Contacts of the helix formed by residues 884 - 895 (chain A) in PDB entry 6C90
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 884 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567A TYR* 5.6 0.8 - - - -
883A ALA* 1.3 71.4 - - - +
885A GLU* 1.3 64.2 + - - +
886A LEU* 3.0 11.1 + - - +
887A LEU* 2.7 32.7 + - + -
888A LEU* 3.1 23.7 + - - +
912A PHE* 4.6 3.8 + - + -
958A TYR* 2.6 38.6 + - - -
962A PHE* 3.9 20.7 - - + -
1104A MLI 4.7 4.9 - - - +
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Residues in contact with GLU 885 (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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566A THR* 3.9 8.1 - - - -
567A TYR* 3.2 24.1 + - + +
568A ASN* 2.7 41.6 + - + +
877A ALA* 3.8 18.8 - - + +
880A ILE* 3.4 32.9 - - + +
881A SER 4.6 3.5 - - - +
883A ALA 2.7 16.2 + - - +
884A ASP* 1.3 73.2 + - - +
886A LEU* 1.3 63.6 + - - +
889A THR* 2.8 34.1 + - - +
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Residues in contact with LEU 886 (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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567A TYR* 3.7 38.4 - - + +
571A LEU* 5.6 0.4 - - + -
857A VAL* 3.7 22.0 - - + -
858A LEU* 3.7 24.2 - - + -
861A LEU* 4.3 5.4 - - + -
863A PHE* 3.6 31.8 - - + -
884A ASP* 3.0 7.1 + - - +
885A GLU* 1.3 80.9 - - - +
887A LEU* 1.3 61.9 + - - +
889A THR* 2.6 20.2 + - - -
890A GLU* 3.1 12.6 + - - +
942A ILE* 4.0 27.1 - - + -
946A SER* 5.1 1.1 - - - +
1104A MLI 5.6 1.1 - - - +
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Residues in contact with LEU 887 (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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884A ASP* 2.7 25.1 + - + +
886A LEU* 1.3 73.9 - - - +
888A LEU* 1.3 58.9 + - - +
890A GLU* 3.3 1.4 + - - +
891A MET* 2.9 48.4 + - + +
912A PHE* 3.6 16.2 - - + -
935A MET* 4.3 5.2 - - - +
938A CYS* 3.6 26.0 - - + -
939A ALA* 3.8 24.0 - - + +
942A ILE* 3.4 15.2 - - + +
958A TYR* 3.8 8.7 + - - +
962A PHE* 3.5 35.7 - - + -
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Residues in contact with LEU 888 (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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880A ILE* 4.0 21.5 - - + -
883A ALA* 3.6 28.0 - - + -
884A ASP 3.1 21.7 + - - +
887A LEU* 1.3 76.5 - - - +
889A THR* 1.3 58.0 + - - +
891A MET* 3.4 13.1 + - + +
892A MET* 3.0 26.7 + - - +
897A PHE* 4.1 7.8 - - + -
909A LEU* 3.7 24.7 - - + -
912A PHE* 3.5 33.7 - - + -
1003A LEU* 4.0 17.9 - - + -
1007A MET* 4.2 8.7 - - + +
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Residues in contact with THR 889 (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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863A PHE* 3.1 22.4 - - - -
873A LYS* 4.8 3.4 - - - -
876A VAL* 3.9 13.5 - - + -
877A ALA* 3.5 34.3 - - + +
880A ILE* 3.8 13.7 - - + -
885A GLU 2.8 16.1 + - - +
886A LEU 2.6 21.5 + - - -
888A LEU* 1.3 73.1 - - - +
890A GLU* 1.3 59.0 + - - +
892A MET* 2.9 9.2 + - - +
893A PHE* 2.8 36.0 + - - -
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Residues in contact with GLU 890 (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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861A LEU* 4.0 15.6 - - - +
863A PHE* 4.2 6.0 - - + -
873A LYS* 2.7 36.1 + - - +
886A LEU 3.1 11.8 + - - +
887A LEU 3.3 4.5 + - - +
889A THR* 1.3 81.1 + - - +
891A MET* 1.3 57.0 + - - +
893A PHE 3.3 0.9 + - - +
894A ASN* 2.9 56.1 + - - +
938A CYS* 3.6 11.7 - - - -
941A ARG* 2.9 35.6 + - - +
942A ILE* 4.0 12.8 - - + -
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Residues in contact with MET 891 (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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887A LEU* 2.9 36.0 + - + +
888A LEU* 3.5 7.9 - - + +
890A GLU* 1.3 76.2 - - - +
892A MET* 1.3 63.7 + - - +
894A ASN 3.4 0.2 + - - -
895A GLY 3.2 4.0 + - - -
896A LEU* 3.1 51.7 + - + +
897A PHE* 3.5 31.1 - - + -
908A LEU* 3.8 22.4 - - + -
912A PHE* 3.5 29.6 - - + -
935A MET* 3.7 20.2 - - + -
938A CYS* 4.0 8.7 - - + -
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Residues in contact with MET 892 (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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876A VAL* 3.9 20.9 - - + -
880A ILE* 5.1 1.8 - - + -
888A LEU 3.0 10.4 + - - +
889A THR* 2.9 11.7 + - - +
891A MET* 1.3 76.8 - - - +
893A PHE* 1.3 65.1 + - + +
895A GLY* 3.3 13.3 + - - -
897A PHE* 3.9 12.5 + - + -
898A ASN* 4.6 2.9 - - - +
1007A MET* 3.7 28.3 - - + -
1010A ALA* 3.8 21.8 - - + -
1011A ALA* 4.3 15.7 - - - +
1014A ILE* 4.5 13.2 - - + -
1016A ASN* 5.5 0.7 - - - +
1019A LEU* 3.6 27.7 - - + +
1023A PHE* 4.3 10.1 - - + -
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Residues in contact with PHE 893 (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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872A MET* 5.7 1.1 - - + -
873A LYS* 3.7 60.6 - - + +
876A VAL* 4.0 29.4 - - + -
889A THR* 2.8 20.4 + - - +
890A GLU 4.0 2.7 - - - +
892A MET* 1.3 83.9 - - + +
894A ASN* 1.3 65.0 + - - +
895A GLY 3.3 0.6 + - - -
1014A ILE* 4.2 21.8 - - + -
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Residues in contact with ASN 894 (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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873A LYS* 5.9 0.2 - - - +
890A GLU* 2.9 39.0 + - - +
892A MET 3.3 0.2 - - - -
893A PHE* 1.3 81.6 + - - +
895A GLY* 1.3 61.0 + - - +
896A LEU* 3.6 20.1 + - + +
938A CYS* 3.8 6.9 - - - +
941A ARG* 2.8 27.6 + - - +
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Residues in contact with GLY 895 (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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891A MET 3.2 3.2 + - - -
892A MET 3.3 9.1 + - - -
893A PHE 3.3 1.2 + - - -
894A ASN* 1.3 78.5 - - - +
896A LEU* 1.3 64.5 + - - +
897A PHE 3.1 3.8 - - - -
898A ASN* 2.9 38.3 + - - +
899A ASP* 4.1 5.9 + - - +
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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