Contacts of the helix formed by residues 1014 - 1030 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012B GLU* 3.0 22.8 + - - +
1013B GLY* 1.3 78.8 - - - +
1015B GLY* 1.3 58.8 + - - +
1016B VAL 3.1 2.0 - - - -
1017B THR 2.6 27.0 + - - -
1018B LYS 2.9 9.4 + - - -
1046B ARG* 3.5 36.8 - - - -
1204B ARG* 4.7 6.5 - - - -
2019B NCO 5.3 0.9 - - - +
2021B UDP 3.3 40.2 - - - +
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Residues in contact with GLY1015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014B CYS* 1.3 70.0 - - - +
1016B VAL* 1.3 56.5 + - - +
1018B LYS* 4.2 0.4 - - - -
1019B PHE* 2.7 32.9 + - - +
1307B TYR* 3.7 10.4 - - - -
2017B CL 4.2 7.6 - - - -
2019B NCO 3.8 5.2 - - - -
2021B UDP 2.6 44.7 + - - -
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Residues in contact with VAL1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B MET* 4.4 7.2 - - - -
1009B ARG* 6.3 0.9 - - - +
1012B GLU* 3.2 23.8 - - + +
1014B CYS 2.9 2.2 + - - -
1015B GLY* 1.3 75.0 - - - +
1017B THR* 1.3 60.4 + - - +
1019B PHE* 4.0 4.6 - - - +
1020B SER* 2.8 29.1 + - - -
1081B ASN* 3.7 37.5 - - + +
1082B SER* 4.3 12.6 - - - -
1114B HIS* 4.2 22.2 - - + -
1115B ASP* 5.3 2.0 - - - +
2019B NCO 4.0 17.0 - - - +
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Residues in contact with THR1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B MET* 4.1 12.3 - - + +
1011B LEU* 3.7 24.7 - - + +
1012B GLU* 2.4 35.7 + - - -
1013B GLY* 2.6 28.9 + - - -
1014B CYS 2.6 9.2 + - - -
1016B VAL* 1.3 69.7 - - - +
1018B LYS* 1.3 65.2 + - - +
1020B SER* 3.2 3.3 + - - -
1021B LEU* 2.9 36.3 + - + +
1050B HIS* 4.2 16.2 - - + +
1052B HIS* 5.3 1.3 - - - +
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Residues in contact with LYS1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014B CYS 2.9 8.2 + - - +
1015B GLY* 3.7 4.3 - - - +
1017B THR* 1.3 77.6 - - - +
1019B PHE* 1.3 62.3 + - - +
1021B LEU* 3.2 6.5 + - + +
1022B GLU* 2.9 55.7 + - + +
1050B HIS* 3.7 35.0 + - + +
1178B MET* 3.9 12.7 - - - -
1183B VAL* 5.1 5.5 - - - +
1277B ASN* 3.5 15.6 + - - -
1307B TYR* 3.2 41.7 - - + -
1311B GLU* 3.8 12.8 - - - -
2021B UDP 4.1 5.8 - - - +
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Residues in contact with PHE1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015B GLY 2.7 23.4 + - - +
1016B VAL 4.0 2.2 - - - +
1018B LYS* 1.3 74.4 - - - +
1020B SER* 1.3 55.0 + - - +
1022B GLU* 3.2 1.2 + - - +
1023B GLN* 2.8 60.1 + - - +
1081B ASN* 3.3 28.0 - - - -
1112B TYR* 3.8 26.2 - + - -
1114B HIS* 3.3 30.3 - + + -
1174B PHE* 3.9 11.4 - + - -
1176B PRO* 4.0 6.1 - - + -
1177B PRO* 3.8 22.7 - - + -
1307B TYR* 3.2 29.3 - - + +
1391B PHE* 3.9 11.4 - + - -
1394B GLN* 4.5 0.9 - - - -
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Residues in contact with SER1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005B ILE* 3.6 14.5 - - - +
1007B MET* 2.9 29.0 - - - +
1016B VAL 2.8 19.6 + - - -
1017B THR 3.4 8.7 - - - -
1019B PHE* 1.3 75.9 - - - +
1021B LEU* 1.3 60.1 + - - +
1023B GLN* 3.3 7.3 + - - +
1024B ARG* 2.8 27.7 + - - +
1036B LEU* 4.3 5.3 - - - +
1081B ASN* 3.2 25.3 + - - +
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Residues in contact with LEU1021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B MET* 5.6 1.1 - - + -
1011B LEU* 6.1 0.7 - - + -
1017B THR* 2.9 22.7 + - + +
1018B LYS* 3.5 10.5 - - + +
1020B SER* 1.3 76.2 - - - +
1022B GLU* 1.3 62.5 + - + +
1024B ARG* 2.9 7.2 + - + +
1025B ASP* 2.9 37.1 + - - +
1036B LEU* 3.5 29.8 - - + -
1050B HIS* 3.8 32.5 - - + -
1051B ASP 4.0 17.5 - - - +
1052B HIS* 4.2 9.4 - - + -
1055B PHE* 3.8 16.8 - - + -
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Residues in contact with GLU1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018B LYS* 2.9 54.5 + - + +
1019B PHE 3.8 3.1 - - - +
1021B LEU* 1.3 77.6 - - + +
1023B GLN* 1.3 62.2 + - - +
1025B ASP* 3.5 15.0 + - - +
1026B TRP* 3.1 18.7 + - - +
1177B PRO 3.6 23.1 - - - +
1178B MET* 3.8 7.4 - - - +
1179B ASP* 3.2 34.0 + - - +
1183B VAL* 5.4 2.3 - - - +
1307B TYR* 4.1 2.9 - - + +
1387B SER* 4.0 2.8 + - - -
1391B PHE* 3.4 14.6 - - + -
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Residues in contact with GLN1023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005B ILE* 3.7 14.3 - - + +
1019B PHE* 2.8 27.1 + - + +
1020B SER* 3.4 2.8 - - - +
1022B GLU* 1.3 75.6 - - - +
1024B ARG* 1.3 68.5 + - - +
1026B TRP* 3.6 1.4 + - - +
1027B PHE* 3.1 43.3 + - + -
1079B ILE* 3.1 36.6 - - - +
1081B ASN* 3.2 29.7 - - - +
1112B TYR* 3.7 15.2 + - - -
1391B PHE* 3.3 24.8 - - + -
1394B GLN* 5.1 0.2 + - - -
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Residues in contact with ARG1024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005B ILE* 3.7 14.6 - - + +
1020B SER 2.8 14.6 + - - +
1021B LEU* 3.2 11.1 + - - +
1023B GLN* 1.3 79.9 - - - +
1025B ASP* 1.3 80.5 + - - +
1026B TRP 3.0 1.7 + - - -
1027B PHE* 3.2 1.9 + - - +
1028B ILE* 3.1 45.5 + - + +
1034B VAL* 3.8 23.6 + - + +
1036B LEU* 4.1 13.4 - - + +
1055B PHE* 3.1 72.0 - - - +
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Residues in contact with ASP1025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021B LEU* 2.9 25.3 + - - +
1022B GLU* 3.9 18.8 - - - +
1023B GLN 3.4 0.4 - - - -
1024B ARG* 1.3 91.7 + - - +
1026B TRP* 1.3 55.4 + - - +
1028B ILE* 3.8 8.7 - - - +
1029B LYS* 2.8 30.9 + - - +
1179B ASP* 6.2 2.9 - - + -
1182B LYS* 5.9 5.4 - - - +
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Residues in contact with TRP1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022B GLU 3.1 11.4 + - - +
1023B GLN 4.0 2.0 - - - +
1024B ARG 3.0 0.2 + - - -
1025B ASP* 1.3 73.4 - - - +
1027B PHE* 1.3 119.6 + + - +
1028B ILE 3.1 1.8 - - - -
1029B LYS* 3.0 14.9 + - + +
1030B ASN* 2.8 61.3 + - + +
1032B HIS* 4.8 0.4 - + - -
1387B SER* 3.5 31.1 + - - -
1388B SER* 4.8 6.5 + - - +
1391B PHE* 3.3 51.5 - + + +
1392B LYS* 3.9 15.5 - - + +
1395B PHE* 3.6 37.0 - + + -
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Residues in contact with PHE1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B ILE* 3.6 33.4 - - + -
1005B ILE* 4.9 2.5 - - + -
1023B GLN* 3.1 44.7 + - + +
1024B ARG 3.2 1.8 + - - -
1026B TRP* 1.3 101.0 - + - +
1028B ILE* 1.3 64.1 + - - +
1030B ASN 3.0 10.6 + - - -
1031B GLY 3.2 1.0 + - - -
1032B HIS* 3.0 36.5 + + + +
1034B VAL* 3.4 21.1 - - + -
1077B ILE* 5.6 2.2 - - + -
1079B ILE* 3.6 25.1 - - + -
1391B PHE* 5.6 2.5 - + - -
1395B PHE* 3.6 27.1 - + + -
1398B ILE* 4.8 11.2 - - + -
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Residues in contact with ILE1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024B ARG* 3.1 56.9 + - + +
1025B ASP* 3.8 8.3 - - - +
1026B TRP 3.1 0.2 - - - -
1027B PHE* 1.3 72.8 - - - +
1029B LYS* 1.3 59.7 + - - +
1030B ASN 2.8 10.8 + - - -
1031B GLY* 2.9 13.3 + - - -
1032B HIS 3.6 11.8 + - - +
1034B VAL* 3.7 20.6 - - + +
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Residues in contact with LYS1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025B ASP 2.8 25.5 + - - +
1026B TRP* 3.0 15.2 + - + +
1028B ILE* 1.3 73.4 - - - +
1030B ASN* 1.3 73.5 + - - +
1031B GLY 3.5 0.4 - - - -
1179B ASP* 3.6 25.3 + - - -
1182B LYS* 6.2 1.6 - - - +
1387B SER* 6.3 0.7 - - - -
1388B SER* 6.4 2.2 - - - +
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Residues in contact with ASN1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026B TRP* 2.8 51.7 + - + +
1027B PHE 3.0 5.3 + - - +
1028B ILE 2.8 1.0 + - - -
1029B LYS* 1.3 94.2 - - - +
1031B GLY* 1.3 60.8 + - - +
1032B HIS* 3.5 18.8 + - + +
1392B LYS* 6.0 2.4 - - - +
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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