Contacts of the helix formed by residues 1128 - 1133 (chain B) in PDB entry 3I8E
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 ASP1128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1125B THR* 3.5 32.3 + - + -
1126B ALA 3.1 1.0 - - - -
1127B ASP* 1.3 78.8 + - - +
1129B LEU* 1.3 65.6 + - + +
1130B ILE 3.6 0.7 - - - -
1131B LYS* 3.4 19.1 - - - +
1132B VAL* 3.2 29.6 + - - +
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Residues in contact with LEU1129 (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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1050B LEU* 4.0 22.4 - - + -
1051B LEU* 6.2 0.7 - - + -
1054B MET* 3.7 29.6 - - + -
1097B PHE* 4.2 18.4 - - + -
1108B VAL* 6.4 0.9 - - + -
1109B VAL* 5.1 10.8 - - + -
1125B THR 5.1 6.7 - - - +
1126B ALA 3.6 18.7 + - - +
1128B ASP* 1.3 85.9 - - + +
1130B ILE* 1.3 53.8 + - - +
1131B LYS 2.7 15.3 + - - -
1132B VAL* 3.9 23.1 - - + +
1133B VAL* 2.9 28.7 + - + +
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Residues in contact with ILE1130 (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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628B LYS* 4.1 39.3 - - + +
1097B PHE* 3.8 9.8 - - + -
1098B LEU* 3.9 25.2 - - + +
1102B ARG* 5.7 5.6 - - - +
1105B MET* 4.1 29.4 - - + -
1126B ALA 4.1 1.8 + - - +
1127B ASP* 3.1 39.7 - - + +
1129B LEU* 1.3 75.9 - - - +
1131B LYS* 1.3 57.1 + - + +
1133B VAL 4.6 0.4 - - - -
1134B GLU* 3.0 29.5 - - - +
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Residues in contact with LYS1131 (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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630B THR* 5.5 13.5 - - - -
1127B ASP 4.4 7.0 - - - +
1128B ASP* 3.4 24.7 - - - +
1129B LEU 2.7 1.2 - - - -
1130B ILE* 1.3 82.2 - - + +
1132B VAL* 1.3 59.0 + - + +
1133B VAL 3.4 0.4 - - - -
1134B GLU* 3.4 11.2 + - - +
1135B GLU* 3.1 40.2 + - + +
1138B ARG* 5.1 0.7 + - - -
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Residues in contact with VAL1132 (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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1047B TRP* 3.7 35.4 - - + -
1050B LEU* 5.6 9.4 - - + -
1051B LEU* 5.4 6.5 - - + -
1054B MET* 6.5 0.2 - - + -
1128B ASP* 3.2 21.5 - - - +
1129B LEU* 2.9 26.9 + - + +
1131B LYS* 1.3 73.9 - - + +
1133B VAL* 1.3 60.9 + - + +
1134B GLU 3.1 1.8 - - - -
1135B GLU* 3.0 35.1 + - - +
1136B LEU* 3.6 11.3 + - + +
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Residues in contact with VAL1133 (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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1054B MET* 3.8 34.5 - - + -
1094B ILE* 3.4 28.0 - - + +
1095B GLU* 3.9 11.7 - - + +
1097B PHE* 4.2 10.1 - - + -
1098B LEU* 3.6 30.7 - - + -
1129B LEU* 2.9 17.6 + - + +
1132B VAL* 1.3 77.8 - - + +
1134B GLU* 1.3 60.2 + - - +
1136B LEU* 3.4 13.3 + - + +
1137B THR* 3.4 18.9 + - - +
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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