Contacts of the helix formed by residues 831 - 847 (chain E) in PDB entry 6BAA
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 831 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829E ASN 3.8 2.2 + - - -
830E LEU* 1.3 76.7 - - - +
832E GLY* 1.3 61.7 + - - +
833E GLY* 3.2 6.5 - - - -
834E GLN* 3.3 13.1 + - - +
835E ARG* 2.8 29.0 + - - +
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Residues in contact with GLY 832 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777E PRO* 4.4 8.3 - - - +
830E LEU 4.0 0.2 + - - -
831E SER* 1.3 73.2 - - - +
833E GLY* 1.3 56.9 + - - +
835E ARG* 3.5 7.5 + - - +
836E GLN* 2.9 27.9 + - - +
859E ALA* 4.1 9.4 - - - +
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Residues in contact with GLY 833 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831E SER* 3.2 4.2 - - - -
832E GLY* 1.3 74.8 - - - +
834E GLN* 1.3 58.7 + - - +
836E GLN* 3.3 3.3 + - - +
837E ARG* 2.9 29.5 + - - +
859E ALA* 3.5 30.8 + - - +
860E LEU* 5.3 3.2 - - - +
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Residues in contact with GLN 834 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811E ASP* 5.5 11.9 - - + -
830E LEU* 4.2 10.5 - - + -
831E SER* 3.3 25.3 + - - +
833E GLY* 1.3 75.1 - - - +
835E ARG* 1.3 56.9 + - - +
837E ARG* 3.4 7.4 + - - +
838E ILE* 2.9 30.0 + - - +
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Residues in contact with ARG 835 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777E PRO* 3.7 25.8 - - + +
779E LEU* 5.7 9.4 - - + -
830E LEU* 4.5 8.9 - - + +
831E SER 2.8 21.0 + - - +
832E GLY* 3.6 7.9 - - - +
834E GLN* 1.3 73.6 - - - +
836E GLN* 1.3 55.5 + - - +
838E ILE* 3.3 8.5 + - - +
839E SER* 2.9 28.2 + - - -
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Residues in contact with GLN 836 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777E PRO* 4.2 9.8 - - + +
832E GLY 2.9 18.0 + - - +
833E GLY* 3.6 5.2 - - - +
835E ARG* 1.3 75.3 - - - +
837E ARG* 1.3 57.9 + - - +
839E SER* 3.2 7.6 + - - -
840E VAL* 2.9 29.0 + - - +
856E PRO* 4.7 13.7 - - + +
859E ALA* 4.3 15.9 - - + -
860E LEU* 6.6 0.2 - - + -
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Residues in contact with ARG 837 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806E CYS* 3.9 27.6 - - + +
833E GLY 2.9 17.2 + - - +
834E GLN* 3.7 7.2 - - - +
836E GLN* 1.3 75.2 - - - +
838E ILE* 1.3 55.8 + - - +
840E VAL* 3.4 8.5 + - - +
841E ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 838 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779E LEU* 6.1 4.5 - - + -
787E ASN* 4.8 15.3 - - + +
788E ILE* 5.3 1.2 - - - -
834E GLN 2.9 18.9 + - - +
835E ARG* 3.5 8.7 - - - +
837E ARG* 1.3 75.9 - - - +
839E SER* 1.3 56.7 + - - +
841E ALA* 3.3 7.2 + - - +
842E ARG* 2.9 29.9 + - - +
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Residues in contact with SER 839 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772E TYR 5.2 2.9 - - - +
773E ALA* 5.4 13.8 - - - +
774E SER 5.7 4.3 - - - -
777E PRO* 4.8 12.3 - - - -
778E TRP 5.4 7.2 - - - -
835E ARG 2.9 13.8 + - - -
836E GLN* 3.5 10.8 - - - -
838E ILE* 1.3 75.7 - - - +
840E VAL* 1.3 63.1 + - - +
842E ARG* 3.3 8.2 + - - +
843E ALA* 3.0 23.9 + - - +
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Residues in contact with VAL 840 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773E ALA* 5.6 5.5 - - - +
806E CYS* 5.8 2.0 - - + -
836E GLN 2.9 17.4 + - - +
837E ARG* 3.6 8.7 - - - +
839E SER* 1.3 77.0 - - - +
841E ALA* 1.3 57.0 + - - +
843E ALA* 3.3 6.8 + - - +
844E LEU* 2.9 30.4 + - - +
856E PRO* 5.7 9.2 - - + -
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Residues in contact with ALA 841 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788E ILE* 4.9 10.7 - - + +
802E VAL* 4.5 15.6 - - + +
806E CYS* 3.8 21.0 - - + +
837E ARG 2.9 18.3 + - - +
838E ILE* 3.3 8.7 + - - +
840E VAL* 1.3 76.0 - - - +
842E ARG* 1.3 57.0 + - - +
844E LEU* 3.8 6.0 - - - +
845E TYR* 2.8 32.2 + - - +
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Residues in contact with ARG 842 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787E ASN 3.8 19.1 - - - +
788E ILE* 3.7 15.3 - - - +
789E THR 5.5 0.5 - - - +
790E PHE* 4.6 12.4 - - + +
838E ILE 2.9 17.0 + - - +
839E SER* 3.5 9.0 - - - +
841E ALA* 1.3 77.0 - - - +
843E ALA* 1.3 56.5 + - - +
845E TYR* 3.4 2.1 + - - +
846E GLN* 3.0 29.7 + - - +
1217E PHE* 6.0 7.2 - - + -
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Residues in contact with ALA 843 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771E ALA* 4.5 23.8 - - + +
772E TYR 4.5 15.0 - - - +
773E ALA* 5.3 5.2 - - + -
839E SER 3.0 13.5 + - - +
840E VAL* 3.6 9.9 - - - +
842E ARG* 1.3 77.4 - - - +
844E LEU* 1.3 63.3 + - - +
846E GLN* 3.3 17.9 + - - +
847E GLN* 3.7 4.5 + - - -
848E THR 4.7 1.4 + - - -
851E VAL* 5.7 5.2 - - + -
1217E PHE* 5.7 5.3 - - + -
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Residues in contact with LEU 844 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798E ARG* 3.0 22.3 + - - -
802E VAL* 5.5 7.4 - - + -
805E ALA* 6.5 0.7 - - + -
840E VAL 2.9 16.9 + - - +
841E ALA* 3.9 6.5 - - - +
843E ALA* 1.3 75.0 - - - +
845E TYR* 1.3 60.2 + - - +
847E GLN* 3.3 8.5 + - - -
875E GLU* 6.0 6.3 - - + -
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Residues in contact with TYR 845 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788E ILE* 3.7 21.5 - - + +
789E THR* 3.8 11.4 - - - -
792E SER* 3.2 29.8 - - - -
793E PRO 2.9 12.3 + - - -
794E PHE* 3.3 9.6 - + - +
795E ASN* 2.9 30.7 + - + +
798E ARG* 3.6 34.3 + - + +
799E TYR* 3.5 35.4 - + + -
802E VAL* 4.4 8.6 - - + +
841E ALA 2.8 19.0 + - - +
842E ARG 3.7 4.3 - - - +
844E LEU* 1.3 77.5 - - - +
846E GLN* 1.3 61.9 + - - +
847E GLN* 3.2 6.1 + - - +
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Residues in contact with GLN 846 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771E ALA* 5.4 3.6 - - + -
789E THR 5.8 3.1 - - - +
790E PHE* 6.4 1.8 - - + -
842E ARG 3.0 17.6 + - - +
843E ALA* 3.6 9.6 - - - +
844E LEU 3.3 0.8 - - - -
845E TYR* 1.3 79.3 - - - +
847E GLN* 1.3 66.9 + - - +
848E THR* 3.2 10.4 + - - +
1217E PHE* 6.1 5.6 - - + -
1219E TYR* 4.5 18.7 + - + +
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Residues in contact with GLN 847 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798E ARG* 3.9 21.8 - - - +
843E ALA 3.7 2.8 + - - -
844E LEU 3.3 10.0 + - - -
845E TYR 3.1 5.3 - - - +
846E GLN* 1.3 79.0 - - - +
848E THR* 1.3 64.9 + - - +
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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