Contacts of the helix formed by residues 1109 - 1123 (chain B) in PDB entry 1AIS
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 LEU1109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1108B ASN* 1.3 86.8 - - + +
1110B ALA* 1.3 61.1 + - - +
1112B ALA* 3.6 8.6 - - - +
1113B LEU* 3.3 22.7 + - - +
1137B TYR* 4.8 7.9 - - + +
1138B ARG* 5.4 12.1 - - + -
1141B VAL* 4.5 35.2 - - + -
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Residues in contact with ALA1110 (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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1108B ASN 3.1 4.8 - - - +
1109B LEU* 1.3 77.3 - - - +
1111B PHE* 1.3 57.6 + - - +
1112B ALA 3.2 0.2 - - - -
1113B LEU* 3.7 5.1 + - - +
1114B SER* 2.7 32.4 + - - -
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Residues in contact with PHE1111 (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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1108B ASN* 3.3 15.0 + - - +
1110B ALA* 1.3 77.5 - - - +
1112B ALA* 1.3 64.8 + - - +
1114B SER* 3.2 11.1 + - - -
1115B GLU* 3.1 67.7 + - + +
1118B ARG* 4.6 21.3 - - - -
1151B ILE* 4.7 9.2 - - + -
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Residues in contact with ALA1112 (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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1108B ASN 2.9 16.9 + - - +
1109B LEU* 3.6 9.6 - - - +
1111B PHE* 1.3 75.4 - - - +
1113B LEU* 1.3 63.5 + - - +
1115B GLU* 3.2 25.8 + - - +
1116B LEU 3.2 8.5 + - - -
1137B TYR* 3.8 37.0 - - + +
1151B ILE* 4.0 3.6 - - + +
1155B MET* 3.8 16.3 - - + +
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Residues in contact with LEU1113 (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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1109B LEU 3.3 13.6 + - - +
1110B ALA* 4.2 4.9 - - - +
1112B ALA* 1.3 78.4 - - - +
1114B SER* 1.3 61.4 + - - +
1116B LEU* 3.3 12.8 - - + +
1117B ASP* 2.9 42.6 + - - +
1130B GLU* 4.7 7.0 - - - +
1134B ALA* 3.7 30.1 - - + -
1138B ARG* 5.2 3.4 - - - +
1155B MET* 4.4 3.6 - - + +
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Residues in contact with SER1114 (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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1110B ALA 2.7 19.2 + - - -
1111B PHE* 3.2 19.1 + - - -
1112B ALA 3.1 0.4 - - - -
1113B LEU* 1.3 77.0 - - - +
1115B GLU* 1.3 63.0 + - - +
1117B ASP* 3.4 20.6 + - - +
1118B ARG* 3.4 22.1 + - - +
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Residues in contact with GLU1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111B PHE* 3.1 49.9 + - + +
1112B ALA* 3.2 12.5 + - - +
1114B SER* 1.3 73.3 - - - +
1116B LEU* 1.3 59.9 + - - +
1117B ASP 3.1 0.2 - - - -
1118B ARG* 3.0 24.1 + - - +
1119B ILE* 2.9 41.0 + - + +
1151B ILE* 3.3 24.1 - - - +
1152B GLU* 3.7 29.3 + - + +
1155B MET* 4.8 3.6 - - + +
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Residues in contact with LEU1116 (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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1112B ALA 3.2 8.9 + - - +
1113B LEU* 3.3 20.6 - - + +
1115B GLU* 1.3 80.0 - - - +
1117B ASP* 1.3 50.9 - - - +
1119B ILE* 3.4 10.8 + - - +
1120B THR* 2.8 33.7 + - - +
1125B LEU* 5.5 0.7 - - + -
1130B GLU* 3.3 55.2 - - + +
1133B ALA* 4.0 6.1 - - + -
1134B ALA* 3.7 27.6 - - + +
1155B MET* 3.7 24.2 - - + -
1159B VAL* 4.6 7.6 - - + -
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Residues in contact with ASP1117 (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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1113B LEU* 2.9 28.3 + - - +
1114B SER* 3.4 16.3 + - - +
1115B GLU 3.1 0.4 - - - -
1116B LEU* 1.3 76.0 - - - +
1118B ARG* 1.3 58.6 + - + +
1120B THR* 3.1 8.5 - - + +
1121B ALA* 2.9 32.2 + - - +
1130B GLU* 3.1 19.8 - - - +
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Residues in contact with ARG1118 (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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1111B PHE* 4.6 20.4 - - - -
1114B SER* 3.6 17.0 + - - +
1115B GLU* 3.0 27.7 + - - +
1117B ASP* 1.3 77.7 - - + +
1119B ILE* 1.3 53.8 + - + +
1121B ALA* 3.3 3.7 + - - +
1122B GLN* 2.8 57.9 + - - +
1178B ILE 5.7 0.7 - - - +
1180B ARG* 5.4 17.1 - - - +
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Residues in contact with ILE1119 (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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1115B GLU* 2.9 23.7 + - + +
1116B LEU* 3.5 16.4 - - - +
1118B ARG* 1.3 77.0 - - + +
1120B THR* 1.3 52.7 + - - +
1122B GLN* 3.8 0.3 - - - +
1123B LEU* 2.8 62.2 + - + +
1125B LEU* 4.0 3.4 - - + -
1152B GLU 5.8 0.4 - - - +
1155B MET* 3.9 17.9 - - + +
1156B ALA* 4.3 13.5 - - + +
1159B VAL* 3.8 35.9 - - + -
1175B ILE* 5.0 1.1 - - + -
1178B ILE* 3.6 19.5 - - + +
1179B ALA* 5.1 8.3 - - + -
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Residues in contact with THR1120 (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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1116B LEU* 2.8 30.7 + - - +
1117B ASP* 3.1 17.3 - - + +
1119B ILE* 1.3 71.8 - - - +
1121B ALA* 1.3 61.4 + - + +
1124B LYS* 2.7 27.9 + - - -
1125B LEU* 2.8 53.3 + - - +
1130B GLU* 3.6 30.7 + - - +
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Residues in contact with ALA1121 (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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1117B ASP 2.9 21.5 + - - +
1118B ARG* 3.7 5.2 - - - +
1120B THR* 1.3 76.5 - - + +
1122B GLN* 1.3 66.0 + - + +
1124B LYS* 3.4 18.3 + - - +
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Residues in contact with GLN1122 (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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1118B ARG* 2.8 39.3 + - - +
1119B ILE 3.9 2.5 - - - +
1121B ALA* 1.3 79.5 - - + +
1123B LEU* 1.3 61.7 + - - +
1124B LYS* 3.6 13.5 + - - -
1178B ILE* 3.1 61.3 + - + +
1180B ARG* 6.0 0.7 + - - -
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Residues in contact with LEU1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119B ILE* 2.8 42.7 + - + +
1122B GLN* 1.3 73.7 - - - +
1124B LYS* 1.3 71.6 + - - +
1125B LEU* 3.2 19.0 + - + -
1170B ARG* 3.2 30.3 + - - +
1174B GLU* 3.5 49.5 - - + +
1175B ILE* 3.7 25.4 - - + -
1178B ILE* 4.1 16.6 - - + -
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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