Contacts of the helix formed by residues 1015 - 1035 (chain A) in PDB entry 5W0N
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 THR1015 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013A SER 3.7 0.4 + - - -
1014A PRO* 1.3 77.5 - - - +
1016A ILE* 1.3 64.4 + - - +
1017A ILE* 3.5 3.5 + - - +
1018A GLU* 3.0 32.3 + - - +
1019A ASP* 3.0 21.4 + - - +
1055A LYS* 3.7 17.7 - - - +
1011B ASP* 4.3 22.9 - - + +
1012B PHE* 3.7 28.6 - - + -
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Residues in contact with ILE1016 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A PRO 4.0 0.4 + - - -
1015A THR* 1.3 72.3 - - - +
1017A ILE* 1.3 64.1 + - + +
1019A ASP* 3.5 10.6 + - - +
1020A GLN* 3.1 16.8 + - - +
1008B CYS* 6.1 0.7 - - - -
1012B PHE* 4.3 13.9 - - + -
1153B VAL* 3.7 28.3 - - + -
1157B MET* 3.7 36.0 - - + +
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Residues in contact with ILE1017 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A THR* 3.1 7.3 + - - +
1016A ILE* 1.3 77.2 - - + +
1018A GLU* 1.3 65.3 + - + +
1020A GLN* 3.4 8.0 + - - +
1021A ALA* 3.0 22.8 + - + +
1012B PHE* 3.4 33.7 - - + -
1054B PHE* 5.2 9.2 - - + -
1056B GLN* 6.6 0.2 - - + -
1153B VAL* 4.7 8.3 - - + -
1156B LYS* 3.9 34.8 - - + -
1157B MET* 3.7 26.2 - - + -
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Residues in contact with GLU1018 (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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1014A PRO* 3.2 17.7 - - + +
1015A THR* 3.0 41.2 + - - +
1017A ILE* 1.3 78.4 - - + +
1019A ASP* 1.3 61.4 + - - +
1021A ALA* 3.4 9.1 + - - +
1022A ARG* 3.3 26.9 + - - +
1055A LYS* 3.3 34.1 + - - +
1056A GLN* 5.7 2.5 + - - -
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Residues in contact with ASP1019 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A PRO* 3.5 29.8 - - - +
1015A THR 3.0 15.6 + - - +
1016A ILE* 3.8 11.6 - - - +
1017A ILE 3.3 0.2 - - - -
1018A GLU* 1.3 74.4 - - - +
1020A GLN* 1.3 65.6 + - - +
1022A ARG* 3.0 26.0 + - - +
1023A GLU* 3.3 10.7 + - - +
1048A SER* 5.1 7.8 - - - +
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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
----------------------------------------------------------
1016A ILE 3.1 17.2 + - - +
1017A ILE* 3.4 9.0 + - - +
1019A ASP* 1.3 75.0 - - - +
1021A ALA* 1.3 62.7 + - - +
1023A GLU* 3.1 11.1 + - + +
1024A HIS* 2.9 52.7 + - + +
1156B LYS* 3.0 40.9 + - - +
1157B MET* 3.3 37.2 + - + +
1159B ASP* 4.6 6.1 - - - +
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Residues in contact with ALA1021 (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 ILE* 3.0 15.2 + - + +
1018A GLU* 3.5 12.8 - - - +
1019A ASP 3.2 0.2 - - - -
1020A GLN* 1.3 78.0 + - - +
1022A ARG* 1.3 62.6 + - + +
1024A HIS* 3.2 12.5 + - - +
1025A ILE* 2.9 33.8 + - + +
1114A SER* 5.8 5.2 - - - -
1116A LEU* 6.5 0.9 - - + -
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Residues in contact with ARG1022 (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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1014A PRO* 4.8 6.6 - - - +
1018A GLU* 3.3 15.5 + - - +
1019A ASP* 3.0 23.4 + - - +
1021A ALA* 1.3 76.9 - - + +
1023A GLU* 1.3 61.7 + - - +
1025A ILE* 3.3 10.2 + - - +
1026A ARG* 3.1 21.0 + - - +
1044A LEU* 4.1 10.4 - - + +
1048A SER* 2.9 34.3 + - - +
1053A GLY* 6.4 0.7 - - - -
1054A PHE 3.2 14.5 + - - -
1055A LYS 3.1 25.5 + - - -
1057A SER* 2.8 23.9 + - - +
1058A ASP 3.1 21.6 + - - -
1059A LEU* 3.6 22.8 - - + +
1116A LEU* 3.8 21.1 - - + +
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Residues in contact with GLU1023 (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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1019A ASP 3.3 6.5 + - - +
1020A GLN* 3.1 13.3 + - + +
1022A ARG* 1.3 77.8 - - - +
1024A HIS* 1.3 64.8 + - + +
1026A ARG* 2.8 46.5 + - - -
1027A GLN* 2.9 33.2 + - - +
1044A LEU* 4.2 12.9 - - + +
1049A LYS* 5.0 9.2 + - - +
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Residues in contact with HIS1024 (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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1020A GLN* 2.9 55.6 + - + -
1021A ALA* 3.2 12.3 + - - +
1023A GLU* 1.3 79.9 - - + +
1025A ILE* 1.3 57.8 + - + +
1027A GLN* 3.3 19.8 + - - +
1028A ASN* 2.9 30.1 + - - +
1159B ASP* 4.6 20.0 + - + -
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Residues in contact with ILE1025 (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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1021A ALA* 2.9 22.7 + - + +
1022A ARG* 3.5 10.5 - - - +
1023A GLU 3.2 0.2 - - - -
1024A HIS* 1.3 73.7 - - + +
1026A ARG* 1.3 65.5 + - - +
1028A ASN* 3.1 6.6 + - + +
1029A LEU* 2.8 40.6 + - + +
1059A LEU* 3.4 23.3 - - + -
1111A HIS* 3.7 36.6 - - + +
1114A SER* 3.5 31.9 - - - +
1116A LEU* 4.4 13.5 - - + -
1118A VAL* 4.8 3.4 - - + -
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Residues in contact with ARG1026 (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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1022A ARG 3.1 10.9 + - - +
1023A GLU* 2.8 40.5 + - - +
1025A ILE* 1.3 79.6 - - - +
1027A GLN* 1.3 81.5 + - - +
1029A LEU* 3.4 6.5 + - - +
1030A GLU* 3.0 56.1 + - - +
1042A LEU* 3.0 45.3 + - + +
1043A SER* 4.3 1.1 - - - +
1044A LEU* 3.9 35.0 - - + +
1059A LEU* 4.5 1.3 - - - +
1061A VAL* 5.1 3.4 - - + -
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Residues in contact with GLN1027 (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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1023A GLU* 2.9 22.9 + - - +
1024A HIS* 3.5 24.5 + - - +
1025A ILE 3.1 0.2 - - - -
1026A ARG* 1.3 96.9 - - - +
1028A ASN* 1.3 63.1 + - - +
1030A GLU* 3.4 6.1 + - - +
1031A SER* 3.2 29.3 + - - +
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Residues in contact with ASN1028 (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 HIS 2.9 17.0 + - - +
1025A ILE* 3.6 6.7 - - + +
1027A GLN* 1.3 77.7 - - - +
1029A LEU* 1.3 66.9 + - - +
1031A SER* 3.3 6.0 + - - -
1032A PHE* 3.0 21.8 + - - +
1090A HIS* 2.9 32.6 + - - -
1111A HIS* 5.5 5.9 + - - +
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Residues in contact with LEU1029 (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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1025A ILE* 2.8 42.5 + - + +
1026A ARG* 4.9 2.5 - - - -
1028A ASN* 1.3 75.0 - - - +
1030A GLU* 1.3 57.5 + - - +
1032A PHE* 3.8 3.1 - - + +
1033A ILE* 2.9 39.5 + - + +
1042A LEU* 3.5 18.2 - - + -
1059A LEU* 5.1 1.3 - - + -
1061A VAL* 5.1 3.4 - - + -
1087A LEU* 4.6 7.0 - - + -
1090A HIS* 4.4 11.2 - - + -
1093A LEU* 4.0 32.3 - - + -
1109A PHE* 3.8 26.2 - - + -
1111A HIS* 5.4 1.6 - - + -
1118A VAL* 4.1 11.0 - - + -
1120A ILE* 4.8 6.3 - - + -
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Residues in contact with GLU1030 (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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1026A ARG* 3.0 41.5 + - - +
1027A GLN* 3.7 6.6 - - - +
1029A LEU* 1.3 78.4 - - - +
1031A SER* 1.3 58.4 + - - +
1033A ILE* 3.9 2.8 - - - +
1034A ARG* 3.0 63.3 + - - +
1040A THR* 3.8 15.3 - - - +
1041A LYS* 3.4 11.3 - - - +
1042A LEU* 3.0 40.3 + - + +
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Residues in contact with SER1031 (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 GLN* 3.2 16.0 + - - +
1028A ASN* 3.3 8.3 + - - -
1030A GLU* 1.3 75.9 + - - +
1032A PHE* 1.3 66.1 + - - +
1034A ARG* 3.2 21.9 + - - +
1035A GLN* 3.4 16.5 + - - +
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Residues in contact with PHE1032 (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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1028A ASN* 3.0 17.9 + - - +
1029A LEU 3.8 4.0 - - - +
1031A SER* 1.3 77.2 - - - +
1033A ILE* 1.3 68.2 + - + +
1035A GLN* 3.2 44.9 + - - +
1036A ASP* 4.2 4.8 - - - +
1086A VAL* 3.3 36.3 - - + -
1087A LEU* 4.4 5.8 - - + -
1089A LYS* 3.7 19.1 - - + -
1090A HIS* 3.5 59.5 - + + +
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Residues in contact with ILE1033 (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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1029A LEU* 2.9 22.9 + - + +
1030A GLU 4.1 2.2 - - - +
1032A PHE* 1.3 81.3 - - + +
1034A ARG* 1.3 58.0 + - - +
1036A ASP* 3.1 6.1 + - - +
1037A PHE* 2.8 34.0 + - + +
1040A THR* 3.7 27.6 - - + +
1042A LEU* 4.2 22.7 - - + -
1063A MET* 4.4 2.5 - - + -
1083A LEU* 3.7 34.8 - - + -
1086A VAL* 4.4 9.2 - - + -
1087A LEU* 4.1 21.8 - - + -
1120A ILE* 4.4 9.6 - - + -
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Residues in contact with ARG1034 (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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1030A GLU* 3.0 53.1 + - - +
1031A SER* 3.5 14.1 + - - +
1032A PHE 3.2 0.4 - - - -
1033A ILE* 1.3 75.2 - - - +
1035A GLN* 1.3 65.1 + - - +
1036A ASP 3.3 0.5 + - - -
1037A PHE 3.5 14.8 - - - +
1038A PRO* 3.3 21.8 - - + +
1039A GLY* 4.2 9.1 - - - +
1040A THR* 2.9 35.0 + - - +
1041A LYS* 4.7 3.6 - - - +
1066A ASN* 4.6 13.5 - - - +
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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 SER 3.4 10.2 + - - +
1032A PHE* 3.3 42.7 - - - +
1033A ILE 3.1 0.6 - - - -
1034A ARG* 1.3 78.3 - - - +
1036A ASP* 1.3 66.1 + - - +
1038A PRO* 4.9 1.7 - - - +
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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
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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