Contacts of the helix formed by residues 738 - 754 (chain T) in PDB entry 1BGX
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 738 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201T GLU* 6.3 1.6 - - - -
202T LYS* 3.7 27.0 - - - +
206T LYS* 4.6 7.8 - - - +
505T LYS* 6.2 2.0 - - - +
736T ARG 3.8 2.0 + - - -
737T VAL* 1.3 76.3 - - + +
739T SER* 1.3 61.8 + - - +
741T ARG* 3.5 17.3 - - - +
742T GLU* 3.3 51.4 + - - +
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Residues in contact with SER 739 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLY* 5.7 7.6 - - - +
28H SER* 6.1 0.2 - - - -
505T LYS* 5.1 13.2 + - - +
737T VAL* 3.2 13.6 - - - +
738T LYS* 1.3 79.6 - - - +
740T VAL* 1.3 63.3 + - - +
742T GLU* 4.3 3.3 - - - +
743T ALA* 3.5 21.3 + - - +
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Residues in contact with VAL 740 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H THR 4.8 3.4 - - - +
73H SER 4.1 15.5 - - - +
75H ASN* 5.6 11.2 - - + -
732T ASP* 2.6 54.8 - - - +
735T ALA* 3.8 17.3 - - + -
737T VAL* 3.4 25.0 + - + +
738T LYS 3.4 0.4 - - - -
739T SER* 1.3 81.8 - - - +
741T ARG* 1.3 61.9 + - - +
742T GLU 3.4 0.2 - - - -
743T ALA* 3.6 3.4 + - - +
744T ALA* 3.3 10.0 + - - +
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Residues in contact with ARG 741 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171T LYS* 3.0 72.9 + - + +
205T ARG 4.4 15.2 + - - -
206T LYS* 4.4 17.2 - - - +
209T GLU* 3.9 15.6 + - - -
715T ARG* 5.5 3.4 - - - +
732T ASP 4.4 3.6 - - - -
735T ALA* 4.2 12.7 - - + +
736T ARG 5.4 1.6 - - - -
737T VAL 3.4 18.0 + - - +
738T LYS* 3.5 21.5 - - + +
740T VAL* 1.3 78.3 - - - +
742T GLU* 1.3 65.3 + - + +
744T ALA* 3.3 6.1 + - - +
745T GLU* 3.1 46.6 + - - +
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Residues in contact with GLU 742 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206T LYS* 3.5 29.3 + - - +
674T SER* 6.4 1.8 - - - -
738T LYS* 3.3 42.1 + - - +
739T SER* 4.6 4.0 - - - +
740T VAL 3.4 0.4 - - - -
741T ARG* 1.3 84.3 + - - +
743T ALA* 1.3 62.1 + - - +
745T GLU* 3.6 17.7 + - - +
746T ARG* 3.3 59.4 + - - +
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Residues in contact with ALA 743 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H SER* 4.2 23.1 - - - +
30H THR* 4.8 9.7 + - - +
31H SER* 5.5 2.2 - - - +
732T ASP* 4.8 2.5 - - - +
739T SER 3.5 18.2 + - - +
740T VAL* 3.6 6.2 + - - +
741T ARG 3.3 0.6 - - - -
742T GLU* 1.3 78.0 - - - +
744T ALA* 1.3 61.0 + - - +
746T ARG* 3.8 11.7 - - - +
747T MET* 3.7 18.0 + - - +
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Residues in contact with ALA 744 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730T VAL* 5.9 1.3 - - + +
732T ASP* 3.3 48.0 - - + +
733T LEU* 3.7 21.7 - - + +
740T VAL 3.3 9.3 + - - +
741T ARG 3.5 5.6 - - - +
742T GLU 3.2 0.4 - - - -
743T ALA* 1.3 78.1 - - - +
745T GLU* 1.3 63.3 + - - +
746T ARG 3.2 0.4 - - - -
747T MET* 3.2 8.5 + - - +
748T ALA* 3.2 15.2 + - - +
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Residues in contact with GLU 745 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171T LYS* 3.5 30.3 + - - +
205T ARG* 6.1 0.7 - - - +
206T LYS* 5.8 2.9 + - - +
711T LEU* 3.6 29.9 - - + +
715T ARG* 4.8 2.1 + - - -
733T LEU* 4.0 10.3 - - + -
741T ARG* 3.1 39.0 + - - +
742T GLU* 4.0 20.8 - - - +
743T ALA 3.5 0.2 - - - -
744T ALA* 1.3 75.0 - - - +
746T ARG* 1.3 66.5 + - - +
748T ALA* 3.1 14.6 + - - +
749T PHE* 3.2 31.9 - - + -
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Residues in contact with ARG 746 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671T TYR* 3.4 41.5 + - + +
672T GLY* 5.6 0.2 - - - -
673T MET* 4.1 12.7 + - - +
674T SER* 3.5 33.9 + - - +
677T ARG* 4.3 30.7 - - - +
742T GLU* 3.3 51.2 + - - +
743T ALA* 3.8 12.3 - - - +
745T GLU* 1.3 82.6 - - - +
747T MET* 1.3 60.3 + - + +
748T ALA 3.5 0.4 + - - -
749T PHE* 4.6 2.8 - - - -
750T ASN* 3.3 21.1 + - - +
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Residues in contact with MET 747 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H THR* 4.4 29.8 - - + +
31H SER* 5.8 2.0 - - - -
52H TYR* 6.4 1.8 - - + -
570T ALA* 5.5 10.5 - - - -
571T THR* 5.6 7.0 - - - -
720T VAL* 4.6 2.4 - - - +
728T ARG* 5.1 19.5 - - + +
730T VAL* 5.1 13.7 - - + -
743T ALA 3.7 10.7 + - - +
744T ALA* 3.2 10.9 + - - +
745T GLU 3.1 0.6 - - - -
746T ARG* 1.3 81.8 - - + +
748T ALA* 1.3 66.4 + - - +
749T PHE 3.7 0.2 - - - -
750T ASN* 3.6 29.5 + - - +
751T MET* 3.8 12.6 + - - +
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Residues in contact with ALA 748 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710T THR* 4.3 8.7 - - + +
711T LEU* 5.6 2.5 - - + -
714T GLY* 5.4 0.9 - - - -
720T VAL* 3.3 30.9 - - + +
730T VAL* 6.1 1.3 - - - -
733T LEU* 4.1 22.7 - - + -
744T ALA 3.2 10.9 + - - +
745T GLU* 3.1 12.7 + - - +
747T MET* 1.3 80.6 - - - +
749T PHE* 1.3 65.9 + - + +
750T ASN 3.1 4.0 + - - -
752T PRO* 3.2 16.5 - - - +
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Residues in contact with PHE 749 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669T VAL 5.0 4.3 - - - +
670T LEU 3.1 11.9 - - - +
671T TYR* 3.5 32.3 - - - -
672T GLY* 3.8 13.9 - - - -
706T TRP* 4.6 13.6 - - + -
707T ILE* 4.0 31.6 - - + -
710T THR* 4.0 27.1 - - + -
711T LEU* 4.0 24.7 - - + -
745T GLU* 3.2 31.9 - - + -
746T ARG* 4.3 3.1 - - - -
748T ALA* 1.3 76.8 - - + +
750T ASN* 1.3 58.0 + - - +
751T MET 3.6 0.7 - - - -
752T PRO* 3.9 6.2 - - - +
753T VAL* 3.4 19.1 - - - +
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Residues in contact with ASN 750 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571T THR* 4.3 5.5 - - - +
670T LEU* 3.1 29.4 + - - +
671T TYR* 3.7 13.0 - - - +
746T ARG 3.3 20.8 + - - +
747T MET* 3.8 26.7 - - + +
748T ALA 3.1 0.6 - - - -
749T PHE* 1.3 78.6 - - - +
751T MET* 1.3 60.8 + - - +
752T PRO 3.6 0.4 - - - -
753T VAL* 4.2 2.0 - - - +
754T GLN* 2.8 57.9 + - - +
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Residues in contact with MET 751 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570T ALA* 3.9 6.1 - - + +
571T THR* 3.2 43.3 - - + +
720T VAL* 3.4 37.9 - - + +
722T THR* 3.8 13.9 - - + +
726T ARG* 3.7 18.8 - - + +
727T ARG 3.3 26.7 - - - +
728T ARG* 3.9 15.0 - - + -
747T MET* 3.8 9.2 + - - +
748T ALA 3.8 1.0 + - - -
750T ASN* 1.3 77.4 - - - +
752T PRO* 1.3 66.6 - - + +
753T VAL 3.2 1.8 - - - -
755T GLY* 3.0 23.1 + - - -
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Residues in contact with PRO 752 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618T VAL* 3.6 1.4 - - - +
622T LEU* 3.5 28.0 - - + +
706T TRP* 4.1 21.8 - - + -
710T THR* 4.6 7.4 - - + -
720T VAL* 4.2 9.9 - - + +
721T GLU 4.2 17.7 - - - +
722T THR* 4.0 10.1 - - + -
748T ALA 3.2 19.1 - - - +
749T PHE* 3.9 7.9 - - - -
750T ASN 3.9 0.9 - - - -
751T MET* 1.3 91.8 - - + +
753T VAL* 1.3 58.4 + - - +
756T THR* 3.0 22.0 + - - -
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Residues in contact with VAL 753 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615T GLU* 3.4 38.7 - - + +
618T VAL* 4.3 13.2 - - + +
619T LEU* 4.3 16.8 - - + +
622T LEU* 5.9 0.2 - - + -
669T VAL 5.6 0.4 - - - +
670T LEU* 4.2 23.1 - - + +
706T TRP* 3.9 19.3 - - + -
749T PHE 3.4 22.4 - - - +
750T ASN 4.2 3.4 - - - +
751T MET 3.2 0.4 - - - -
752T PRO* 1.3 81.2 - - - +
754T GLN* 1.3 66.0 + - + +
755T GLY 3.3 0.2 - - - -
757T ALA* 3.3 24.3 + - - +
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Residues in contact with GLN 754 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571T THR* 4.0 18.1 - - + +
573T ARG* 3.3 31.5 + - - +
615T GLU* 3.2 26.9 + - - +
670T LEU* 4.7 8.3 - - + +
750T ASN* 2.8 46.5 + - - +
753T VAL* 1.3 78.6 - - + +
755T GLY* 1.3 62.0 + - - +
757T ALA* 4.1 3.3 - - - +
758T ALA* 3.5 21.3 + - - +
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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