Contacts of the helix formed by residues 1131 - 1139 (chain C) in PDB entry 5VZU
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 THR1131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1129C GLY 5.7 0.7 - - - +
1130C LYS* 1.3 73.9 - - - +
1132C PRO* 1.3 66.7 - - - +
1133C GLU* 3.4 22.1 + - - +
1134C GLU* 2.7 48.5 + - - +
1135C ILE* 3.0 27.2 + - - +
89D SER* 4.2 1.3 - - - -
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Residues in contact with PRO1132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131C THR* 1.3 85.8 - - - +
1133C GLU* 1.3 79.3 + - - +
1135C ILE* 3.5 1.3 + - + +
1136C ARG* 3.1 38.9 + - - +
89D SER* 3.6 36.3 - - - +
92D GLN* 3.8 36.6 - - + +
93D VAL* 4.1 6.3 - - + -
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Residues in contact with GLU1133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131C THR* 3.4 21.4 - - - +
1132C PRO* 1.3 92.2 - - - +
1134C GLU* 1.3 65.3 + - + +
1136C ARG* 3.3 36.6 + - - +
1137C LYS* 3.1 31.7 + - - +
1154C ARG* 5.2 7.5 + - - -
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Residues in contact with GLU1134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129C GLY 4.4 1.2 - - - +
1130C LYS* 3.1 26.0 - - + +
1131C THR* 2.7 56.5 + - - +
1133C GLU* 1.3 72.5 - - + +
1135C ILE* 1.3 60.4 + - - +
1137C LYS* 3.0 12.4 + - - +
1138C THR* 2.7 32.4 + - - +
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Residues in contact with ILE1135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127C ILE* 4.0 27.6 - - + -
1130C LYS* 3.8 27.8 - - + +
1131C THR 3.0 19.0 + - - +
1132C PRO 3.7 3.8 - - - +
1134C GLU* 1.3 78.4 - - - +
1136C ARG* 1.3 63.4 + - - +
1138C THR* 3.1 8.5 + - - -
1139C PHE* 3.1 40.1 + - + +
1141C ILE* 5.0 4.0 - - + -
67D LEU* 5.7 0.7 - - + -
89D SER* 4.0 14.1 - - - -
90D LEU* 4.3 14.1 - - + +
93D VAL* 3.3 33.7 - - + -
97D PHE* 5.1 2.2 - - + -
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Residues in contact with ARG1136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132C PRO* 3.1 19.6 + - - +
1133C GLU* 3.3 46.3 + - - +
1135C ILE* 1.3 78.1 - - - +
1137C LYS* 1.3 61.1 + - + +
1140C ASN* 3.0 8.3 + - - -
1141C ILE* 2.8 52.4 + - + +
1142C LYS 4.5 0.2 - - - -
1143C ASN* 4.2 33.8 + - - +
92D GLN 4.4 3.4 + - - -
93D VAL* 3.4 43.7 + - + +
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Residues in contact with LYS1137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133C GLU* 3.1 37.3 + - - +
1134C GLU* 3.0 11.4 + - - +
1136C ARG* 1.3 78.1 - - + +
1138C THR* 1.3 67.6 + - - +
1139C PHE 3.2 1.0 + - - -
1140C ASN* 3.3 18.5 + - - +
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Residues in contact with THR1138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C GLN* 2.2 34.4 + - - +
1126C MET* 5.3 8.5 - - + -
1130C LYS* 4.0 27.8 + - - +
1134C GLU* 2.7 24.6 + - - +
1135C ILE* 3.1 8.8 + - - -
1137C LYS* 1.3 77.5 - - - +
1139C PHE* 1.3 67.2 - - + +
1140C ASN* 5.4 0.7 - - - +
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Residues in contact with PHE1139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C GLN* 3.3 28.0 - - - +
1101C PHE* 3.8 15.7 - + - -
1123C VAL* 4.5 7.6 - - + -
1126C MET* 4.1 37.0 - - + -
1127C ILE* 4.0 22.4 - - + -
1130C LYS* 6.4 1.1 - - + -
1135C ILE* 3.1 28.4 + - + +
1138C THR* 1.3 87.1 - - + +
1140C ASN* 1.3 71.8 + - - +
1141C ILE* 3.4 21.8 + - + +
66D SER* 4.7 12.8 - - - -
67D LEU* 3.7 38.6 - - + -
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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