Contacts of the helix formed by residues 1014 - 1030 (chain A) in PDB entry 1Y6G
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 CYS1014 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012A GLU* 2.8 29.1 + - - +
1013A GLY* 1.3 77.1 - - - +
1015A GLY* 1.3 63.7 + - - +
1016A VAL 3.4 2.0 - - - -
1017A THR 3.1 0.3 + - - -
1018A LYS* 2.8 28.2 + - - +
1046A ARG* 3.6 33.2 - - - -
1050A HIS* 3.9 0.2 - - - -
1204A ARG* 4.1 11.4 - - - +
1403A NCO 4.9 1.8 - - - +
1404A UDP 3.2 38.1 - - - +
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Residues in contact with GLY1015 (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 CYS* 1.3 79.9 - - - +
1016A VAL* 1.3 50.8 + - - +
1018A LYS* 3.0 5.4 + - - +
1019A PHE* 2.6 37.9 + - - +
1114A HIS* 5.4 0.9 - - - -
1307A TYR* 3.7 5.7 - - - -
1403A NCO 4.3 4.0 - - - -
1404A UDP 2.7 40.8 + - - -
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Residues in contact with VAL1016 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A MET* 4.1 15.9 - - + -
1012A GLU* 2.7 32.6 + - + +
1014A CYS 3.4 0.4 - - - -
1015A GLY* 1.3 75.5 - - - +
1017A THR* 1.3 59.6 + - - +
1019A PHE* 3.6 7.5 + - - +
1020A SER* 2.8 28.8 + - - +
1081A ASN* 3.8 12.5 - - + +
1082A SER* 4.8 13.2 - - - +
1114A HIS* 3.4 45.5 - - + +
1403A NCO 4.2 9.5 + - - +
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Residues in contact with THR1017 (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 MET* 3.9 16.3 - - + +
1011A LEU* 3.6 25.6 - - + +
1012A GLU* 2.4 43.3 + - - +
1013A GLY* 2.8 27.4 + - - -
1014A CYS 3.1 5.8 + - - -
1016A VAL* 1.3 69.2 - - - +
1018A LYS* 1.3 66.0 + - - +
1020A SER* 3.6 3.1 + - - -
1021A LEU* 3.1 33.4 + - + +
1050A HIS* 4.3 10.8 - - + +
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Residues in contact with LYS1018 (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 CYS 2.8 13.5 + - - +
1015A GLY* 3.0 4.2 + - - +
1017A THR* 1.3 75.1 - - - +
1019A PHE* 1.3 66.0 + - - +
1021A LEU* 2.9 12.4 + - + +
1022A GLU* 2.8 48.9 + - - +
1050A HIS* 3.2 35.1 + - + +
1178A MET* 4.5 8.9 - - - -
1183A VAL* 6.0 2.8 - - - +
1277A ASN* 4.3 7.9 + - - -
1307A TYR* 3.1 35.2 - - + -
1311A GLU* 3.9 17.9 + - - -
1404A UDP 3.9 5.2 - - - +
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Residues in contact with PHE1019 (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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1015A GLY 2.6 19.3 + - - +
1016A VAL 3.6 4.9 - - - +
1018A LYS* 1.3 73.3 - - - +
1020A SER* 1.3 53.8 + - - +
1022A GLU* 3.3 2.1 + - - +
1023A GLN* 2.7 61.1 + - - +
1081A ASN* 3.2 28.5 - - - -
1112A TYR* 3.8 29.6 - + - -
1114A HIS* 3.3 28.3 - + + +
1174A PHE* 4.1 11.9 - + - -
1176A PRO* 4.0 10.1 - - + -
1177A PRO* 3.8 9.9 - - + -
1307A TYR* 3.2 25.9 - - + +
1391A PHE* 3.7 20.2 - + - -
1394A GLN* 4.4 1.1 - - - -
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Residues in contact with SER1020 (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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1005A ILE* 3.7 19.0 - - - +
1007A MET* 3.7 17.8 - - - +
1016A VAL 2.8 17.6 + - - -
1017A THR 3.8 5.4 - - - -
1018A LYS 3.2 0.6 - - - -
1019A PHE* 1.3 76.3 - - - +
1021A LEU* 1.3 53.0 + - - +
1023A GLN* 3.4 12.8 - - - +
1024A ARG* 2.7 36.0 + - - +
1036A LEU* 3.8 13.5 - - - -
1081A ASN* 3.1 16.1 + - - -
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Residues in contact with LEU1021 (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 MET* 5.6 0.9 - - + -
1017A THR* 3.1 22.4 - - + +
1018A LYS* 2.9 13.0 + - + +
1020A SER* 1.3 74.1 - - - +
1022A GLU* 1.3 62.1 + - + +
1024A ARG* 3.1 5.1 + - - +
1025A ASP* 2.8 38.0 + - - +
1036A LEU* 4.2 16.6 - - + -
1050A HIS* 3.5 37.5 - - + -
1051A ASP 3.8 12.3 - - - +
1052A HIS* 4.2 10.5 - - + -
1055A PHE* 3.5 33.7 - - + -
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Residues in contact with GLU1022 (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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1018A LYS* 2.8 40.5 + - - +
1019A PHE 3.5 7.0 - - - +
1021A LEU* 1.3 75.6 - - - +
1023A GLN* 1.3 63.3 + - - +
1025A ASP* 3.3 11.4 + - - +
1026A TRP* 3.0 18.7 + - - +
1177A PRO 3.4 22.2 - - - +
1178A MET* 3.0 29.0 - - + +
1179A ASP* 3.0 26.4 + - - +
1182A LYS* 5.6 4.2 - - - -
1183A VAL* 5.4 2.1 - - - +
1307A TYR* 3.8 10.3 - - + +
1387A SER* 3.6 5.9 + - - -
1391A PHE* 3.6 9.3 - - + -
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Residues in contact with GLN1023 (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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1005A ILE* 3.6 14.3 - - + +
1019A PHE* 2.7 44.9 + - + +
1020A SER* 3.4 3.1 - - - +
1022A GLU* 1.3 75.0 - - - +
1024A ARG* 1.3 61.9 + - - +
1026A TRP* 3.1 2.9 + - - +
1027A PHE* 3.0 48.8 + - + -
1079A ILE* 3.3 26.8 - - - +
1081A ASN* 3.5 17.0 - - - +
1112A TYR* 3.5 22.2 + - - -
1391A PHE* 3.5 23.1 - - + -
1394A GLN* 5.2 0.2 + - - -
1398A ILE* 5.5 0.2 - - - +
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Residues in contact with ARG1024 (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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1005A ILE* 3.8 15.2 - - + +
1020A SER 2.7 20.2 + - - +
1021A LEU* 3.5 6.0 - - - +
1023A GLN* 1.3 73.2 - - - +
1025A ASP* 1.3 79.8 + - - +
1027A PHE* 3.9 2.4 - - - +
1028A ILE* 3.0 49.5 + - + +
1034A VAL* 3.9 25.4 + - + +
1036A LEU* 4.4 15.5 - - + +
1055A PHE* 3.3 63.7 - - - +
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Residues in contact with ASP1025 (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 LEU* 2.8 22.4 + - - +
1022A GLU* 3.6 13.1 - - - +
1024A ARG* 1.3 98.4 + - - +
1026A TRP* 1.3 56.8 + - - +
1028A ILE* 4.0 4.1 - - - +
1029A LYS* 3.0 32.2 + - - +
1179A ASP* 6.3 0.7 - - + -
1182A LYS* 3.4 32.9 + - - +
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Residues in contact with TRP1026 (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 GLU 3.0 9.4 + - - +
1023A GLN 3.1 2.9 + - - +
1025A ASP* 1.3 74.8 - - - +
1027A PHE* 1.3 87.6 + + - +
1029A LYS* 3.6 14.3 + - + +
1030A ASN* 3.1 55.6 + - + +
1032A HIS* 5.1 0.2 - + - -
1387A SER* 3.3 40.6 + - - -
1388A SER* 3.8 9.7 - - - +
1391A PHE* 3.2 50.5 - + + -
1392A LYS* 3.7 28.0 - - + -
1395A PHE* 3.8 33.2 - + + -
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Residues in contact with PHE1027 (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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1003A ILE* 3.4 39.9 - - + -
1005A ILE* 4.8 2.0 - - + -
1023A GLN* 3.0 54.5 + - + +
1024A ARG 3.9 0.4 - - - +
1026A TRP* 1.3 88.6 - + - +
1028A ILE* 1.3 67.7 + - - +
1030A ASN 2.9 12.6 + - - -
1031A GLY 3.1 7.3 + - - -
1032A HIS* 3.2 27.2 + + + +
1034A VAL* 3.6 17.7 - - + -
1077A ILE* 5.6 2.5 - - + -
1079A ILE* 3.9 13.0 - - + -
1391A PHE* 5.4 3.4 - + - -
1395A PHE* 3.8 26.7 - + + -
1398A ILE* 4.9 14.8 - - + -
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Residues in contact with ILE1028 (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 ARG* 3.0 56.8 + - + +
1025A ASP* 4.0 4.3 - - - +
1027A PHE* 1.3 79.0 - - - +
1029A LYS* 1.3 56.4 + - - +
1031A GLY* 2.4 31.0 + - - -
1032A HIS 3.7 18.4 - - - +
1034A VAL* 4.1 14.8 - - + +
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Residues in contact with LYS1029 (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 ASP 3.0 21.8 + - - +
1026A TRP* 3.7 15.8 - - + +
1028A ILE* 1.3 79.5 - - - +
1030A ASN* 1.3 67.2 + - - +
1031A GLY 3.4 1.7 + - - -
1179A ASP* 4.9 14.8 - - - +
1182A LYS* 6.0 2.2 - - - +
1388A SER* 5.1 13.1 - - - -
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Residues in contact with ASN1030 (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 GLY 4.6 2.9 - - - +
1026A TRP* 3.1 59.1 + - + +
1027A PHE 2.9 6.6 + - - +
1028A ILE 2.8 0.2 + - - -
1029A LYS* 1.3 86.8 + - - +
1031A GLY* 1.3 66.4 + - - +
1032A HIS* 3.6 16.7 + - + +
1392A LYS* 4.4 13.9 - - - +
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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