Contacts of the helix formed by residues 862 - 879 (chain A) in PDB entry 3IAY
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 862 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A LYS* 2.7 24.8 + - + +
857A ILE* 4.2 1.2 + - - +
860A GLU* 3.7 20.0 + - + +
861A ARG* 1.3 75.0 - - - +
863A VAL* 1.3 60.8 + - - +
864A ASP* 3.6 10.0 + - - +
865A GLY* 3.0 26.1 + - - -
866A ALA* 3.0 19.8 + - - +
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Residues in contact with VAL 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A ILE* 4.3 28.7 - - + -
861A ARG 3.9 2.6 + - - -
862A ASN* 1.3 74.2 - - - +
864A ASP* 1.3 59.8 + - - +
866A ALA* 3.1 3.5 + - - +
867A LEU* 2.8 39.3 + - + +
970A VAL* 6.4 0.7 - - + -
973A ILE* 3.8 23.6 - - + -
974A ILE* 3.7 29.6 - - + -
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Residues in contact with ASP 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A ASN* 3.7 8.0 - - - +
863A VAL* 1.3 81.5 - - - +
865A GLY* 1.3 57.9 + - - +
867A LEU* 3.2 12.1 + - - +
868A ALA* 2.9 28.9 + - - +
871A ARG* 4.8 2.9 + - - +
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Residues in contact with GLY 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A LYS* 4.0 11.5 + - - +
862A ASN* 3.0 29.5 + - - -
864A ASP* 1.3 72.5 - - - +
866A ALA* 1.3 64.9 + - - +
868A ALA* 3.4 7.6 + - - +
869A PHE* 3.0 23.6 + - - +
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Residues in contact with ALA 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A VAL* 4.1 15.8 - - + +
856A LYS* 3.8 20.3 - - + +
857A ILE* 3.9 28.3 - - + -
862A ASN 3.0 13.3 + - - +
863A VAL* 3.1 8.7 + - + +
865A GLY* 1.3 76.0 - - - +
867A LEU* 1.3 60.3 + - + +
869A PHE* 3.2 4.2 + - - +
870A VAL* 3.0 33.2 + - - +
970A VAL* 5.7 0.4 - - + -
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Residues in contact with LEU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A VAL* 2.8 35.2 + - + +
864A ASP* 3.2 10.1 + - - +
866A ALA* 1.3 74.2 - - + +
868A ALA* 1.3 66.7 + - - +
870A VAL* 3.2 5.9 + - + +
871A ARG* 2.9 59.6 + - - +
970A VAL* 4.6 14.8 - - + -
974A ILE* 4.1 18.2 - - + -
978A GLN* 4.0 19.3 - - - +
982A MET* 3.7 29.1 - - + +
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Residues in contact with ALA 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A ASP 2.9 16.3 + - - +
865A GLY* 3.7 7.4 - - - +
867A LEU* 1.3 76.4 - - - +
869A PHE* 1.3 59.1 + - - +
871A ARG* 3.5 16.7 + - - +
872A GLU* 3.0 30.1 + - - +
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Residues in contact with PHE 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A ILE* 5.3 2.2 - - + -
849A VAL* 3.8 43.7 - - + -
852A LYS* 3.7 40.4 - - + -
853A VAL* 4.3 11.2 - - + -
856A LYS* 4.1 17.5 - - - -
865A GLY 3.0 17.7 + - - +
866A ALA 3.5 3.1 - - - +
867A LEU 3.2 0.2 - - - -
868A ALA* 1.3 78.7 - - - +
870A VAL* 1.3 57.3 + - - +
872A GLU* 3.3 10.0 + - + +
873A THR* 2.9 43.4 + - - -
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Residues in contact with VAL 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A VAL* 4.6 6.3 - - + -
853A VAL* 3.6 25.8 - - + -
866A ALA 3.0 20.5 + - - +
867A LEU* 3.2 9.6 + - + +
869A PHE* 1.3 76.4 - - - +
871A ARG* 1.3 57.4 + - - +
873A THR* 3.1 8.6 + - - -
874A ILE* 2.9 41.5 + - + +
962A LEU* 5.1 3.6 - - + -
966A ILE* 4.1 19.7 - - + -
970A VAL* 5.5 0.9 - - + -
982A MET* 3.9 22.4 - - + -
983A PHE* 4.0 16.6 - - + -
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Residues in contact with ARG 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A ASP* 4.8 2.8 + - - +
867A LEU* 2.9 54.6 + - - +
868A ALA* 3.8 16.0 - - - +
870A VAL* 1.3 75.5 - - - +
872A GLU* 1.3 63.0 + - - +
874A ILE* 3.3 11.4 + - + +
875A ASN* 3.0 22.7 + - - +
978A GLN* 4.7 7.3 - - - +
982A MET* 4.2 24.0 - - + +
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Residues in contact with GLU 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A ALA 3.0 17.9 + - - +
869A PHE* 3.6 11.0 - - + +
871A ARG* 1.3 76.9 - - - +
873A THR* 1.3 58.2 + - - +
875A ASN* 3.2 16.7 + - - +
876A ASP* 2.9 50.1 + - - +
881A ARG* 4.4 8.3 + - - +
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Residues in contact with THR 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A LEU* 3.9 18.6 - - + -
849A VAL* 3.8 32.5 - - + +
869A PHE* 2.9 29.8 + - - -
870A VAL* 3.3 11.8 - - - -
872A GLU* 1.3 73.3 - - - +
874A ILE* 1.3 67.4 + - - +
876A ASP* 3.1 10.5 + - + +
877A ILE* 3.0 23.6 + - + +
882A VAL* 5.9 0.2 - - + -
962A LEU* 4.0 17.7 - - + -
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Residues in contact with ILE 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A VAL* 2.9 28.1 + - + +
871A ARG* 3.6 11.9 - - + +
873A THR* 1.3 76.5 - - - +
875A ASN* 1.3 63.5 + - - +
877A ILE* 3.3 6.3 + - - +
878A LEU* 3.1 30.2 + - + +
958A LEU* 3.8 24.9 - - + -
962A LEU* 4.3 5.6 - - + -
982A MET* 3.6 28.3 - - + +
983A PHE* 3.7 26.0 - - + -
985A VAL 3.6 24.5 - - - +
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Residues in contact with ASN 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ARG 3.0 13.6 + - - +
872A GLU* 3.4 21.4 + - - +
874A ILE* 1.3 79.1 - - - +
876A ASP* 1.3 60.4 + - - +
878A LEU* 3.4 3.9 + - - +
879A HIS* 2.9 64.0 + - - +
881A ARG* 5.6 3.6 - - - +
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Residues in contact with ASP 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A GLU* 2.9 30.6 + - - +
873A THR* 3.1 12.0 + - + +
875A ASN* 1.3 76.0 + - - +
877A ILE* 1.3 65.7 + - - +
879A HIS 3.3 0.5 + - - -
880A ASN 3.1 4.0 + - - -
881A ARG* 2.5 82.9 + - + +
882A VAL* 3.8 15.7 - - + -
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Residues in contact with ILE 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A LEU* 3.8 24.9 - - + -
873A THR* 3.0 18.5 + - + +
874A ILE* 3.6 6.7 - - - +
876A ASP* 1.3 76.4 - - - +
878A LEU* 1.3 64.8 + - + +
880A ASN* 3.1 12.3 + - - -
882A VAL* 3.9 18.8 - - + -
887A LEU* 5.8 1.3 - - + -
954A SER* 3.2 45.7 + - - +
957A TYR* 4.4 5.2 - - + -
958A LEU* 4.1 27.1 - - + +
962A LEU* 3.8 29.8 - - + -
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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
----------------------------------------------------------
874A ILE* 3.1 24.0 + - + +
875A ASN* 4.0 4.9 - - - +
877A ILE* 1.3 80.9 - - + +
879A HIS* 1.3 72.5 + - + +
880A ASN* 3.3 1.6 + - - +
954A SER* 4.9 6.3 - - - -
955A ARG* 3.8 58.1 - - + +
958A LEU* 4.0 14.1 - - + -
985A VAL* 4.0 26.9 - - + +
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Residues in contact with HIS 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ASN* 2.9 48.6 + - - +
876A ASP 4.5 0.4 - - - +
877A ILE 3.2 0.2 - - - -
878A LEU* 1.3 85.5 - - + +
880A ASN* 1.3 71.0 + - - +
881A ARG* 3.2 21.7 + - - +
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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
------------------------------------------------------------
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