Contacts of the helix formed by residues 1136 - 1145 (chain I) in PDB entry 3AOI
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 LYS1136 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124I GLN* 5.0 12.6 - - - +
1134I LEU 3.4 2.8 + - - -
1135I ARG* 1.3 73.7 - - - +
1137I ARG* 1.3 66.5 + - - +
1138I ALA* 3.1 6.3 + - + +
1139I ASP* 3.0 28.3 + - - +
1140I ILE* 3.0 19.9 + - - +
26Y LEU* 5.2 11.7 - - - +
27Y GLN* 6.3 1.6 - - - +
30Y THR* 5.6 4.4 + - - -
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Residues in contact with ARG1137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135I ARG 3.5 2.5 + - - -
1136I LYS* 1.3 71.5 - - - +
1138I ALA* 1.3 56.9 + - - +
1140I ILE* 3.4 8.3 + - - +
1141I GLU* 2.7 58.1 + - + +
1172I HIS* 3.0 39.4 + - - -
1175I ILE* 4.7 20.1 - - + +
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Residues in contact with ALA1138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136I LYS* 3.1 4.8 - - + +
1137I ARG* 1.3 78.1 - - - +
1139I ASP* 1.3 62.2 + - - +
1141I GLU* 2.8 38.4 + - - +
1142I ALA* 2.9 11.1 + - - +
1362I LYS* 3.7 32.1 - - + +
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Residues in contact with ASP1139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124I GLN* 5.7 0.7 - - - +
1135I ARG* 4.2 13.2 + - - +
1136I LYS* 3.0 42.0 + - + +
1138I ALA* 1.3 77.6 - - - +
1140I ILE* 1.3 64.0 + - - +
1142I ALA* 2.9 25.2 + - - +
1143I GLY* 3.1 5.9 + - - -
1357I ARG* 3.2 60.8 + - - +
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Residues in contact with ILE1140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120I VAL* 5.4 1.9 - - - +
1121I PRO 5.7 0.2 - - - +
1122I LEU* 4.2 13.9 - - + +
1134I LEU* 4.1 25.1 - - + -
1135I ARG* 2.8 48.5 - - + +
1136I LYS 3.0 6.0 + - - +
1137I ARG* 3.7 7.0 - - - +
1139I ASP* 1.3 74.9 - - - +
1141I GLU* 1.3 62.6 + - - +
1143I GLY* 3.4 1.8 + - - -
1144I LEU* 3.0 47.0 + - + +
1171I VAL* 4.3 1.3 - - + -
1175I ILE* 3.8 35.4 - - + -
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Residues in contact with GLU1141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776I GLU* 4.7 6.4 - - - +
1137I ARG* 2.7 58.3 + - + +
1138I ALA* 2.8 12.1 + - - +
1140I ILE* 1.3 77.2 - - + +
1142I ALA* 1.3 57.3 + - - +
1145I TYR* 2.7 41.7 + - + +
1168I MET* 3.8 35.3 - - + +
1171I VAL* 4.4 7.6 - - + -
1172I HIS* 4.7 2.0 + - + -
1175I ILE* 5.2 3.8 - - + -
1362I LYS* 3.8 19.3 + - - +
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Residues in contact with ALA1142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138I ALA 2.9 7.7 + - - +
1139I ASP* 2.9 20.1 + - - +
1141I GLU* 1.3 77.0 - - - +
1143I GLY* 1.3 54.7 + - - +
1353I GLN* 5.1 5.8 - - - +
1357I ARG* 5.2 2.5 - - - +
1362I LYS* 6.2 2.0 - - - -
1363I LEU 4.1 16.6 - - - +
1364I HIS* 3.1 35.3 + - - +
1365I ASP* 2.9 19.5 + - - +
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Residues in contact with GLY1143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120I VAL* 3.8 19.4 - - - +
1139I ASP 3.1 9.2 + - - -
1140I ILE* 3.4 2.2 + - - -
1142I ALA* 1.3 77.0 - - - +
1144I LEU* 1.3 58.6 + - - +
1147I ARG* 2.4 38.5 + - - +
1346I ARG* 6.0 1.6 - - - -
1365I ASP* 3.1 18.1 + - - -
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Residues in contact with LEU1144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120I VAL* 4.2 18.2 - - + -
1121I PRO 5.9 0.2 - - - +
1122I LEU* 4.6 16.2 - - + -
1140I ILE* 3.0 41.2 + - + +
1143I GLY* 1.3 78.4 - - - +
1145I TYR* 1.3 71.4 + - - +
1146I GLY 3.4 0.3 + - - -
1147I ARG* 2.8 23.3 + - + +
1166I LEU* 3.9 20.0 - - + +
1171I VAL* 3.4 22.7 - - + -
1174I LEU* 4.5 7.4 - - + -
1186I VAL* 3.8 36.6 - - + -
1188I VAL* 5.5 1.1 - - + -
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Residues in contact with TYR1145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770I LEU* 5.0 2.6 - - - +
775I GLY* 4.2 19.4 - - - -
916I TYR* 3.0 38.7 + + - -
920I LEU* 5.0 4.3 - - + +
1141I GLU* 2.7 30.9 + - + +
1143I GLY 3.9 0.2 - - - -
1144I LEU* 1.3 78.6 - - - +
1146I GLY* 1.3 73.2 + - - +
1147I ARG* 2.8 1.7 + - - +
1168I MET* 4.0 34.5 - - + -
1171I VAL* 4.0 10.9 - - + +
1207I TYR* 4.2 22.4 - + - -
1208I ASP* 4.1 22.3 + - + -
1212I ALA* 5.0 7.8 - - - +
1364I HIS* 3.0 34.0 + + + +
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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