Contacts of the helix formed by residues 873 - 887 (chain A) in PDB entry 5Z58
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 ASN 873 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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869A GLN* 2.9 38.2 + - - +
870A ALA* 3.9 4.5 - - - +
871A TYR 3.4 0.2 - - - -
872A ASP* 1.3 81.4 - - + +
874A PRO* 1.3 66.0 - - - +
875A HIS 3.4 2.0 - - - -
876A GLU* 2.8 46.5 + - + +
877A ALA* 3.4 4.5 + - - +
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Residues in contact with PRO 874 (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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1041 PHE* 4.6 21.3 - - + -
1081 ARG* 5.5 8.3 - - + -
836A THR* 5.2 7.0 - - + -
839A LEU* 4.1 16.3 - - + +
870A ALA 3.5 13.2 - - - +
871A TYR* 3.5 15.0 - - - +
872A ASP 3.4 8.3 - - - +
873A ASN* 1.3 87.2 - - - +
875A HIS* 1.3 69.7 + - + +
877A ALA* 2.8 21.3 + - + +
878A LEU* 2.9 19.4 + - + +
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Residues in contact with HIS 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4661 PHE* 3.9 10.7 - - + -
4681 LYS* 5.7 1.6 - - + -
4691 PRO* 4.1 37.3 - - + +
830A LEU* 6.1 2.9 - - + -
835A ASP* 4.9 12.6 + - - -
836A THR* 5.0 16.1 - - + +
873A ASN 3.4 0.6 - - - -
874A PRO* 1.3 85.0 - - + +
876A GLU* 1.3 62.7 + - - +
878A LEU* 3.3 11.0 + - + +
879A SER* 2.9 25.5 + - - -
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Residues in contact with GLU 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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4661 PHE* 3.7 38.3 - - + +
869A GLN* 4.0 15.5 + - - -
873A ASN* 2.8 44.4 + - + +
874A PRO 3.1 0.6 - - - -
875A HIS* 1.3 79.2 - - - +
877A ALA* 1.3 63.3 + - - +
879A SER* 3.2 2.1 + - - -
880A ARG* 2.9 34.4 + - + +
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Residues in contact with ALA 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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839A LEU* 4.3 14.6 - - + -
870A ALA* 4.3 19.7 - - + -
873A ASN* 3.4 5.2 + - - +
874A PRO* 2.8 16.8 + - + +
876A GLU* 1.3 76.1 - - - +
878A LEU* 1.3 56.1 + - - +
880A ARG* 3.3 26.7 + - - +
881A ILE* 2.9 41.2 + - + +
917A ILE* 5.6 1.1 - - + -
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Residues in contact with LEU 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A ASP* 3.4 42.6 - - + +
836A THR* 4.4 6.5 - - + +
839A LEU* 3.7 35.7 - - + -
874A PRO* 2.9 17.6 + - + +
875A HIS* 3.8 15.7 - - + +
877A ALA* 1.3 77.1 - - - +
879A SER* 1.3 57.9 + - - +
881A ILE* 3.2 10.5 + - + +
882A LYS* 2.9 46.4 + - - +
921A TYR* 4.5 22.2 - - + +
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Residues in contact with SER 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4581 ASP* 4.9 9.7 - - - +
4661 PHE* 3.4 40.2 - - - -
830A LEU* 5.4 12.4 - - - +
875A HIS 2.9 8.6 + - - -
876A GLU 3.7 0.9 - - - -
878A LEU* 1.3 72.5 - - - +
880A ARG* 1.3 67.1 + - - +
882A LYS* 3.3 8.3 + - - +
883A ARG* 2.9 24.5 + - - +
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Residues in contact with ARG 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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866A LEU* 4.4 12.3 - - - +
869A GLN* 5.4 4.9 - - - +
870A ALA* 5.8 1.4 - - - +
876A GLU* 2.9 25.9 + - + +
877A ALA* 3.5 33.3 + - - +
879A SER* 1.3 75.6 - - - +
881A ILE* 1.3 67.8 + - - +
883A ARG* 3.1 37.4 + - - +
884A HIS* 2.9 45.0 + - - +
914A LEU* 3.9 29.8 + - - +
917A ILE* 4.7 15.4 - - - +
918A THR* 5.4 1.8 + - - -
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Residues in contact with ILE 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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839A LEU* 4.6 4.9 - - + -
877A ALA* 2.9 27.9 + - + +
878A LEU* 3.5 15.0 - - + +
879A SER 3.2 0.2 - - - -
880A ARG* 1.3 81.5 - - - +
882A LYS* 1.3 63.8 + - - +
884A HIS* 2.9 12.2 + - - +
885A LEU* 2.9 30.7 + - + +
917A ILE* 4.0 24.2 - - + -
918A THR* 3.8 34.1 - - + +
921A TYR* 3.9 39.0 - - + -
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Residues in contact with LYS 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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827A PHE* 3.8 22.7 - - + -
828A PRO* 3.6 27.8 - - + +
829A PRO 2.3 36.1 + - - -
830A LEU* 3.2 22.3 + - + +
832A TYR* 5.1 2.6 - - - +
835A ASP* 5.2 5.9 + - - +
878A LEU* 2.9 32.3 + - - +
879A SER* 3.9 6.5 - - - +
881A ILE* 1.3 76.7 - - + +
883A ARG* 1.3 56.7 + - - +
885A LEU* 3.7 9.2 - - + +
886A LEU* 2.9 38.7 + - + +
921A TYR* 4.5 12.8 - - + -
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Residues in contact with ARG 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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879A SER* 2.9 14.5 + - - +
880A ARG* 3.3 41.0 + - - +
881A ILE 3.0 0.2 - - - -
882A LYS* 1.3 74.7 - - - +
884A HIS* 1.3 72.4 + - - +
886A LEU* 3.2 7.0 + - - -
887A THR* 2.8 40.1 + - + +
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Residues in contact with HIS 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ARG* 2.9 54.2 + - + +
881A ILE* 2.9 6.3 + - - +
883A ARG* 1.3 84.6 + - - +
885A LEU* 1.3 58.2 + - - +
887A THR* 2.8 23.8 + - - -
888A GLN* 3.0 44.5 + - + +
891A PHE* 6.1 0.6 - - + -
914A LEU* 5.5 12.2 - - + +
915A GLU* 6.3 3.1 - - + +
918A THR* 3.9 30.0 + - + -
1008A TYR* 4.2 9.5 - - + +
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Residues in contact with LEU 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A PHE* 4.0 14.8 - - + -
828A PRO* 5.6 3.8 - - + -
881A ILE* 2.9 39.0 + - + +
882A LYS* 3.8 10.8 - - + +
883A ARG 3.3 0.2 - - - -
884A HIS* 1.3 72.2 - - - +
886A LEU* 1.3 62.5 + - - +
887A THR 3.7 0.2 + - - -
889A ARG* 3.7 18.0 + - - -
918A THR* 4.0 7.4 - - + -
921A TYR* 5.0 11.4 - - + -
922A LEU* 4.4 20.0 - - + -
1004A ASN* 4.0 12.6 - - - +
1005A ILE* 4.3 17.5 - - + -
1008A TYR* 3.5 46.5 - - + +
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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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4541 LYS* 5.1 16.8 - - + +
4561 VAL* 5.3 13.7 - - + -
827A PHE* 3.7 36.1 - - + -
882A LYS* 2.9 23.8 + - + +
883A ARG* 3.8 7.2 - - - +
884A HIS 3.1 0.4 - - - -
885A LEU* 1.3 80.9 - - - +
887A THR* 1.3 65.2 + - + +
889A ARG* 3.5 13.0 + - - -
1004A ASN* 3.9 30.0 - - - +
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Residues in contact with THR 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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883A ARG* 2.8 31.4 + - + +
884A HIS* 2.8 8.3 + - - -
886A LEU* 1.3 88.1 - - + +
888A GLN* 1.3 78.1 + - - +
889A ARG* 3.0 24.3 + - - +
97L LEU* 5.2 2.5 - - - +
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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