Contacts of the helix formed by residues 874 - 890 (chain A) in PDB entry 1TXD
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 GLY 874 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873A SER* 1.3 76.7 + - - +
875A PRO* 1.3 70.6 - - - +
877A GLU* 3.1 9.8 + - - +
878A GLU* 3.1 27.0 + - - +
966A HIS* 5.2 1.2 - - - -
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Residues in contact with PRO 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A THR 5.9 0.2 - - - +
873A SER 4.0 2.0 - - - +
874A GLY* 1.3 82.8 - - - +
876A GLY* 1.3 56.8 + - - +
878A GLU* 3.8 9.4 - - + +
879A LYS* 3.0 30.7 + - - +
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Residues in contact with GLY 876 (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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870A THR 3.7 11.3 + - - -
871A TRP 3.4 24.4 - - - +
873A SER 3.2 6.3 + - - -
874A GLY 3.2 1.2 - - - -
875A PRO* 1.3 76.2 - - - +
877A GLU* 1.3 62.6 + - - +
879A LYS* 3.6 4.5 + - - +
880A LEU* 3.2 22.9 + - - +
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Residues in contact with GLU 877 (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 PHE 3.4 14.4 - - - +
873A SER* 3.4 12.5 + - - +
874A GLY 3.1 12.3 + - - +
876A GLY* 1.3 72.9 - - - +
878A GLU* 1.3 64.7 + - + +
880A LEU* 3.3 1.0 + - - +
881A LYS* 2.8 48.6 + - + +
966A HIS* 2.8 32.2 + - - -
969A GLN* 3.4 31.9 + - - +
970A ILE* 3.6 28.0 + - + +
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Residues in contact with GLU 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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874A GLY 3.1 18.1 + - - +
875A PRO* 3.4 8.5 + - + +
876A GLY 3.4 0.2 - - - -
877A GLU* 1.3 79.9 - - + +
879A LYS* 1.3 64.3 + - - +
881A LYS* 4.1 18.8 + - - -
882A HIS* 3.1 50.9 + - + +
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Residues in contact with LYS 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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837A ASP* 5.7 3.8 - - - +
840A GLN* 6.6 0.4 - - - -
841A LEU* 3.8 31.2 - - + +
875A PRO 3.0 18.6 + - - +
876A GLY* 4.0 5.2 - - - +
878A GLU* 1.3 77.3 - - - +
880A LEU* 1.3 61.8 + - - +
882A HIS* 4.3 1.6 - - - +
883A ALA* 3.1 25.5 + - + +
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Residues in contact with LEU 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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838A ILE* 6.2 0.4 - - + -
841A LEU* 3.6 33.2 - - + -
842A HIS* 4.4 9.6 - - + +
845A LEU* 5.4 2.2 - - + -
871A TRP 5.1 1.6 - - - +
872A PHE* 3.8 34.8 - - + -
876A GLY 3.2 17.8 + - - +
877A GLU 4.0 1.6 - - - +
879A LYS* 1.3 75.0 - - - +
881A LYS* 1.3 58.6 + - - +
883A ALA 3.3 0.3 + - - -
884A ALA* 2.9 38.2 + - + +
933A GLN* 4.7 0.7 - - - +
937A LEU* 4.2 19.1 - - + -
940A TYR* 4.3 15.0 - - + -
970A ILE* 4.1 23.3 - - + -
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Residues in contact with LYS 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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877A GLU* 2.8 44.2 + - + +
878A GLU* 4.1 22.6 + - - -
880A LEU* 1.3 75.4 - - - +
882A HIS* 1.3 69.4 + - + +
885A ALA* 2.9 32.2 + - - +
969A GLN* 5.1 6.8 + - - +
970A ILE* 3.9 28.0 - - + +
973A PHE* 3.5 49.7 - - + +
974A VAL* 3.8 4.8 - - - +
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Residues in contact with HIS 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 GLU* 3.1 46.5 + - + +
879A LYS* 4.3 1.6 - - - +
881A LYS* 1.3 90.6 - - + +
883A ALA* 1.3 62.6 + - - +
885A ALA* 3.9 5.1 - - - +
886A THR* 3.2 27.2 + - - -
973A PHE* 4.1 20.9 - + - -
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Residues in contact with ALA 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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834A ASN* 2.9 32.3 + - - +
837A ASP* 4.9 11.4 - - + -
838A ILE* 3.8 15.4 - - + +
841A LEU* 4.2 12.6 - - + -
879A LYS* 3.1 20.4 + - + +
880A LEU 4.0 1.6 - - - +
882A HIS* 1.3 76.8 - - - +
884A ALA* 1.3 66.2 + - - +
885A ALA 3.3 0.3 + - - -
886A THR 3.3 1.0 + - - -
887A PHE 3.0 9.7 + - - -
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Residues in contact with ALA 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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838A ILE* 4.1 9.5 - - - +
880A LEU* 2.9 19.1 + - + +
883A ALA* 1.3 77.4 - - - +
885A ALA* 1.3 58.7 + - - +
887A PHE* 4.6 0.7 - - - +
888A CYS* 2.8 41.6 + - - +
933A GLN* 4.2 9.0 - - - +
937A LEU* 3.5 40.8 - - + -
974A VAL* 4.0 3.6 - - + -
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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 LYS 2.9 21.7 + - - +
882A HIS* 3.9 4.3 - - - +
884A ALA* 1.3 76.7 - - - +
886A THR* 1.3 53.3 + - - +
889A SER* 2.5 42.1 + - - -
973A PHE* 3.7 24.9 - - + -
974A VAL* 3.8 13.0 - - + +
977A ALA* 4.2 15.0 - - + -
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Residues in contact with THR 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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833A SER* 4.4 7.8 + - - -
834A ASN* 3.6 26.7 - - + +
882A HIS 3.2 16.7 + - - -
885A ALA* 1.3 76.1 - - - +
887A PHE* 1.3 68.5 + - - +
889A SER* 3.5 4.7 + - - -
890A ASN* 3.3 23.3 + - + +
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Residues in contact with PHE 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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806A LEU* 5.7 0.4 - - + -
809A LEU* 4.5 12.3 - - + -
831A ILE 5.3 2.5 - - - -
832A PHE* 3.9 18.6 - + - -
833A SER* 3.6 15.0 - - - -
834A ASN* 3.1 20.4 + - - +
835A LEU* 4.0 12.6 - - + -
838A ILE* 3.7 28.3 - - + -
883A ALA 3.0 14.5 + - - +
884A ALA* 4.2 2.5 - - - +
886A THR* 1.3 76.6 - - - +
888A CYS* 1.3 64.4 + - - +
890A ASN* 3.3 13.0 + - - +
891A GLN* 3.5 7.4 + - + +
930A ILE* 3.5 48.2 - - + -
933A GLN* 3.6 25.8 - - + -
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Residues in contact with CYS 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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884A ALA* 2.8 32.7 + - - +
887A PHE* 1.3 77.9 - - - +
889A SER* 1.3 59.3 + - - +
891A GLN* 3.3 24.0 - - - +
892A PRO* 4.2 1.9 - - - +
933A GLN* 3.7 19.5 - - - -
934A MET* 3.6 40.6 - - + -
937A LEU* 5.0 1.1 - - - -
974A VAL* 3.9 20.4 - - + -
978A VAL* 3.6 16.8 - - + +
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Residues in contact with SER 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 2.5 24.5 + - - -
886A THR* 3.5 6.8 + - - -
888A CYS* 1.3 76.7 - - - +
890A ASN* 1.3 58.4 + - - +
891A GLN 3.3 0.2 - - - -
892A PRO* 3.3 12.6 - - - +
893A PHE* 4.0 2.9 - - - -
977A ALA* 3.5 33.1 - - - +
978A VAL* 3.9 10.0 - - - +
981A ALA* 3.0 27.6 - - - +
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Residues in contact with ASN 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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829A ARG 3.9 1.9 + - - -
830A LYS* 3.0 33.5 + - - +
831A ILE 4.3 1.6 + - - -
833A SER* 3.6 27.7 + - - +
886A THR 3.3 15.9 + - - +
887A PHE 3.4 5.8 - - - +
888A CYS 3.2 0.2 - - - -
889A SER* 1.3 82.1 + - - +
891A GLN* 1.3 50.9 + - - +
892A PRO* 3.4 1.6 - - - -
893A PHE* 2.9 27.7 + - - +
894A ALA* 2.8 36.5 + - - +
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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