Contacts of the helix formed by residues 767 - 783 (chain A) in PDB entry 6S1M
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 SER 767 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A PRO* 5.1 1.1 - - - -
765A VAL* 3.4 6.4 - - - +
766A SER* 1.3 80.1 + - - +
768A VAL* 1.3 64.9 + - - +
769A ALA* 3.2 2.9 - - - -
770A GLU* 3.2 35.1 + - - -
771A ALA* 3.1 19.5 + - - +
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Residues in contact with VAL 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 4.6 7.9 - - + -
766A SER 4.9 2.0 - - - +
767A SER* 1.3 73.2 - - - +
769A ALA* 1.3 56.9 + - - +
771A ALA* 3.9 5.9 - - - +
772A MET* 2.9 38.7 + - + +
797A VAL* 4.1 16.2 - - + -
799A PHE* 4.0 25.8 - - + -
814A PHE* 3.6 36.6 - - + -
817A ARG* 3.4 33.3 - - - +
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Residues in contact with ALA 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A SER* 3.2 2.6 - - - -
768A VAL* 1.3 79.2 - - - +
770A GLU* 1.3 61.2 + - + +
772A MET* 3.4 6.0 + - - +
773A ALA* 3.0 28.5 + - - +
817A ARG* 4.6 21.3 - - + +
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Residues in contact with GLU 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A VAL* 3.6 28.4 - - + +
766A SER 5.1 0.2 + - - -
767A SER* 3.2 31.7 + - - +
769A ALA* 1.3 75.8 - - + +
771A ALA* 1.3 60.9 + - - +
773A ALA* 3.4 6.1 + - - +
774A LEU* 3.0 36.7 + - + +
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Residues in contact with ALA 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 4.3 24.2 - - + +
599A ALA* 4.7 2.0 - - + +
763A PHE* 4.7 16.4 - - + -
765A VAL* 3.7 14.6 - - + +
767A SER 3.1 15.5 + - - +
768A VAL* 3.9 4.7 - - - +
770A GLU* 1.3 74.5 - - - +
772A MET* 1.3 59.3 + - - +
774A LEU* 3.9 3.8 - - - +
775A GLY* 2.9 27.5 + - - -
794A PHE* 4.3 2.3 - - - -
797A VAL* 4.4 12.3 - - + -
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Residues in contact with MET 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768A VAL* 2.9 28.0 + - + +
769A ALA* 3.7 5.2 - - - +
771A ALA* 1.3 74.7 - - - +
773A ALA* 1.3 63.6 + - - +
775A GLY* 3.9 0.3 - - - -
776A ARG* 3.0 47.4 + - - +
794A PHE* 3.9 26.0 - - + -
797A VAL* 4.0 9.9 - - + -
814A PHE* 3.8 24.0 - - + +
815A SER 3.7 20.6 - - - +
816A SER* 3.6 34.5 - - - +
817A ARG* 4.0 7.9 - - - -
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Residues in contact with ALA 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769A ALA 3.0 17.2 + - - +
770A GLU* 3.8 7.2 - - - +
772A MET* 1.3 77.0 - - - +
774A LEU* 1.3 63.9 + - + +
776A ARG* 3.4 5.5 + - - +
777A GLU* 3.1 23.3 + - - +
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Residues in contact with LEU 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A TYR* 4.5 10.8 - - + -
745A TYR* 5.0 20.6 - - + -
746A SER* 6.5 1.6 - - - -
763A PHE* 4.2 28.3 - - + -
765A VAL* 5.2 14.4 - - + -
770A GLU* 3.0 22.3 + - + +
771A ALA* 4.2 2.7 - - - +
773A ALA* 1.3 78.8 - - + +
775A GLY* 1.3 57.3 + - - +
777A GLU* 3.4 22.1 + - + +
778A ALA* 2.9 28.8 + - - +
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Residues in contact with GLY 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A LEU* 3.7 5.3 - - - +
763A PHE* 4.1 17.9 - - - -
771A ALA 2.9 18.8 + - - -
774A LEU* 1.3 73.9 - - - +
776A ARG* 1.3 60.7 + - - +
778A ALA* 3.3 2.6 + - - +
779A ALA* 3.0 29.6 + - - +
794A PHE* 3.4 20.9 - - - -
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Residues in contact with ARG 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A MET* 3.0 44.7 + - - +
773A ALA* 3.9 5.4 - - - +
775A GLY* 1.3 72.3 - - - +
777A GLU* 1.3 64.8 + - - +
779A ALA* 3.9 0.6 - - - +
780A ASP* 3.1 37.9 + - - +
794A PHE* 3.6 33.9 - - + +
815A SER 4.6 12.9 + - - -
816A SER* 6.2 0.6 - - - +
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Residues in contact with GLU 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739A TYR* 4.1 13.0 + - + +
745A TYR* 4.9 13.4 + - - -
773A ALA 3.1 15.3 + - - +
774A LEU* 3.6 24.6 - - + +
776A ARG* 1.3 76.6 - - - +
778A ALA* 1.3 55.7 + - - +
780A ASP* 3.8 3.6 - - - +
781A TRP* 2.9 34.6 + - + +
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Residues in contact with ALA 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A LEU* 4.2 15.3 - - + -
735A VAL* 5.4 5.4 - - + -
739A TYR* 3.3 30.7 + - + +
763A PHE* 4.3 9.0 - - + -
774A LEU 2.9 17.2 + - - +
775A GLY 3.3 5.6 + - - +
777A GLU* 1.3 74.8 - - - +
779A ALA* 1.3 60.4 + - - +
781A TRP* 3.6 0.4 - - - +
782A VAL* 2.9 38.4 + - + +
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Residues in contact with ALA 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A LEU* 4.2 7.7 - - + +
775A GLY 3.0 15.4 + - - +
776A ARG 3.9 3.4 - - - +
778A ALA* 1.3 75.4 - - - +
780A ASP* 1.3 67.3 + - - +
783A SER* 2.9 30.4 + - - -
792A LEU* 3.8 15.3 - - + +
793A GLU* 3.8 12.6 - - - +
794A PHE* 3.5 30.3 - - + +
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Residues in contact with ASP 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A ARG* 3.1 23.2 + - - +
777A GLU* 4.2 3.5 - - - +
779A ALA* 1.3 82.6 - - - +
781A TRP* 1.3 63.0 + - - +
783A SER* 3.9 12.8 + - - -
784A GLY* 4.2 3.5 + - - -
792A LEU 4.8 4.0 - - - +
793A GLU* 5.7 0.7 - - - -
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Residues in contact with TRP 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734A LEU* 4.9 13.9 + - + +
738A LYS* 3.3 48.4 - - + +
739A TYR* 3.7 21.3 - + - +
777A GLU* 2.9 23.1 + - + +
778A ALA 3.6 1.6 - - - +
779A ALA 3.2 0.2 - - - -
780A ASP* 1.3 77.0 - - - +
782A VAL* 1.3 84.9 + - + +
784A GLY* 3.4 12.3 + - - -
785A HIS* 4.5 25.1 + - - -
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Residues in contact with VAL 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A PHE* 5.5 0.7 - - + -
730A LYS* 6.5 0.2 - - + -
731A THR* 4.7 19.5 - - + +
734A LEU* 4.7 22.2 - - + -
735A VAL* 4.2 22.9 - - + +
778A ALA* 2.9 20.6 + - + +
781A TRP* 1.3 94.6 - - + +
783A SER* 1.3 63.3 + - - +
784A GLY 3.0 1.4 + - - -
785A HIS* 3.5 21.9 + - - +
786A PHE* 4.0 14.3 - - + -
792A LEU* 3.7 22.4 - - + -
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Residues in contact with SER 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A ALA 2.9 18.2 + - - -
780A ASP* 4.1 8.5 - - - -
781A TRP 3.2 0.6 - - - -
782A VAL* 1.3 77.4 - - - +
784A GLY* 1.3 55.6 + - - +
785A HIS 3.1 6.3 + - - -
786A PHE* 3.9 17.9 + - - +
790A ILE 4.1 9.2 - - - +
791A ARG* 4.2 9.4 - - - +
792A LEU* 2.7 39.4 + - - +
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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