Contacts of the helix formed by residues 877 - 892 (chain A) in PDB entry 2XT6
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 877 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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866A LYS* 5.5 0.5 - - - +
867A ARG* 5.2 2.1 + - - -
870A MET* 3.4 23.6 - - + +
875A ARG 3.5 3.8 + - - -
876A ILE* 1.4 78.9 - - - +
878A TRP* 1.3 59.0 + - - +
879A ALA* 4.1 9.6 - - - +
880A PHE* 2.9 29.8 + - - +
881A ALA* 3.0 21.3 + - - +
1045A PRO* 3.6 4.5 - - - -
1073A LEU 4.2 15.6 - - - +
1078A ALA 4.7 0.9 - - - -
1079A VAL* 4.4 12.3 - - + -
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Residues in contact with TRP 878 (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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877A ASP* 1.3 71.4 - - - +
879A ALA* 1.3 67.6 + - - +
881A ALA* 3.1 4.4 + - - +
882A GLU* 3.1 24.3 + - - +
1042A PRO* 3.4 38.1 - - + -
1044A THR 3.7 27.4 - - - -
1045A PRO* 3.4 18.1 - - + +
1048A TYR* 3.3 54.1 - + + -
1067A PHE 5.0 0.4 - - - -
1068A THR* 4.3 12.6 - - + -
1069A PRO* 3.3 25.2 - - + +
1072A MET* 3.6 27.8 - - + +
1073A LEU* 3.6 37.9 + - + -
1078A ALA 4.7 1.5 + - - +
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Residues in contact with ALA 879 (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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867A ARG* 3.8 5.2 - - - +
877A ASP* 3.5 9.9 + - - +
878A TRP* 1.3 84.1 - - - +
880A PHE* 1.4 59.9 + - - +
882A GLU* 3.5 10.4 - - - +
883A LEU* 3.4 24.1 + - - +
910A GLN* 3.3 49.8 - - + +
911A ARG* 4.9 2.8 - - - +
1073A LEU* 4.3 5.5 + - + +
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Residues in contact with PHE 880 (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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843A ILE* 4.1 12.8 - - + -
844A GLY* 4.0 6.1 - - - -
847A HIS* 4.2 9.6 - + - -
867A ARG* 3.2 61.4 - - + +
870A MET* 3.7 22.2 - - + -
871A ALA* 3.7 24.7 - - + -
876A ILE* 3.7 13.7 - - + -
877A ASP* 2.9 21.8 + - - +
879A ALA* 1.4 71.0 - - - +
881A ALA* 1.4 55.7 + - - +
882A GLU 3.1 1.8 - - - -
883A LEU* 3.1 7.2 + - + +
884A LEU* 2.7 63.8 + - + +
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Residues in contact with ALA 881 (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 ILE* 3.8 6.4 - - - +
877A ASP 3.0 14.6 + - - +
878A TRP 3.4 9.0 - - - +
880A PHE* 1.4 74.5 - - - +
882A GLU* 1.4 55.3 + - - +
884A LEU* 3.5 9.0 + - - +
885A ALA* 3.1 23.9 + - - +
1045A PRO* 3.3 37.5 - - + +
1048A TYR* 5.2 1.3 - - + -
1049A PHE* 3.5 11.9 - - - +
1085A PHE* 4.0 11.0 - - + -
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Residues in contact with GLU 882 (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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878A TRP* 3.1 13.5 + - + +
879A ALA* 3.5 13.1 - - - +
880A PHE 3.1 0.2 - - - -
881A ALA* 1.4 75.9 - - - +
883A LEU* 1.4 59.7 + - - +
885A ALA* 3.2 4.9 + - - +
886A LEU* 3.0 40.8 + - + +
898A LEU* 4.6 4.5 - - - +
911A ARG* 2.8 47.3 + - - +
972A LEU* 5.9 1.3 - - + -
1008A LEU* 3.7 8.1 - - - +
1048A TYR* 2.6 48.1 + - + +
1052A LEU* 4.0 10.5 - - + -
1068A THR* 5.4 0.9 - - - +
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Residues in contact with LEU 883 (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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843A ILE* 4.0 3.2 - - - +
847A HIS* 4.3 8.5 - - + +
867A ARG* 3.3 43.5 - - - +
879A ALA 3.4 9.8 + - - +
880A PHE* 3.1 11.4 + - + +
882A GLU* 1.4 72.9 - - + +
884A LEU* 1.4 57.0 + - - +
886A LEU* 4.5 7.2 - - + -
887A GLY* 2.7 32.9 + - - -
911A ARG* 3.4 32.5 - - + +
912A HIS 5.3 1.3 - - - +
913A ALA* 4.6 13.7 - - + -
927A LEU* 3.4 34.9 - - + +
943A PHE* 4.8 5.2 - - + -
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Residues in contact with LEU 884 (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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840A LEU* 3.8 35.9 - - + +
843A ILE* 3.4 29.3 - - + +
876A ILE* 3.9 36.3 - - + -
880A PHE* 2.7 48.8 + - + +
881A ALA* 3.5 5.4 - - - +
883A LEU* 1.4 72.4 - - - +
885A ALA* 1.4 56.3 + - - +
888A SER* 2.9 32.1 + - - -
1049A PHE* 3.7 13.0 - - + -
1085A PHE* 4.1 8.3 - - + -
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Residues in contact with ALA 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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881A ALA 3.1 10.6 + - - +
882A GLU 3.2 7.6 + - - +
884A LEU* 1.4 75.2 - - - +
886A LEU* 1.3 60.1 + - - +
888A SER* 2.8 19.1 + - - -
889A LEU* 3.2 18.7 + - - +
1049A PHE* 3.4 37.8 - - + +
1052A LEU* 4.0 23.3 - - + -
1053A ARG* 3.8 4.3 - - + +
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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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882A GLU* 3.0 30.9 + - + +
883A LEU* 5.0 4.3 - - + -
885A ALA* 1.3 74.4 - - - +
887A GLY* 1.3 57.1 + - - +
889A LEU* 3.2 10.0 + - + +
890A ILE* 3.0 35.7 + - + +
896A VAL* 3.9 24.0 - - + +
898A LEU* 4.0 27.8 - - + -
927A LEU* 4.0 11.7 - - + -
943A PHE* 4.1 7.6 - - + -
970A MET* 4.4 16.2 - - + -
972A LEU* 3.8 30.3 - - + -
1052A LEU* 4.5 7.6 - - + -
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Residues in contact with GLY 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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843A ILE* 3.9 7.4 - - - -
883A LEU 2.7 24.0 + - - -
884A LEU 4.0 0.4 - - - -
886A LEU* 1.3 73.8 - - - +
888A SER* 1.3 54.6 + - - +
890A ILE* 3.4 7.2 + - - +
891A ALA* 3.0 27.7 + - - +
927A LEU* 3.6 11.8 - - - +
930A LEU* 3.8 19.5 - - - +
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Residues in contact with SER 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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835A VAL* 4.0 10.1 - - - -
839A MET* 3.8 33.8 - - - +
843A ILE* 3.6 1.0 - - - +
884A LEU 2.9 16.4 + - - -
885A ALA 2.8 20.4 + - - -
887A GLY* 1.3 71.3 - - - +
889A LEU* 1.4 59.4 + - - +
891A ALA* 3.4 2.4 + - - +
892A GLU* 3.0 33.8 + - - +
1049A PHE* 4.2 1.5 - - - -
1053A ARG* 3.3 25.5 - - - -
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Residues in contact with LEU 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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885A ALA 3.2 22.3 + - - +
886A LEU* 3.2 11.6 + - + +
888A SER* 1.4 73.7 + - - +
890A ILE* 1.4 64.4 + - - +
892A GLU* 3.1 15.3 + - + +
893A GLY 3.3 0.7 + - - -
894A LYS* 3.0 44.7 + - + +
896A VAL* 4.2 4.0 - - + -
970A MET* 3.9 38.6 - - + -
1052A LEU 4.3 11.0 - - - +
1053A ARG* 3.7 25.6 - - - +
1056A GLY* 4.7 1.6 - - - -
1057A LYS* 3.8 25.6 - - + -
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Residues in contact with ILE 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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886A LEU 3.0 28.1 + - - +
887A GLY* 3.6 10.5 - - - +
889A LEU* 1.4 73.5 - - - +
891A ALA* 1.4 56.9 + - - +
893A GLY 2.9 16.5 + - - -
894A LYS 3.4 8.5 - - - +
896A VAL* 3.8 10.1 - - + -
927A LEU* 4.1 16.6 - - + +
930A LEU* 3.9 2.2 - - + -
931A ALA* 3.7 31.0 - - + +
939A THR* 3.0 14.2 + - - -
941A GLY* 3.4 4.3 - - - -
942A LYS 3.8 31.9 - - - +
943A PHE* 3.6 36.1 - - + +
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Residues in contact with ALA 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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839A MET* 3.8 28.3 - - + -
842A ARG* 4.5 6.1 - - - +
887A GLY 3.0 16.9 + - - +
888A SER 3.5 6.5 - - - +
889A LEU 3.3 0.2 - - - -
890A ILE* 1.4 74.7 - - - +
892A GLU* 1.3 57.5 + - - +
893A GLY 3.2 3.2 + - - -
930A LEU* 3.4 27.1 + - + +
933A ASN* 4.3 4.5 - - - +
939A THR* 3.4 17.8 - - + +
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Residues in contact with GLU 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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835A VAL* 4.4 6.8 - - - +
839A MET* 5.0 8.8 - - + +
888A SER* 3.0 14.8 + - - +
889A LEU* 3.1 11.4 + - + +
891A ALA* 1.3 73.5 - - - +
893A GLY* 1.3 57.8 + - - +
894A LYS* 3.6 1.3 + - + -
939A THR* 4.8 0.7 - - - -
1053A ARG* 2.9 43.2 + - - -
1057A LYS* 2.9 25.0 + - - +
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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