Contacts of the helix formed by residues 860 - 876 (chain E) in PDB entry 6C3P
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 ASP 860 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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858E ALA 3.6 1.4 + - - -
859E LEU* 1.3 74.4 - - - +
861E ILE* 1.3 64.3 + - + +
862E HIS* 3.4 7.5 + - - -
863E LEU* 3.2 25.7 + - - +
864E SER* 2.7 30.5 + - - -
1378E GLY 5.0 4.9 - - - +
1379E ARG* 3.2 15.1 - - - +
1380E THR* 2.8 42.2 + - - +
1537E HIS* 5.5 14.4 - - + +
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Residues in contact with ILE 861 (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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860E ASP* 1.3 73.9 - - + +
862E HIS* 1.3 105.0 + - + +
864E SER* 4.1 5.6 - - - -
865E ASP* 2.9 39.4 + - - +
889E LYS* 4.8 11.4 - - + +
1537E HIS 4.9 11.6 + - - +
1538E ARG* 5.3 9.4 - - - +
1539E VAL* 6.2 3.1 - - + -
1576E PHE* 4.4 23.6 - - + +
1579E ALA* 5.2 9.0 - - + -
1580E ASP* 3.6 32.1 - - - +
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Residues in contact with HIS 862 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860E ASP* 3.3 8.8 + - - +
861E ILE* 1.3 102.5 - - + +
863E LEU* 1.3 66.4 + - + +
865E ASP* 3.8 3.4 - - - +
866E HIS* 3.0 27.0 + - - +
1379E ARG* 3.3 45.1 - - + +
1576E PHE* 3.3 31.0 - + - -
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Residues in contact with LEU 863 (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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805E CYS 5.6 0.2 - - - +
806E SER* 4.1 18.6 + - - +
810E ASP* 5.4 0.4 - - - +
836E ARG* 3.2 47.3 - - - +
859E LEU* 3.7 19.5 - - + -
860E ASP* 3.2 19.5 + - - +
862E HIS* 1.3 86.2 - - + +
864E SER* 1.3 61.1 + - - +
866E HIS* 4.0 5.6 - - - +
867E LEU* 2.8 34.1 + - - +
1380E THR* 4.0 22.2 - - + -
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Residues in contact with SER 864 (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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856E PHE* 4.0 20.7 + - - +
859E LEU* 3.5 25.1 + - - +
860E ASP 2.7 24.4 + - - -
861E ILE* 3.9 3.8 - - - -
863E LEU* 1.3 76.3 - - - +
865E ASP* 1.3 63.9 + - - +
867E LEU* 3.9 0.7 - - - +
868E MET* 2.9 28.1 + - - +
889E LYS* 3.3 27.8 + - - -
892E TYR* 4.4 1.1 - - - -
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Residues in contact with ASP 865 (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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861E ILE* 2.9 30.9 + - - +
862E HIS* 3.8 3.4 - - - +
864E SER* 1.3 73.5 - - - +
866E HIS* 1.3 65.0 + - - +
868E MET* 4.1 0.2 - - - +
869E GLN* 2.9 32.1 + - - +
889E LYS* 4.1 5.0 + - - -
891E GLN* 5.3 3.1 - - - +
892E TYR* 2.0 39.1 + - - +
1579E ALA* 4.8 14.8 - - - +
1580E ASP* 5.6 0.9 - - - +
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Residues in contact with HIS 866 (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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803E GLU 3.5 17.1 + - - -
804E ALA 4.5 0.7 - - - -
806E SER* 3.3 33.3 + - - +
862E HIS 3.0 16.9 + - - +
863E LEU* 4.0 5.6 - - - +
865E ASP* 1.3 77.1 - - - +
867E LEU* 1.3 63.9 + - - +
869E GLN* 4.7 7.6 - - + -
870E ALA* 2.9 35.3 + - + +
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Residues in contact with LEU 867 (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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804E ALA 3.4 17.2 + - - +
805E CYS* 4.1 30.3 - - + +
806E SER* 5.6 0.4 + - - +
836E ARG* 4.7 5.2 - - + -
839E VAL* 4.1 30.7 - - + -
843E LEU* 5.3 4.9 - - + -
852E LEU* 5.9 1.3 - - + -
855E PRO* 5.2 2.7 - - + +
856E PHE* 4.2 15.7 - - + -
859E LEU* 3.7 25.1 - - + -
863E LEU 2.8 22.4 + - - +
864E SER* 3.9 2.2 - - - +
866E HIS* 1.3 73.5 - - - +
868E MET* 1.3 68.5 + - - +
871E GLY* 2.8 28.2 + - - -
872E ILE* 3.7 9.8 + - + -
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Residues in contact with MET 868 (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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708E LEU* 4.4 15.3 - - + -
710E MET* 3.9 16.8 - - + -
856E PHE* 3.6 22.4 - - + -
864E SER 2.9 21.9 + - - +
865E ASP 4.1 1.1 - - - +
867E LEU* 1.3 73.8 - - - +
869E GLN* 1.3 69.2 + - - +
872E ILE* 2.8 48.6 + - + +
873E LEU 3.5 0.3 + - - -
885E LEU* 5.7 3.8 - - + -
892E TYR* 3.2 59.9 - - + -
895E HIS* 4.0 13.5 - - + +
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Residues in contact with GLN 869 (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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865E ASP* 2.9 25.9 + - - +
866E HIS* 3.9 6.2 - - + +
868E MET* 1.3 76.5 - - - +
870E ALA* 1.3 59.8 + - - +
873E LEU* 2.7 48.6 - - + +
892E TYR* 5.5 3.0 + - + -
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Residues in contact with ALA 870 (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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803E GLU 4.7 0.4 - - - +
804E ALA* 3.9 21.3 - - + -
866E HIS* 2.9 34.7 + - + +
869E GLN* 1.3 77.4 - - - +
871E GLY* 1.3 57.4 + - - +
873E LEU* 3.8 4.0 - - - +
874E GLU* 2.9 30.5 + - - +
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Residues in contact with GLY 871 (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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804E ALA* 3.8 19.7 - - - +
843E LEU* 4.8 11.6 - - - +
867E LEU* 2.8 18.5 + - - -
870E ALA* 1.3 75.8 - - - +
872E ILE* 1.3 56.4 + - - -
874E GLU* 3.0 9.3 + - - +
875E LEU* 2.9 34.4 + - - +
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Residues in contact with ILE 872 (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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708E LEU* 3.5 35.2 - - + -
843E LEU* 5.4 2.0 - - + -
852E LEU* 4.3 13.5 - - + -
856E PHE* 5.4 2.2 - - + -
867E LEU* 3.7 7.8 + - + +
868E MET* 2.8 50.3 + - + +
871E GLY* 1.3 72.2 - - - -
873E LEU* 1.3 56.0 + - - +
875E LEU* 3.2 23.0 + - + +
876E LEU* 2.9 33.3 + - + +
883E VAL* 4.7 4.0 - - + -
885E LEU* 4.2 22.0 - - + -
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Residues in contact with LEU 873 (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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868E MET 3.5 0.4 + - - -
869E GLN* 2.7 37.8 + - + +
870E ALA* 3.9 2.9 - - - +
872E ILE* 1.3 77.7 - - - +
874E GLU* 1.3 55.7 + - - +
876E LEU* 3.7 8.7 - - + +
877E ARG* 2.8 60.7 + - - +
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Residues in contact with GLU 874 (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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800E MET* 3.6 42.6 - - + +
801E VAL* 6.0 1.0 - - - +
804E ALA* 6.2 1.1 - - + -
843E LEU* 5.6 1.7 - - - +
870E ALA 2.9 16.1 + - - +
871E GLY* 3.3 10.1 - - - +
873E LEU* 1.3 76.1 - - - +
875E LEU* 1.3 76.4 + - - +
877E ARG* 3.0 18.1 + - + +
878E ASP* 2.8 31.1 + - - +
881E ARG* 4.3 8.6 + - - -
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Residues in contact with LEU 875 (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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843E LEU* 3.8 24.0 - - + -
850E VAL* 4.8 4.0 - - + -
852E LEU* 5.4 0.9 - - + -
871E GLY 2.9 14.4 + - - +
872E ILE* 3.5 27.4 - - + +
874E GLU* 1.3 82.8 - - - +
876E LEU* 1.3 58.0 + - - +
878E ASP* 2.9 30.9 + - - +
881E ARG* 3.4 56.3 - - + +
883E VAL* 3.6 40.8 - - + -
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Residues in contact with LEU 876 (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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706E GLY 4.3 13.5 - - - +
707E GLN 4.5 0.9 - - - -
708E LEU* 3.6 52.9 - - + +
872E ILE* 2.9 20.6 + - + +
873E LEU* 3.7 7.4 - - + +
875E LEU* 1.3 74.5 - - - +
877E ARG* 1.3 59.2 + - - +
878E ASP 3.3 7.8 - - - +
881E ARG 5.4 2.7 - - - +
883E VAL* 5.0 5.6 - - + -
895E HIS 5.1 3.6 - - - +
897E ASP* 3.8 15.0 - - - +
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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