Contacts of the helix formed by residues 123 - 133 (chain H) in PDB entry 3WBR
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 123 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165F VAL* 4.9 6.5 - - - -
167F PHE* 4.6 6.5 - - - -
91H GLN* 5.0 9.5 + - - +
121H ILE* 3.7 3.5 - - - +
122H ASN* 1.3 90.8 - - + +
124H ARG* 1.3 63.7 + - - +
125H GLU* 3.5 17.3 + - - +
126H GLU* 3.0 26.6 + - - +
127H GLN* 3.0 21.1 + - - +
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Residues in contact with ARG 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F VAL* 5.2 8.7 - - + +
167F PHE* 3.5 34.4 - - + -
123H THR* 1.3 72.1 - - - +
125H GLU* 1.3 72.6 + - - +
127H GLN* 3.1 4.3 + - - +
128H ASP* 2.8 60.2 + - - +
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H PHE* 3.7 19.9 - - + -
91H GLN* 4.8 5.6 - - - +
123H THR* 3.3 18.8 - - - +
124H ARG* 1.3 89.8 + - - +
126H GLU* 1.3 56.8 + - - +
128H ASP* 3.4 9.5 + - - +
129H PHE* 2.9 29.5 + - - +
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Residues in contact with GLU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H PHE* 3.6 15.8 - - + -
91H GLN* 5.4 4.0 - - - +
95H TYR* 2.6 30.6 + - + +
119H VAL* 4.7 0.3 - - - +
120H VAL 3.1 11.8 - - - +
121H ILE* 4.1 2.9 - - + -
122H ASN* 2.9 32.7 + - - +
123H THR* 3.0 23.0 + - - +
125H GLU* 1.3 74.3 - - - +
127H GLN* 1.3 64.5 + - - +
129H PHE* 3.2 2.3 + - - +
130H ILE* 3.0 37.5 + - + +
207H LYS* 2.7 26.2 + - - +
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Residues in contact with GLN 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F PHE* 3.6 55.1 - - + +
121H ILE* 3.5 20.1 - - + +
123H THR 3.0 7.1 + - - +
124H ARG 3.1 8.3 + - - +
126H GLU* 1.3 74.2 - - - +
128H ASP* 1.3 68.2 + - - +
130H ILE* 3.3 7.7 + - - +
131H ILE* 3.0 40.9 + - + +
183H ILE* 3.6 23.1 - - - +
191H TRP* 4.9 1.8 + - - +
192H GLY* 4.7 6.3 - - - +
193H TRP* 3.1 20.7 + - - +
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Residues in contact with ASP 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ARG* 2.8 46.5 + - - +
125H GLU* 3.6 9.4 - - - +
127H GLN* 1.3 79.2 - - - +
129H PHE* 1.3 62.8 + - - +
131H ILE* 3.5 14.1 + - - +
132H GLN* 3.5 28.2 + - - +
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Residues in contact with PHE 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H THR* 3.5 24.5 - - + -
89H SER 3.3 28.0 - - - -
90H PHE* 3.6 35.4 - + + -
95H TYR* 3.5 37.9 - + + -
125H GLU 2.9 17.8 + - - +
126H GLU 3.2 5.1 + - - +
128H ASP* 1.3 74.1 - - - +
130H ILE* 1.3 68.7 + - + +
132H GLN* 3.0 39.0 - - - +
133H ASN* 3.2 27.3 + - - -
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Residues in contact with ILE 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H TYR* 4.1 21.3 - - + -
97H ILE* 5.6 0.7 - - + -
119H VAL* 3.7 18.4 - - + -
121H ILE* 3.7 35.0 - - + -
126H GLU* 3.0 28.6 + - + +
127H GLN* 3.3 6.7 + - - +
129H PHE* 1.3 77.2 - - + +
131H ILE* 1.3 58.9 + - - +
133H ASN* 2.9 25.7 + - - +
134H LEU* 3.3 29.9 - - + +
183H ILE* 4.7 9.4 - - + -
205H ILE* 3.8 21.8 - - + -
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Residues in contact with ILE 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H GLN* 3.0 41.5 + - + +
128H ASP* 3.6 14.6 - - - +
129H PHE 3.3 0.2 - - - -
130H ILE* 1.3 76.0 - - - +
132H GLN* 1.3 61.4 + - + +
134H LEU* 3.0 32.5 + - - +
183H ILE* 4.3 11.0 - - + -
191H TRP* 3.5 59.7 - - + +
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Residues in contact with GLN 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H ASP* 3.5 15.4 + - - +
129H PHE* 3.0 37.0 - - + +
131H ILE* 1.3 81.7 - - + +
133H ASN* 1.3 64.8 + - - +
134H LEU 3.4 2.8 - - - +
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Residues in contact with ASN 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H THR* 3.0 34.9 + - - +
95H TYR* 5.5 2.1 - - + +
97H ILE* 3.7 35.6 - - + +
129H PHE* 3.2 39.0 + - + -
130H ILE* 2.9 13.0 + - - +
132H GLN* 1.3 85.8 - - - +
134H LEU* 1.3 57.9 + - - +
135H LYS* 5.5 1.2 - - - +
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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