Contacts of the helix formed by residues 1019 - 1039 (chain A) in PDB entry 1WER
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 GLN1019 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A HIS* 3.6 36.1 + - + +
1012A LEU 4.7 1.5 + - - +
1015A GLU* 2.9 40.4 + - - +
1016A ARG 3.2 15.4 + - - +
1017A GLY* 3.8 2.5 - - - -
1018A ALA* 1.3 84.2 + - - +
1020A GLN* 1.3 67.4 + - - +
1021A HIS 3.3 0.7 - - - -
1022A VAL* 3.2 6.5 + - - +
1023A LEU* 3.1 42.1 + - + +
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Residues in contact with GLN1020 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A SER 3.3 25.1 + - - +
1014A ASN* 4.3 7.5 + - - +
1015A GLU 3.4 23.5 + - - +
1016A ARG* 3.6 16.3 - - - +
1017A GLY 3.1 15.4 + - - +
1019A GLN* 1.3 82.2 - - - +
1021A HIS* 1.3 65.0 + - - +
1023A LEU* 3.3 3.4 + - - +
1024A LYS* 3.1 54.6 + - - +
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Residues in contact with HIS1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A GLY 4.5 0.8 + - - -
1018A ALA 4.1 9.3 + - - +
1019A GLN 3.3 0.2 - - - -
1020A GLN* 1.3 81.0 - - - +
1022A VAL* 1.3 66.6 + - + +
1024A LYS* 3.5 19.7 + - - +
1025A LYS* 3.2 36.1 + - + +
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Residues in contact with VAL1022 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A LEU* 3.9 16.2 - - + +
732A GLN* 3.7 21.3 - - - +
734A GLU* 4.6 5.8 - - - +
736A HIS* 3.9 32.1 - - + +
737A VAL* 3.4 31.0 - - + +
1018A ALA 4.8 2.0 - - - +
1019A GLN 3.2 7.5 + - - +
1021A HIS* 1.3 79.9 - - + +
1023A LEU* 1.3 52.9 + - + +
1025A LYS* 3.1 15.1 - - - +
1026A LEU* 2.7 30.8 + - - +
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Residues in contact with LEU1023 (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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736A HIS 4.3 9.2 - - - +
737A VAL* 4.6 4.5 - - - -
740A ALA* 3.5 29.6 - - + -
1009A LEU* 4.7 4.9 - - + +
1012A LEU* 3.8 38.1 - - + +
1013A SER* 3.8 15.7 - - - +
1019A GLN* 3.1 35.1 + - + +
1020A GLN* 3.3 3.3 + - - +
1022A VAL* 1.3 76.6 - - + +
1024A LYS* 1.3 59.7 + - - +
1026A LEU* 3.2 23.7 + - + +
1027A LEU* 3.1 31.9 + - - +
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Residues in contact with LYS1024 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A SER* 4.2 12.8 - - - +
1014A ASN* 6.1 0.9 - - - +
1020A GLN* 3.1 58.7 + - + +
1021A HIS* 3.9 18.7 - - - +
1023A LEU* 1.3 73.3 - - - +
1025A LYS* 1.3 61.9 + - - +
1027A LEU* 3.3 10.7 + - - +
1028A ALA* 3.1 23.6 + - - +
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Residues in contact with LYS1025 (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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729A LEU* 3.7 29.9 - - + +
732A GLN* 4.6 9.9 + - - +
1021A HIS* 3.2 25.0 + - + +
1022A VAL* 3.1 21.2 - - - +
1024A LYS* 1.3 79.4 - - - +
1026A LEU* 1.3 54.6 + - - +
1028A ALA* 3.4 7.6 - - + +
1029A ILE* 3.0 39.0 + - + +
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Residues in contact with LEU1026 (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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726A PHE* 3.7 33.7 - - + -
729A LEU* 3.5 15.0 - - + -
737A VAL* 4.0 25.4 - - + -
740A ALA* 5.3 0.2 - - + -
741A LEU* 5.3 0.9 - - + -
1002A CYS* 4.1 8.3 - - - -
1009A LEU* 4.2 28.9 - - + -
1022A VAL 2.7 16.6 + - - +
1023A LEU* 3.4 30.5 - - + +
1024A LYS 3.2 0.4 - - - -
1025A LYS* 1.3 74.6 - - - +
1027A LEU* 1.3 59.0 + - + +
1029A ILE* 3.3 2.4 + - - +
1030A THR* 2.9 40.2 + - - +
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Residues in contact with LEU1027 (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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1006A SER* 3.7 29.2 - - - +
1009A LEU* 4.2 13.5 - - + +
1010A ARG* 3.6 36.1 - - + +
1013A SER* 3.3 34.1 - - - +
1023A LEU 3.1 14.5 + - - +
1024A LYS* 3.3 7.4 + - - +
1026A LEU* 1.3 73.2 - - + +
1028A ALA* 1.3 67.3 + - - +
1030A THR* 3.3 11.3 + - + +
1031A GLU* 3.0 26.6 + - - +
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Residues in contact with ALA1028 (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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1024A LYS 3.1 13.5 + - - +
1025A LYS* 3.4 13.5 - - + +
1027A LEU* 1.3 74.9 - - - +
1029A ILE* 1.3 64.8 + - + +
1031A GLU* 3.0 16.9 + - - +
1032A LEU* 3.0 14.3 + - - +
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Residues in contact with ILE1029 (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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725A GLU* 3.6 44.2 - - + +
726A PHE* 3.5 32.8 - - + -
729A LEU* 3.6 27.1 - - + -
1025A LYS* 3.0 23.1 + - + +
1026A LEU* 3.3 5.1 + - - +
1028A ALA* 1.3 75.2 - - + +
1030A THR* 1.3 57.2 + - - +
1032A LEU* 3.3 10.2 + - + +
1033A LEU* 3.0 38.5 + - + +
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Residues in contact with THR1030 (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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726A PHE* 5.0 1.7 - - - -
999A HIS* 3.0 30.7 + - + -
1002A CYS* 3.6 21.8 - - + +
1003A VAL* 3.7 38.4 - - + +
1006A SER* 5.4 5.6 - - - -
1026A LEU* 2.9 29.1 + - - +
1027A LEU* 3.5 11.8 - - + +
1028A ALA 3.2 0.2 - - - -
1029A ILE* 1.3 76.0 - - - +
1031A GLU* 1.3 62.8 + - + +
1034A GLN* 3.2 11.9 + - + +
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Residues in contact with GLU1031 (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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1027A LEU 3.0 11.6 + - - +
1028A ALA* 3.0 10.2 + - - +
1030A THR* 1.3 76.7 - - + +
1032A LEU* 1.3 59.4 + - - +
1034A GLN* 3.1 16.4 + - - +
1035A GLN* 2.8 46.9 + - - +
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Residues in contact with LEU1032 (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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725A GLU* 5.1 18.2 - - + -
1028A ALA 3.0 11.5 + - - +
1029A ILE* 3.7 10.8 - - + +
1031A GLU* 1.3 77.6 - - - +
1033A LEU* 1.3 60.0 + - + +
1035A GLN* 3.0 25.8 + - + +
1036A LYS* 2.9 52.5 + - + +
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Residues in contact with LEU1033 (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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718A MET* 3.5 24.3 - - + +
722A GLU* 3.1 28.5 - - + +
723A TYR* 4.2 12.6 - - + -
725A GLU* 3.4 20.9 - - - +
726A PHE* 3.8 13.2 - - + -
999A HIS* 3.4 35.4 - - + +
1029A ILE* 3.0 27.1 + - + +
1032A LEU* 1.3 79.7 - - + +
1034A GLN* 1.3 57.6 + - - +
1036A LYS* 4.0 8.1 - - + +
1037A GLN* 3.2 31.4 + - - +
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Residues in contact with GLN1034 (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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999A HIS* 3.6 15.7 - - - +
1003A VAL* 3.5 32.4 - - + +
1030A THR* 3.2 18.0 + - + +
1031A GLU* 3.1 20.9 + - - +
1033A LEU* 1.3 76.6 - - - +
1035A GLN* 1.3 63.7 + - - +
1037A GLN* 3.7 11.6 + - - +
1038A ASN* 3.7 17.7 + - - +
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Residues in contact with GLN1035 (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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1031A GLU* 2.8 43.5 + - - +
1032A LEU* 3.0 30.9 + - + +
1034A GLN* 1.3 75.4 - - - +
1036A LYS* 1.3 64.1 + - + +
1037A GLN 2.9 4.9 + - - -
1038A ASN 4.0 0.3 - - - -
1039A GLN* 3.2 31.1 + - + +
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Residues in contact with LYS1036 (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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718A MET* 3.5 26.3 - - + +
722A GLU* 2.8 35.0 + - + +
725A GLU* 5.9 0.4 + - - -
1032A LEU* 2.9 41.0 + - + +
1033A LEU* 4.1 7.2 - - + +
1035A GLN* 1.3 76.8 - - + +
1037A GLN* 1.3 63.4 + - - +
1039A GLN* 3.5 28.4 + - - +
1041A THR* 6.1 0.3 - - - +
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Residues in contact with GLN1037 (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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718A MET* 4.4 20.2 + - - +
723A TYR* 4.6 14.4 + - - -
996A ALA* 6.1 0.2 - - - +
999A HIS* 4.4 16.8 + - - -
1033A LEU 3.2 22.7 + - - +
1034A GLN* 3.7 15.3 + - - +
1035A GLN 2.9 2.2 + - - -
1036A LYS* 1.3 81.2 - - - +
1038A ASN* 1.3 62.0 + - + +
1039A GLN 3.2 5.6 + - - +
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Residues in contact with ASN1038 (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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1034A GLN* 3.7 8.6 + - - +
1035A GLN 3.4 4.1 + - - -
1037A GLN* 1.3 80.8 - - + +
1039A GLN* 1.3 63.3 + - - +
1040A TYR 3.7 0.7 + - - -
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Residues in contact with GLN1039 (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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1035A GLN* 3.2 18.7 + - + +
1036A LYS* 3.5 33.9 + - - +
1037A GLN 3.2 5.0 - - - +
1038A ASN* 1.3 80.8 - - - +
1040A TYR* 1.3 72.8 + - - +
1041A THR* 3.3 17.1 + - + +
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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
------------------------------------------------------------
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