 4.2 21.8 - - + +
743O GLU* 5.6 5.6 - - + -
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Residues in contact with GLU 708 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521O ASN 5.5 3.1 - - - +
522O ASP 4.4 16.2 - - - +
523O GLY* 4.8 8.4 - - - +
525O TYR* 5.3 4.2 + - - -
706O CYS 2.5 11.4 + - - +
707O LYS* 1.3 76.3 - - + +
709O ARG* 1.3 58.3 + - - +
711O ARG* 3.6 32.6 + - + +
712O ASP* 4.1 5.2 + - - +
740O LEU 5.4 1.6 - - - +
743O GLU* 3.3 30.6 - - + +
744O LEU* 3.3 32.6 + - - +
754O HIS* 5.9 0.2 - - - -
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Residues in contact with ARG 709 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658O LEU* 4.0 18.6 - - - +
662O ARG* 3.3 36.6 - - - +
665O PHE* 5.5 9.2 - - + -
701O PHE* 3.7 36.9 - - + -
706O CYS* 3.5 35.3 + - + -
707O LYS 3.1 0.6 - - - -
708O GLU* 1.3 77.6 - - - +
710O ILE* 1.3 66.4 + - - +
712O ASP* 3.4 16.9 + - - +
713O VAL 3.6 3.1 + - - -
754O HIS* 3.0 51.2 + - + +
755O LEU* 5.3 3.2 - - - +
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Residues in contact with ILE 710 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698O LYS* 3.7 41.1 - - + +
701O PHE* 3.9 24.3 - - + +
702O ALA* 4.9 7.2 - - + +
707O LYS* 3.0 41.2 - - + +
709O ARG* 1.3 74.3 - - - +
711O ARG* 1.3 68.2 + - - +
712O ASP 2.9 2.0 - - - -
713O VAL* 2.7 28.4 + - + +
714O VAL* 2.9 21.5 + - + +
740O LEU* 3.8 12.3 - - + -
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Residues in contact with ARG 711 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707O LYS 2.8 21.0 + - - +
708O GLU* 3.6 23.8 + - - +
710O ILE* 1.3 72.9 - - - +
712O ASP* 1.3 60.2 + - - +
714O VAL* 3.0 5.0 + - - +
715O TYR* 2.8 32.1 + - - +
737O PHE* 3.6 29.5 - - + -
740O LEU* 3.6 33.0 + - + +
741O HIS* 3.5 28.5 + - - -
743O GLU 3.8 19.2 + - - -
744O LEU 4.4 3.3 + - - -
745O PRO* 3.8 27.7 - - - +
746O SER 4.7 0.4 - - - +
749O VAL* 4.2 16.0 + - - +
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Residues in contact with ASP 712 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665O PHE* 3.8 12.8 - - + -
708O GLU 4.5 5.2 - - - +
709O ARG* 3.4 12.9 + - - +
710O ILE 2.7 3.6 + - - -
711O ARG* 1.3 84.3 + - + +
713O VAL* 1.3 64.2 + - - +
715O TYR* 3.2 9.6 + - - +
716O PHE* 3.0 21.5 + - - +
750O PRO 4.2 3.3 - - - +
751O LEU* 3.0 54.7 + - - +
754O HIS* 5.7 5.1 + - + +
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Residues in contact with VAL 713 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665O PHE* 3.6 36.3 - - + -
694O LEU* 3.4 40.5 - - + +
697O ALA* 4.3 9.2 - - + -
698O LYS* 4.1 21.1 - - + -
701O PHE* 4.5 7.6 - - + -
709O ARG 3.6 1.6 + - - -
710O ILE* 2.7 38.1 + - + +
712O ASP* 1.3 74.4 - - - +
714O VAL* 1.3 67.5 + - + +
716O PHE* 3.3 1.9 + - - +
717O GLN* 2.9 17.6 + - - +
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Residues in contact with VAL 714 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698O LYS* 4.2 17.3 - - - -
710O ILE* 2.9 33.8 + - + +
711O ARG* 3.3 7.4 - - - +
713O VAL* 1.3 79.4 - - + +
715O TYR* 1.3 57.0 + - - +
717O GLN* 2.8 30.4 + - - +
718O ALA* 2.9 12.3 + - - +
733O CYS* 3.2 32.3 - - + +
736O LEU* 3.9 11.4 - - + -
737O PHE* 3.8 18.4 - - + +
740O LEU* 4.2 12.1 - - + -
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Residues in contact with TYR 715 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711O ARG 2.8 12.7 + - - +
712O ASP* 3.3 16.8 - - - +
714O VAL* 1.3 77.4 - - - +
716O PHE* 1.3 71.7 + + + +
718O ALA* 3.1 18.1 + - + +
719O ARG* 2.8 55.7 + - + +
737O PHE* 3.8 38.3 - + + -
751O LEU* 4.5 20.2 - - + -
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Residues in contact with PHE 716 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665O PHE* 4.2 13.0 - + + -
668O ALA 4.9 0.7 - - - -
669O LYS* 4.1 33.2 - - + -
672O VAL* 4.1 20.2 - - + -
694O LEU* 3.3 29.4 - - + -
712O ASP* 3.0 13.5 + - - +
713O VAL 3.5 8.7 - - - +
715O TYR* 1.3 86.6 - + + +
717O GLN* 1.3 62.8 + - - +
719O ARG* 3.3 8.2 + - + +
720O LEU* 3.1 61.3 + - + +
751O LEU* 4.7 15.0 - - + -
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Residues in contact with GLN 717 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691O ILE* 3.9 19.6 - - + +
694O LEU* 3.5 26.6 - - + +
695O ASN* 3.5 34.0 + - - +
698O LYS* 3.8 26.2 - - - +
713O VAL 2.9 8.8 + - - +
714O VAL* 2.8 24.4 + - - +
716O PHE* 1.3 77.3 - - - +
718O ALA* 1.3 60.2 + - - +
720O LEU* 3.1 8.7 + - - +
721O TYR* 3.0 41.5 + - + -
733O CYS* 4.9 8.8 - - - -
736O LEU* 6.1 0.6 - - - +
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Residues in contact with ALA 718 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714O VAL 2.9 10.4 + - - +
715O TYR* 3.4 13.7 - - + +
717O GLN* 1.3 76.1 - - - +
719O ARG* 1.3 61.8 + - + +
721O TYR* 3.3 7.4 + - - +
722O HIS* 3.1 20.4 + - - +
730O ARG* 4.2 11.4 + - + +
733O CYS* 4.1 21.7 - - + +
734O ALA* 4.4 18.4 - - + +
737O PHE* 5.9 0.9 - - + -
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Residues in contact with ARG 719 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715O TYR* 2.8 52.7 + - + +
716O PHE* 3.7 12.3 - - + +
717O GLN 3.3 0.2 - - - -
718O ALA* 1.3 76.2 - - + +
720O LEU* 1.3 69.6 + - + +
722O HIS* 3.3 16.2 + - - +
723O THR* 3.4 11.8 + - - -
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Residues in contact with LEU 720 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668O ALA* 6.2 0.2 - - + -
672O VAL* 3.7 26.9 - - + -
687O LEU* 4.8 15.3 - - + +
690O ALA* 4.8 1.3 - - + -
691O ILE* 3.9 34.5 - - + +
694O LEU* 4.8 5.4 - - + -
716O PHE* 3.1 65.5 + - + +
717O GLN* 3.1 7.4 + - - +
719O ARG* 1.3 79.7 - - + +
721O TYR* 1.3 59.4 + - - +
723O THR* 3.1 12.0 + - - +
724O LEU* 2.9 28.7 + - + +
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Residues in contact with TYR 721 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691O ILE* 3.2 42.0 - - + +
695O ASN* 4.7 7.3 + - - -
717O GLN* 3.0 28.7 + - + -
718O ALA 3.6 6.7 - - - +
719O ARG 3.2 0.2 - - - -
720O LEU* 1.3 78.3 - - - +
722O HIS* 1.3 55.2 + - - +
724O LEU* 3.4 18.3 + - + -
725O GLY* 2.8 24.4 + - - -
726O LYS* 3.3 20.9 + - + +
729O GLU* 3.2 37.4 + - + -
730O ARG* 4.0 14.8 - - + -
733O CYS* 3.4 36.1 - - + -
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Residues in contact with HIS 722 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718O ALA 3.1 12.0 + - - +
719O ARG* 3.4 13.9 - - - +
720O LEU 3.2 0.2 - - - -
721O TYR* 1.3 76.7 - - - +
723O THR* 1.3 61.6 + - - +
725O GLY* 3.4 12.5 + - - -
727O THR* 5.6 2.8 - - + +
730O ARG* 3.5 48.1 + - - +
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Residues in contact with THR 723 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683O LYS* 5.1 13.5 + - + +
687O LEU* 3.4 26.5 - - + -
719O ARG 3.4 5.6 + - - +
720O LEU* 3.1 17.4 + - - +
722O HIS* 1.3 80.2 + - - +
724O LEU* 1.3 67.5 + - - +
725O GLY* 3.1 2.4 + - - -
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Residues in contact with LEU 724 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684O ALA* 3.9 31.2 - - + +
687O LEU* 4.4 13.9 - - + +
688O GLU* 4.1 26.5 - - + +
691O ILE* 4.2 12.3 - - + -
720O LEU* 2.9 15.5 + - + +
721O TYR* 3.7 31.9 - - + +
723O THR* 1.3 76.8 - - - +
725O GLY* 1.3 59.2 + - - +
726O LYS* 3.4 32.2 + - - +
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Residues in contact with GLY 725 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721O TYR 2.8 8.6 + - - -
722O HIS 3.4 10.5 + - - -
723O THR 3.1 3.4 - - - -
724O LEU* 1.3 76.2 - - - +
726O LYS* 1.3 59.5 + - - +
727O THR* 2.8 21.5 + - - +
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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
------------------------------------------------------------
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