Contacts of the helix formed by residues 1070 - 1085 (chain A) in PDB entry 1Y1S
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 GLY1070 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068A GLY 4.2 0.2 - - - +
1069A ILE* 1.3 78.0 - - - +
1071A GLY* 1.3 59.0 + - - -
1072A PRO* 3.4 2.9 - - - -
1073A SER 3.8 0.6 + - - -
1074A THR* 2.6 33.3 + - - -
1197A MET 3.5 14.8 + - - -
1198A GLU* 2.9 13.9 + - - -
4072F PRO* 3.3 23.3 - - - -
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Residues in contact with GLY1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070A GLY* 1.3 70.7 - - - -
1072A PRO* 1.3 62.1 - - - +
1074A THR* 4.0 2.5 - - - -
1075A SER* 2.7 37.4 + - - -
1117A ASP* 5.9 0.2 - - - +
1119A ALA* 4.0 4.9 - - - -
1160A ASP* 4.1 5.2 + - - -
1197A MET 3.9 6.3 + - - -
1198A GLU* 5.1 0.7 - - - -
1201A THR* 3.0 35.3 - - - +
4072F PRO* 4.1 2.6 - - - +
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Residues in contact with PRO1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070A GLY 3.5 3.6 - - - -
1071A GLY* 1.3 88.1 - - - +
1073A SER* 1.3 61.4 + - - +
1075A SER* 2.9 20.9 + - - +
1076A ILE* 3.3 10.9 + - - +
1119A ALA* 4.8 0.4 - - + -
1160A ASP* 4.5 1.8 - - - +
4069F ILE* 4.1 4.5 - - - +
4070F GLY* 3.6 22.0 - - - -
4072F PRO* 3.6 25.1 - - + -
4160F ASP* 3.1 50.7 - - - +
4197F MET* 3.9 12.5 - - + +
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Residues in contact with SER1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A GLU* 2.7 28.7 + - - -
1050A PHE* 3.5 18.6 - - - -
1067A THR 2.7 23.1 - - - +
1068A GLY* 4.4 0.6 - - - -
1069A ILE 3.9 13.7 + - - -
1070A GLY 3.8 1.0 + - - -
1071A GLY 3.4 0.2 - - - -
1072A PRO* 1.3 77.6 - - - +
1074A THR* 1.3 63.1 + - - +
1076A ILE* 3.2 2.9 + - - +
1077A ALA* 3.2 18.9 + - - +
4049F GLU* 5.4 0.2 + - - -
4069F ILE* 2.8 25.2 + - - +
4073F SER* 4.7 0.3 + - - -
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Residues in contact with THR1074 (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 VAL* 6.2 1.1 - - + -
1067A THR* 3.4 30.0 + - + +
1068A GLY 4.1 0.9 + - - -
1070A GLY 2.6 22.0 + - - -
1071A GLY* 3.3 7.6 + - - -
1073A SER* 1.3 78.7 - - - +
1075A SER* 1.3 62.1 + - - +
1077A ALA* 3.4 1.2 + - - +
1078A VAL* 3.1 37.8 + - + +
1091A ARG* 6.3 1.3 - - + -
1198A GLU* 3.5 18.3 - - + +
1201A THR* 4.4 2.2 - - + -
1202A LEU* 4.2 27.8 - - + +
1205A MET* 5.2 0.2 - - - -
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Residues in contact with SER1075 (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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1071A GLY 2.7 20.4 + - - -
1072A PRO 2.9 9.2 + - - -
1074A THR* 1.3 75.7 - - - +
1076A ILE* 1.3 61.5 + - - +
1079A GLU* 3.0 31.0 + - - +
1123A PHE* 4.2 15.9 - - - -
1201A THR* 4.3 3.6 - - - +
1205A MET* 3.6 14.6 - - - +
4161F THR* 3.9 34.5 - - - +
4162F PHE 4.3 1.4 + - - -
4163F TYR* 5.2 2.6 - - - -
4164F PRO* 5.7 0.3 - - - +
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Residues in contact with ILE1076 (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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1008A HIS* 3.5 29.6 - - + +
1009A LEU* 4.6 0.7 - - + -
1050A PHE* 3.9 8.1 - - + -
1072A PRO 3.6 9.4 - - - +
1073A SER* 3.2 7.3 + - - +
1074A THR 3.2 0.2 - - - -
1075A SER* 1.3 81.1 + - - +
1077A ALA* 1.3 62.8 + - - +
1079A GLU* 3.2 1.0 + - - +
1080A GLU* 2.8 60.3 + - - +
4069F ILE* 3.7 42.6 - - + -
4162F PHE* 3.9 26.5 - - + +
4163F TYR* 4.5 7.9 - - + -
4197F MET* 4.7 2.5 - - - -
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Residues in contact with ALA1077 (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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1009A LEU* 3.7 14.2 - - + +
1050A PHE* 4.2 9.2 - - + -
1065A CYS* 4.8 1.6 - - - -
1066A SER 4.2 19.3 - - - +
1067A THR* 4.2 13.0 - - + -
1073A SER 3.2 12.6 + - - +
1074A THR 3.4 3.6 + - - +
1076A ILE* 1.3 79.4 - - - +
1078A VAL* 1.3 55.2 + - + +
1081A LEU* 2.7 51.6 + - + +
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Residues in contact with VAL1078 (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 VAL* 5.2 7.6 - - + -
1067A THR* 5.5 0.7 - - + -
1074A THR* 3.1 25.8 + - + +
1077A ALA* 1.3 74.6 - - + +
1079A GLU* 1.3 65.5 + - - +
1082A ALA* 2.9 26.5 + - - +
1089A PHE* 3.7 39.1 - - + -
1202A LEU* 4.0 21.3 - - + -
1205A MET* 3.8 24.5 - - + -
1206A CYS* 4.1 12.6 - - - -
1211A LEU* 5.1 5.4 - - + -
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Residues in contact with GLU1079 (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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1075A SER 3.0 20.7 + - - +
1076A ILE 3.7 2.2 - - - +
1078A VAL* 1.3 76.4 - - - +
1080A GLU* 1.3 58.9 + - - +
1082A ALA* 3.2 7.4 + - - +
1083A GLN* 2.8 54.7 + - - +
1123A PHE* 5.5 4.3 - - + -
1205A MET* 4.2 8.1 - - + +
1209A GLN* 4.5 14.4 + - - +
4163F TYR* 3.7 28.3 - - + -
4171F THR* 3.4 13.2 - - - +
4172F TYR* 2.8 34.2 + - - +
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Residues in contact with GLU1080 (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 VAL* 3.1 25.7 - - + +
1007A PHE 3.9 1.9 + - - -
1008A HIS* 2.6 52.2 + - - -
1009A LEU* 3.1 25.1 + - + +
1076A ILE* 2.8 26.0 + - - +
1079A GLU* 1.3 74.9 - - + +
1081A LEU* 1.3 65.4 + - - +
1083A GLN* 3.1 9.2 + - - +
1084A LEU* 3.0 25.3 + - - +
4163F TYR* 2.6 28.0 + - + +
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Residues in contact with LEU1081 (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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1009A LEU* 3.7 17.3 - - + -
1011A LEU* 4.1 17.7 - - + -
1016A LEU* 5.7 1.3 - - + -
1022A ALA* 4.3 7.2 - - + -
1024A VAL* 4.1 16.6 - - + -
1063A ILE* 4.4 12.6 - - + -
1065A CYS* 4.0 27.4 - - + -
1077A ALA* 2.7 35.3 + - + +
1080A GLU* 1.3 72.9 - - - +
1082A ALA* 1.3 62.7 + - - +
1084A LEU* 3.0 19.8 + - + +
1085A GLY 3.2 1.0 + - - -
1086A ILE* 3.1 29.0 + - + +
1089A PHE* 3.8 23.8 - - + -
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Residues in contact with ALA1082 (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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1078A VAL 2.9 19.8 + - - +
1079A GLU* 3.3 7.4 - - - +
1081A LEU* 1.3 75.8 - - - +
1083A GLN* 1.3 65.7 + - - +
1085A GLY 3.1 2.6 + - - -
1086A ILE 3.7 16.8 - - - +
1087A ARG* 2.5 25.7 + - - +
1089A PHE* 4.3 7.8 - - + -
1211A LEU* 4.5 9.4 - - + -
4172F TYR* 3.8 26.9 - - + -
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Residues in contact with GLN1083 (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 ASP 4.4 6.1 - - - +
1006A VAL* 4.0 16.1 - - + +
1013A LYS* 3.5 18.4 + - - -
1079A GLU* 2.8 47.1 + - - +
1080A GLU* 3.1 13.9 + - - +
1082A ALA* 1.3 76.9 - - - +
1084A LEU* 1.3 62.3 + - - +
1085A GLY 3.4 0.9 + - - -
4163F TYR* 4.1 15.2 + - - -
4170F ASP 3.7 20.4 + - - +
4171F THR 4.8 1.3 - - - -
4172F TYR* 4.3 14.4 - - + +
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Residues in contact with LEU1084 (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 ASP* 4.2 13.9 - - + +
1006A VAL* 4.0 14.1 - - + -
1009A LEU* 4.6 0.9 - - + -
1011A LEU* 3.6 55.6 - - + +
1012A THR* 3.8 2.9 - - - -
1013A LYS* 3.5 47.2 - - + +
1016A LEU* 3.4 27.0 - - + +
1080A GLU 3.0 17.9 + - - +
1081A LEU* 3.0 18.6 + - + +
1083A GLN* 1.3 78.3 - - - +
1085A GLY* 1.3 55.2 + - - +
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Residues in contact with GLY1085 (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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1013A LYS* 5.3 4.0 - - - -
1016A LEU* 4.7 1.3 - - - -
1019A ALA 4.4 8.4 - - - +
1020A GLN* 4.3 10.0 - - - +
1082A ALA 3.1 6.1 + - - -
1083A GLN 3.2 1.2 - - - -
1084A LEU* 1.3 80.1 - - - +
1086A ILE* 1.3 68.1 + - - +
1087A ARG* 3.3 27.8 + - - +
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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
------------------------------------------------------------
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