Contacts of the helix formed by residues 129 - 138 (chain C) in PDB entry 5TBY
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 THR 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C LYS* 5.7 12.6 - - + +
127C THR* 5.5 2.5 - - - +
128C GLY* 1.3 76.5 - - - +
130C TYR* 1.3 64.5 + - - +
131C GLU* 3.1 30.6 + - - +
132C ASP* 2.9 33.9 + - - +
133C PHE* 3.2 22.5 + - - -
193C MET* 4.8 2.7 - - - -
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Residues in contact with TYR 130 (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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129C THR* 1.3 73.4 - - - +
131C GLU* 1.3 66.5 + - + +
133C PHE* 3.1 12.1 + - - +
134C VAL* 2.7 58.0 + - + +
137C LEU* 6.0 1.8 - - + -
186C GLU* 2.8 35.3 + - + +
189C VAL* 3.6 24.7 - - + -
190C LYS* 3.8 33.1 + - + -
193C MET* 4.5 15.1 - - + -
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Residues in contact with GLU 131 (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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129C THR* 3.1 16.2 + - - +
130C TYR* 1.3 93.2 + - + +
132C ASP* 1.3 63.4 + - - +
133C PHE 3.0 0.2 + - - -
134C VAL* 3.0 30.3 - - + +
135C GLU* 3.0 16.1 + - - +
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Residues in contact with ASP 132 (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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785A ILE* 4.2 18.0 - - + +
787A ARG* 4.9 7.3 + - + -
128C GLY* 3.9 10.8 - - - -
129C THR* 2.9 42.5 + - - +
131C GLU* 1.3 76.2 - - - +
133C PHE* 1.3 64.9 + - + +
135C GLU* 3.7 19.0 - - - +
136C GLY* 3.7 11.6 + - - -
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Residues in contact with PHE 133 (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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785A ILE* 4.5 1.6 - - + -
787A ARG* 3.5 14.4 - - + -
788A ILE* 1.6 49.1 - - + -
791A GLN* 1.7 51.6 - - + -
128C GLY* 3.6 13.7 - - - -
129C THR 3.2 18.4 - - - -
130C TYR* 3.1 4.9 + - - +
131C GLU 3.1 0.4 - - - -
132C ASP* 1.3 81.9 - - + +
134C VAL* 1.3 60.0 + - - +
135C GLU 3.1 1.1 - - - -
136C GLY* 2.9 19.0 + - - +
137C LEU* 3.0 22.6 + - + +
189C VAL* 3.5 35.0 - - + -
192C ILE* 5.6 0.7 - - + -
193C MET* 3.6 7.0 - - + -
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Residues in contact with VAL 134 (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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130C TYR* 2.7 38.7 + - + +
131C GLU* 3.0 37.0 - - + +
133C PHE* 1.3 71.6 - - - +
135C GLU* 1.3 60.7 + - + +
137C LEU* 3.7 13.3 + - + +
138C ARG* 3.0 45.6 + - + +
185C TYR* 6.1 2.7 - - + -
186C GLU* 6.6 0.2 - - + -
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Residues in contact with GLU 135 (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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724A ILE* 3.3 41.2 - - + +
727A PRO* 5.7 1.6 - - - +
780A ARG* 2.7 52.7 + - - +
781A LEU* 4.0 6.5 - - + +
131C GLU 3.0 16.7 + - - +
132C ASP* 3.7 22.1 - - - +
134C VAL* 1.3 77.1 - - + +
136C GLY* 1.3 64.1 + - - +
138C ARG* 3.0 21.5 + - - +
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Residues in contact with GLY 136 (chain C).
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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781A LEU* 4.2 3.1 - - - -
784A ILE* 3.2 30.5 - - - +
785A ILE* 5.6 8.3 - - - -
132C ASP 3.7 5.6 + - - -
133C PHE* 2.9 12.0 + - - -
135C GLU* 1.3 77.0 - - - +
137C LEU* 1.3 60.4 + - - +
138C ARG 3.4 1.2 + - - -
139C VAL* 3.7 3.8 - - - +
140C PHE* 3.0 23.1 - - - -
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Residues in contact with LEU 137 (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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788A ILE* 6.1 4.3 - - + -
130C TYR* 6.0 1.8 - - + +
133C PHE* 3.0 21.0 + - + +
134C VAL* 4.0 12.8 - - + +
135C GLU 3.1 0.2 + - - -
136C GLY* 1.3 74.3 - - - +
138C ARG* 1.3 56.5 + - - +
139C VAL 3.1 4.5 - - - -
140C PHE* 2.9 32.6 + - + +
141C ASP 3.3 9.4 + - - -
153C LEU* 6.3 3.4 - - + -
185C TYR* 3.6 59.6 - - + +
186C GLU* 4.4 3.4 - - - +
188C PHE* 5.7 4.5 - - + -
189C VAL* 3.7 29.8 - - + -
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Residues in contact with ARG 138 (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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720A GLN* 4.5 1.6 - - - +
723A ARG* 1.2 72.4 + - - +
724A ILE* 3.4 31.5 - - + +
777A ARG* 4.7 4.9 + - - -
781A LEU* 5.4 0.4 - - - -
134C VAL* 3.0 34.8 - - + +
135C GLU 3.0 11.6 + - - +
137C LEU* 1.3 73.8 - - - +
139C VAL* 1.3 56.5 + - - +
141C ASP* 4.5 7.9 - - - +
144C GLY* 4.9 13.2 - - - -
185C TYR* 3.4 26.3 + - - -
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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