Contacts of the helix formed by residues 1003 - 1022 (chain A) in PDB entry 4EZJ
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 SER1003 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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995A MET 2.9 23.4 + - - -
996A GLY* 3.3 29.4 - - - -
997A THR* 3.5 2.6 + - - -
1002A THR* 1.3 72.5 + - - +
1004A PRO* 1.4 74.6 - - - +
1005A HIS 3.3 0.2 - - - -
1006A PHE* 3.4 15.4 - - - +
1007A GLN* 3.1 29.7 + - - +
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Residues in contact with PRO1004 (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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995A MET 5.3 0.2 - - - +
1003A SER* 1.4 88.4 - - - +
1005A HIS* 1.4 69.5 + - + +
1007A GLN* 3.7 12.2 - - + +
1008A LYS* 3.2 24.1 + - - +
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Residues in contact with HIS1005 (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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922A GLN* 5.3 5.7 + - - -
925A VAL* 3.9 28.0 - - + +
926A GLU* 6.3 1.6 - - - -
929A VAL* 3.8 14.9 - - + +
994A VAL 4.9 2.5 - - - -
995A MET* 3.2 26.8 + - - +
1003A SER 3.3 0.6 - - - -
1004A PRO* 1.4 85.1 - - + +
1006A PHE* 1.4 59.1 + - - +
1007A GLN 3.3 1.6 - - - -
1008A LYS* 3.2 38.3 - - - +
1009A PHE* 2.9 27.2 + - - +
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Residues in contact with PHE1006 (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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992A LEU* 3.6 33.2 - - + -
995A MET* 3.7 8.8 + - + -
997A THR* 3.9 11.0 - - + -
1002A THR* 3.8 23.6 - - - -
1003A SER* 3.4 23.1 + - - +
1005A HIS* 1.4 73.8 - - - +
1007A GLN* 1.4 59.6 + - - +
1009A PHE* 3.4 16.6 - + - +
1010A GLN* 3.0 67.9 + - + +
1072A ILE* 4.0 20.2 - - + -
1073A GLU* 4.3 0.4 - - - -
1076A ARG* 3.6 36.6 - - - -
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Residues in contact with GLN1007 (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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1002A THR* 3.5 30.4 + - - +
1003A SER 3.1 22.4 + - - +
1004A PRO* 3.7 10.1 - - + +
1006A PHE* 1.4 74.4 - - - +
1008A LYS* 1.4 65.2 + - - +
1010A GLN* 3.6 13.8 + - - +
1011A ASP* 3.4 21.1 + - - +
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Residues in contact with LYS1008 (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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926A GLU* 3.9 33.9 + - + +
929A VAL* 4.3 15.9 - - + -
930A TYR* 5.5 5.2 - - + +
1004A PRO 3.2 12.3 + - - +
1005A HIS* 3.2 43.0 - - - +
1007A GLN* 1.4 77.7 - - - +
1009A PHE* 1.4 60.9 + - - +
1011A ASP* 3.3 6.3 + - - +
1012A ILE* 3.1 36.2 + - + +
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Residues in contact with PHE1009 (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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929A VAL* 3.8 28.0 - - + +
932A CYS* 3.8 14.4 - - - -
933A ALA* 3.7 26.6 - - + +
936A CYS* 4.2 7.4 - - - -
987A LEU* 3.5 39.3 - - + -
995A MET* 3.7 18.4 - - + -
1005A HIS 2.9 17.8 + - - +
1006A PHE* 3.4 24.0 - + - +
1008A LYS* 1.4 72.6 - - - +
1010A GLN* 1.4 66.3 + - - +
1012A ILE* 2.9 26.0 + - - +
1013A CYS* 3.0 29.9 + - - +
1072A ILE* 4.2 13.7 - - + -
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Residues in contact with GLN1010 (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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1002A THR* 4.8 0.9 + - - -
1006A PHE* 3.0 63.6 + - + +
1007A GLN* 3.6 17.3 - - - +
1008A LYS 3.6 0.2 - - - -
1009A PHE* 1.4 75.9 - - + +
1011A ASP* 1.3 56.1 + - - +
1013A CYS* 3.4 3.6 - - - +
1014A VAL* 3.0 33.7 + - - +
1069A LEU* 3.8 24.7 - - + +
1072A ILE* 3.9 20.4 - - + +
1073A GLU* 4.3 9.3 + - - -
1076A ARG* 5.4 0.2 - - - +
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Residues in contact with ASP1011 (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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1007A GLN 3.4 10.2 + - - +
1008A LYS* 3.3 10.9 + - - +
1009A PHE 3.2 1.0 - - - -
1010A GLN* 1.3 75.1 - - - +
1012A ILE* 1.4 62.0 + - + +
1014A VAL* 4.0 5.0 - - - +
1015A LYS* 2.9 60.3 + - - +
1065A LYS* 4.6 13.4 + - - +
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Residues in contact with ILE1012 (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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860A LEU* 5.4 7.6 - - + +
861A ASP 6.1 0.2 - - - -
862A LEU* 3.5 28.7 - - + -
929A VAL* 3.8 26.5 - - + -
930A TYR* 3.7 44.9 - - + +
933A ALA* 4.2 6.1 - - + -
1008A LYS* 3.1 29.1 + - + +
1009A PHE* 2.9 6.4 + - - +
1011A ASP* 1.4 73.5 - - + +
1013A CYS* 1.4 52.6 + - - +
1015A LYS* 3.3 7.6 + - + +
1016A ALA* 2.8 38.1 + - - +
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Residues in contact with CYS1013 (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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933A ALA* 3.8 27.3 - - - +
936A CYS* 4.3 2.7 - - - -
937A VAL* 3.6 10.2 - - - +
1009A PHE* 3.0 39.8 + - - +
1010A GLN* 3.4 12.6 - - - +
1012A ILE* 1.4 73.9 - - - +
1014A VAL* 1.3 52.0 + - - +
1016A ALA* 3.3 3.8 + - - +
1017A TYR* 2.8 36.8 + - - +
1068A PHE* 3.5 31.4 - - + -
1072A ILE* 4.3 1.6 - - + -
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Residues in contact with VAL1014 (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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1010A GLN 3.0 20.9 + - - +
1011A ASP* 4.2 6.3 - - - +
1013A CYS* 1.3 70.4 - - - +
1015A LYS* 1.4 65.2 + - + +
1017A TYR* 3.3 6.8 + - + +
1018A LEU* 3.0 37.2 + - + +
1065A LYS* 3.7 66.4 - - + +
1068A PHE* 4.5 12.8 - - + -
1069A LEU* 4.0 16.8 - - + -
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Residues in contact with LYS1015 (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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860A LEU* 3.5 28.6 - - + +
1011A ASP* 2.9 48.8 + - - +
1012A ILE* 3.6 6.3 - - - +
1014A VAL* 1.4 72.4 - - + +
1016A ALA* 1.4 57.6 + - - +
1018A LEU* 4.1 6.5 - - - +
1019A ALA* 3.2 27.9 + - - +
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Residues in contact with ALA1016 (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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855A TRP* 2.8 43.0 + - + +
860A LEU* 3.9 5.6 - - - +
862A LEU* 3.7 26.0 - - + -
937A VAL* 4.0 7.2 - - + -
1012A ILE 2.8 21.5 + - - +
1013A CYS 3.5 4.9 - - - +
1015A LYS* 1.4 69.2 - - - +
1017A TYR* 1.4 63.2 - - - +
1019A ALA* 3.4 0.3 - - - +
1020A LEU* 3.3 14.9 + - - +
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Residues in contact with TYR1017 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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937A VAL* 3.7 21.1 - - + +
940A PHE* 3.9 14.6 - + - -
941A VAL* 4.9 7.0 - - + -
1013A CYS 2.8 21.2 + - - +
1014A VAL* 3.3 8.0 + - - +
1016A ALA* 1.4 69.6 - - - +
1018A LEU* 1.3 68.8 + - + +
1020A LEU* 3.2 7.2 + - + +
1021A ARG* 3.1 47.2 + - + +
1054A ALA 2.8 28.9 + - - -
1055A LEU* 3.9 2.6 - - + -
1056A THR* 3.2 15.1 + - - -
1064A ALA* 3.4 33.0 - - + -
1065A LYS* 5.1 1.3 - - - -
1067A TYR* 3.4 16.7 - + - -
1068A PHE* 3.6 25.8 - + + -
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Residues in contact with LEU1018 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014A VAL* 3.0 34.3 + - + +
1015A LYS* 4.2 5.8 - - - +
1017A TYR* 1.3 77.8 - - + +
1019A ALA* 1.4 60.6 + - - +
1021A ARG* 3.2 19.9 + - - +
1022A HIS* 3.1 25.2 + - + -
1061A GLU* 3.6 62.3 - - + +
1064A ALA* 3.9 17.7 - - + -
1065A LYS* 4.4 7.9 - - + +
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Residues in contact with ALA1019 (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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854A ILE* 3.9 2.7 - - - +
855A TRP* 3.6 20.2 - - + -
858A GLU* 3.7 27.3 - - + +
860A LEU* 3.8 7.6 - - + -
1015A LYS 3.2 19.6 + - - +
1016A ALA 3.4 8.3 - - - +
1017A TYR 3.2 0.2 - - - -
1018A LEU* 1.4 77.7 - - - +
1020A LEU* 1.4 56.8 + - - +
1022A HIS* 3.7 5.8 + - - +
1023A HIS* 3.2 26.2 - - - -
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Residues in contact with LEU1020 (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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851A MET* 3.8 37.9 - - + -
854A ILE* 3.9 26.5 - - + -
855A TRP* 3.7 33.4 - - + +
937A VAL* 4.1 9.2 - - + -
938A ALA 4.9 0.9 - - - +
941A VAL* 3.9 26.0 - - + -
1016A ALA 3.3 9.8 + - - +
1017A TYR 3.2 8.0 + - - +
1019A ALA* 1.4 75.5 - - - +
1021A ARG* 1.3 60.6 + - - +
1022A HIS 3.2 0.4 - - - -
1023A HIS* 3.0 26.3 + - - +
1024A THR* 3.6 0.7 + - - -
1027A LEU* 3.4 18.7 - - + +
1055A LEU* 4.5 5.1 - - + +
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Residues in contact with ARG1021 (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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1017A TYR* 3.1 43.8 + - + +
1018A LEU* 3.2 22.9 + - - +
1020A LEU* 1.3 72.6 - - - +
1022A HIS* 1.4 56.7 + - + +
1023A HIS 3.1 7.1 + - - -
1024A THR* 2.5 26.7 + - - +
1055A LEU* 2.8 35.5 + - + +
1056A THR* 3.0 23.8 + - - -
1057A VAL* 5.3 0.4 - - - +
1058A GLY 5.1 1.0 - - - +
1059A LYS 3.0 28.9 + - - +
1061A GLU* 4.2 14.8 - - - +
1064A ALA* 3.7 17.5 - - - +
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Residues in contact with HIS1022 (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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858A GLU* 4.1 14.3 + - - +
1018A LEU* 3.1 23.1 + - + -
1019A ALA* 3.8 7.8 - - - +
1020A LEU 3.2 0.8 - - - -
1021A ARG* 1.4 74.9 - - - +
1023A HIS* 1.4 75.8 + - + +
1024A THR 3.7 1.1 - - - -
1061A GLU* 3.4 30.6 + - - +
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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