Contacts of the helix formed by residues 1133 - 1148 (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 ASP1133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1131A VAL 4.0 0.2 + - - -
1132A ALA* 1.3 71.9 - - - +
1134A PHE* 1.3 65.9 + - - +
1135A ALA* 2.8 15.1 + - - +
1136A CYS* 2.7 29.1 + - - +
1137A THR* 2.8 26.2 + - - -
1211A LEU 5.3 0.7 - - - +
1212A ARG* 3.3 33.3 - - + +
1213A ALA* 3.0 31.5 + - - +
5111E THR* 6.1 0.2 - - - -
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Residues in contact with PHE1134 (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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1132A ALA 3.6 2.6 + - - -
1133A ASP* 1.3 74.4 + - - +
1135A ALA* 1.3 60.7 + - + +
1137A THR* 3.5 3.7 + - - -
1138A THR* 2.6 47.6 + - + -
5111E THR* 4.3 9.7 - - + +
5134E PHE* 3.8 22.7 - + - -
5137E THR* 3.5 31.9 - - + -
5138E THR* 3.9 25.1 - - + -
5141E VAL* 3.7 35.7 - - + -
5142E GLU* 6.1 0.4 - - - -
5153E VAL* 3.8 27.4 - - + +
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Residues in contact with ALA1135 (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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1133A ASP* 2.8 17.4 + - - +
1134A PHE* 1.3 78.7 - - + +
1136A CYS* 1.3 55.7 + - - +
1138A THR* 3.2 7.4 + - - -
1139A ALA* 2.9 29.1 + - - +
1212A ARG* 3.7 22.9 - - - +
1252A LEU* 3.7 9.4 - - + +
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Residues in contact with CYS1136 (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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1088A THR* 3.6 31.4 - - - -
1090A LEU* 4.0 5.8 - - + -
1133A ASP* 2.7 21.5 + - - +
1134A PHE 3.4 0.2 - - - -
1135A ALA* 1.3 73.2 - - - +
1137A THR* 1.3 59.3 + - - +
1139A ALA* 3.2 3.8 + - - +
1140A LEU* 3.0 33.6 + - - +
1212A ARG* 3.9 9.4 - - - -
1213A ALA 3.6 32.1 - - - +
1214A GLY* 3.7 9.2 - - - -
1252A LEU* 3.9 16.7 - - - +
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Residues in contact with THR1137 (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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1109A VAL* 3.7 22.9 - - + -
1110A THR 4.2 6.6 + - - +
1111A THR* 4.5 12.7 - - + -
1132A ALA* 3.1 22.7 + - - +
1133A ASP 2.8 17.3 + - - -
1134A PHE* 3.9 4.3 - - - -
1136A CYS* 1.3 74.7 - - - +
1138A THR* 1.3 65.1 + - - +
1140A LEU* 3.5 9.2 + - - +
1141A VAL* 3.1 32.1 + - + +
1153A VAL* 5.1 0.2 - - + -
1214A GLY* 5.3 0.3 - - - -
1215A MET 5.7 0.3 + - - -
5134E PHE* 4.0 23.1 - - + -
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Residues in contact with THR1138 (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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1134A PHE* 2.6 45.6 + - + -
1135A ALA* 3.2 6.9 + - - -
1137A THR* 1.3 77.0 - - - +
1139A ALA* 1.3 64.8 + - - +
1141A VAL* 3.2 3.2 + - + +
1142A GLU* 3.0 45.5 + - + +
5134E PHE* 3.6 20.4 - - + -
5138E THR* 6.1 3.6 - - + -
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Residues in contact with ALA1139 (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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1135A ALA 2.9 13.6 + - - +
1136A CYS 3.4 9.2 - - - +
1138A THR* 1.3 78.4 - - - +
1140A LEU* 1.3 56.4 + - - +
1142A GLU* 4.7 2.5 - - - -
1143A ALA* 3.0 30.0 + - - +
1248A ALA* 3.4 28.2 - - + +
1251A ARG* 3.8 17.8 - - + +
1252A LEU* 3.8 19.1 - - + -
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Residues in contact with LEU1140 (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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1090A LEU* 4.4 7.0 - - + -
1109A VAL* 4.0 20.8 - - + +
1136A CYS 3.0 21.9 + - - +
1137A THR* 3.9 4.9 - - - +
1138A THR 3.2 0.2 - - - -
1139A ALA* 1.3 75.1 - - - +
1141A VAL* 1.3 64.7 + - - +
1143A ALA* 4.4 0.2 - - - -
1144A ALA* 3.2 23.0 + - - +
1214A GLY* 4.0 9.2 - - - -
1215A MET 3.6 39.3 - - - +
1216A VAL* 3.7 24.5 - - + +
1244A ILE* 3.8 9.0 - - + +
1245A VAL* 4.0 16.8 - - + +
1248A ALA* 3.5 21.8 - - + -
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Residues in contact with VAL1141 (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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1109A VAL* 4.4 10.5 - - + -
1137A THR* 3.1 19.9 + - + +
1138A THR 3.2 4.2 + - - +
1140A LEU* 1.3 76.7 - - - +
1142A GLU* 1.3 65.9 + - + +
1144A ALA* 3.5 7.1 - - - +
1145A LYS* 3.4 19.1 + - - +
1151A THR* 5.7 2.4 - - + +
1153A VAL* 3.9 27.6 - - + -
5134E PHE* 3.5 31.4 - - + -
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Residues in contact with GLU1142 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1138A THR* 3.0 37.7 + - + +
1139A ALA* 3.8 3.6 - - - +
1141A VAL* 1.3 79.9 - - + +
1143A ALA* 1.3 59.4 + - - +
1145A LYS* 3.1 12.0 + - + +
1146A SER* 2.8 28.2 + - - -
1251A ARG* 3.0 35.9 + - - +
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Residues in contact with ALA1143 (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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1139A ALA 3.0 18.3 + - - +
1140A LEU 4.0 0.2 - - - +
1142A GLU* 1.3 73.3 - - - +
1144A ALA* 1.3 57.1 + - - +
1146A SER* 3.5 2.4 - - - -
1147A ILE* 2.7 42.0 + - - +
1244A ILE* 3.2 32.3 - - + +
1247A GLU* 3.7 15.3 - - + -
1248A ALA* 3.4 15.0 - - + +
1251A ARG* 4.1 3.1 - - - +
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Residues in contact with ALA1144 (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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1107A VAL* 5.0 1.3 - - + -
1109A VAL* 5.6 0.2 - - + -
1140A LEU 3.2 16.6 + - - +
1141A VAL 3.5 6.7 - - - +
1143A ALA* 1.3 77.3 - - - +
1145A LYS* 1.3 58.1 + - - +
1147A ILE* 3.8 0.7 - - - +
1148A GLY 2.8 24.4 + - - -
1149A ALA* 3.5 12.8 + - - +
1151A THR* 3.3 35.9 - - + +
1244A ILE* 3.7 23.3 - - + +
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Residues in contact with LYS1145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1141A VAL* 3.4 9.9 + - + +
1142A GLU* 3.1 14.0 + - + +
1144A ALA* 1.3 79.7 - - - +
1146A SER* 1.3 60.9 + - - +
1147A ILE 3.4 0.7 + - - -
1148A GLY* 3.4 10.5 + - - -
1149A ALA 5.4 1.1 - - - +
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Residues in contact with SER1146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142A GLU 2.8 16.2 + - - -
1143A ALA* 3.6 3.1 - - - -
1145A LYS* 1.3 78.2 - - - +
1147A ILE* 1.3 64.3 + - - +
1247A GLU* 3.8 20.6 + - - +
1251A ARG* 3.6 17.7 + - - -
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Residues in contact with ILE1147 (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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1143A ALA 2.7 29.4 + - - +
1144A ALA 3.8 2.9 - - - +
1146A SER* 1.3 78.5 - - - +
1148A GLY* 1.3 68.6 + - - +
1240A HIS* 4.3 12.6 - - + -
1243A LYS* 4.1 29.2 - - + +
1244A ILE* 3.8 33.7 - - + -
1247A GLU* 3.8 26.7 - - + +
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Residues in contact with GLY1148 (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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1144A ALA 2.8 9.1 + - - -
1145A LYS* 3.4 9.1 + - - -
1147A ILE* 1.3 82.0 - - - +
1149A ALA* 1.3 65.5 + - - +
1240A HIS* 3.1 13.7 + - - -
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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