Contacts of the helix formed by residues 735 - 750 (chain D) in PDB entry 2BT4
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 VAL 735 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620D LEU* 4.4 3.8 - - + -
628D TYR 4.5 10.5 + - - +
629D GLY* 6.1 0.7 - - - -
631D ASP* 3.4 30.1 - - + +
636D VAL* 3.6 30.1 - - + -
639D LEU* 3.8 23.9 - - + +
707D ILE* 4.2 17.0 - - + +
734D GLY* 1.3 67.0 - - - -
736D GLN* 1.3 58.4 + - + +
737D GLY 3.0 5.6 - - - -
738D TYR* 3.0 37.2 + - + +
739D VAL 3.9 0.9 + - - -
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Residues in contact with GLN 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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143A GLU* 3.4 23.6 + - - +
144A ARG* 3.0 33.8 + - - +
147A ALA* 3.4 15.0 - - - +
639D LEU* 5.1 2.0 - - - -
733D CYS 3.6 10.1 + - - +
734D GLY 3.1 1.0 - - - -
735D VAL* 1.3 81.6 - - - +
737D GLY* 1.3 55.3 + - - +
739D VAL* 2.9 34.2 + - + +
740D PHE* 3.1 40.0 + - + -
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Residues in contact with GLY 737 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705D VAL* 3.6 19.0 - - - +
706D HIS 5.9 0.4 - - - -
730D VAL* 3.8 24.1 - - - +
733D CYS* 3.5 8.3 + - - -
734D GLY 3.0 14.8 + - - -
736D GLN* 1.3 75.7 - - - +
738D TYR* 1.3 61.4 + - - +
740D PHE* 3.3 6.0 + - - +
741D GLY 2.9 17.8 + - - -
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Residues in contact with TYR 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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611D ILE* 4.1 24.7 - - + -
613D ASN* 2.7 29.4 + - - -
617D LEU* 4.2 2.1 - - - +
620D LEU* 5.7 0.2 - - + -
633D LEU* 4.7 3.7 - - + +
636D VAL* 3.8 29.6 - - + -
639D LEU* 5.8 1.1 - - + -
640D CYS* 3.8 15.5 - - - -
677D VAL* 4.3 11.6 - - + +
679D ASN* 3.1 31.4 + - + +
705D VAL* 4.2 13.0 - - + -
707D ILE* 3.8 27.7 - - + +
735D VAL* 3.0 27.1 + - - +
737D GLY* 1.3 77.9 - - - +
739D VAL* 1.3 58.9 + - + +
741D GLY* 3.2 2.1 + - - -
742D VAL* 3.0 31.5 + - - +
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Residues in contact with VAL 739 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D LEU* 4.3 35.7 - - + +
640D CYS* 5.4 0.7 - - - +
643D ALA* 4.0 25.1 - - + -
735D VAL 4.7 0.2 - - - +
736D GLN* 2.9 24.0 + - + +
738D TYR* 1.3 74.8 - - + +
740D PHE* 1.3 63.2 + - + +
742D VAL* 3.3 6.7 + - - +
743D GLU* 2.8 50.6 + - + +
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Residues in contact with PHE 740 (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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130A VAL* 4.9 1.1 - - + -
140A PHE* 3.3 71.3 - + + -
143A GLU* 3.3 22.7 - - + -
144A ARG* 3.9 7.9 - - + -
730D VAL* 4.1 18.6 - - + -
733D CYS* 3.8 26.0 - - + -
736D GLN* 3.1 44.6 + - + -
737D GLY* 3.5 14.6 - - - +
738D TYR 3.3 0.2 - - - -
739D VAL* 1.3 75.3 - - + +
741D GLY* 1.3 64.0 + - - +
743D GLU* 3.2 4.6 + - - -
744D ARG* 2.8 21.2 + - - +
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Residues in contact with GLY 741 (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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677D VAL* 3.7 18.4 - - - -
703D VAL* 4.0 23.2 - - - +
730D VAL* 5.1 0.2 - - - +
737D GLY 2.9 14.8 + - - -
738D TYR 3.2 4.6 + - - -
740D PHE* 1.3 78.1 - - - +
742D VAL* 1.3 60.2 + - - +
744D ARG* 3.2 2.3 + - - +
745D ILE* 3.0 28.8 + - - +
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Residues in contact with VAL 742 (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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609D ILE* 4.0 15.5 - - + +
611D ILE* 4.1 26.5 - - + -
640D CYS* 4.7 7.6 - - + +
643D ALA* 3.9 17.5 - - + +
644D ALA* 3.7 33.0 - - - +
647D HIS* 4.9 2.7 - - + -
651D VAL* 5.0 0.4 - - + -
677D VAL* 4.4 8.3 - - + -
738D TYR 3.0 15.7 + - - +
739D VAL 3.6 6.3 - - - +
741D GLY* 1.3 75.2 - - - +
743D GLU* 1.3 65.3 + - - +
745D ILE* 3.3 5.5 + - - +
746D ALA* 2.9 24.4 + - + +
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Residues in contact with GLU 743 (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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136A GLN* 3.5 14.1 + - - +
140A PHE* 3.2 19.6 - - + -
143A GLU* 2.7 38.4 - - - +
643D ALA* 5.7 0.2 - - + -
647D HIS* 3.5 31.6 + - + +
739D VAL* 2.8 38.1 + - + +
740D PHE* 3.7 6.2 - - - +
742D VAL* 1.3 79.1 - - + +
744D ARG* 1.3 56.3 + - - +
746D ALA* 3.5 6.7 + - - +
747D ALA* 3.1 21.1 + - - +
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Residues in contact with ARG 744 (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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132A GLY 4.4 5.1 + - - -
133A CYS* 3.1 50.5 + - - +
134A GLY* 3.7 7.5 - - - +
136A GLN* 3.0 30.8 + - - +
140A PHE* 3.9 8.5 - - + -
703D VAL* 3.9 21.3 - - + -
727D ASP* 6.3 0.4 - - - +
728D GLY* 5.9 1.1 - - - -
740D PHE 2.8 17.2 + - - +
741D GLY 3.7 3.8 - - - +
742D VAL 3.2 0.2 - - - -
743D GLU* 1.3 74.6 - - - +
745D ILE* 1.3 65.1 + - - +
747D ALA* 3.1 7.1 + - - +
748D LEU* 2.9 65.9 + - + +
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Residues in contact with ILE 745 (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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604D LEU* 4.0 16.2 - - + -
609D ILE* 4.1 20.6 - - + -
674D CYS* 4.4 5.8 - - - +
675D GLY* 4.3 14.1 - - - -
676D ILE 4.0 7.2 - - - +
677D VAL* 4.0 15.0 - - + -
701D PRO* 3.8 36.5 - - + +
703D VAL* 3.7 22.2 - - + -
741D GLY 3.0 19.7 + - - +
742D VAL 3.7 4.3 - - - +
744D ARG* 1.3 77.3 - - - +
746D ALA* 1.3 58.0 + - - +
748D LEU* 3.0 3.5 + - + +
749D ALA* 2.8 31.5 + - + +
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Residues in contact with ALA 746 (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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604D LEU* 3.5 34.3 - - + +
647D HIS* 3.8 25.6 - - + +
742D VAL* 2.9 17.2 + - + +
743D GLU 3.7 5.4 - - - +
745D ILE* 1.3 75.9 - - - +
747D ALA* 1.3 62.5 + - - +
750D GLY* 3.1 20.3 + - - -
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Residues in contact with ALA 747 (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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136A GLN* 3.4 29.8 - - - +
743D GLU 3.1 11.3 + - - +
744D ARG* 3.1 9.8 + - - +
746D ALA* 1.3 78.6 - - - +
748D LEU* 1.3 61.2 + - - +
750D GLY* 3.3 16.2 + - - +
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Residues in contact with LEU 748 (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 PRO* 3.8 30.7 - - + -
702D VAL 5.6 0.2 - - - +
703D VAL* 5.7 0.9 - - + -
727D ASP* 5.1 14.1 - - + -
744D ARG* 2.9 62.7 + - + +
745D ILE* 3.8 3.1 - - + +
747D ALA* 1.3 76.2 - - - +
749D ALA* 1.3 67.2 + - - +
750D GLY 3.2 7.4 - - - +
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Residues in contact with ALA 749 (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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602D ARG 4.3 14.1 - - - +
603D SER* 4.6 10.5 - - - -
604D LEU* 3.6 33.4 - - + +
674D CYS* 4.5 12.6 - - + +
701D PRO* 4.8 4.2 - - + +
745D ILE* 2.8 17.4 + - + +
748D LEU* 1.3 75.5 - - - +
750D GLY* 1.3 66.7 + - - +
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Residues in contact with GLY 750 (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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604D LEU* 5.5 1.4 - - - +
746D ALA 3.1 18.8 + - - -
747D ALA* 3.3 15.7 - - - +
748D LEU 3.2 7.4 - - - +
749D ALA* 1.3 82.4 - - - +
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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