Contacts of the helix formed by residues 126 - 134 (chain B) in PDB entry 2D2C
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 ARG 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B GLU* 2.4 44.1 + - - +
117B VAL* 3.8 19.0 - - + +
118B ASN* 3.3 33.9 - - - +
121B GLN* 5.0 1.1 - - - +
122B ASN 3.5 2.2 + - - -
123B PRO* 2.5 20.4 - - + +
125B ARG* 1.3 74.1 - - - +
127B PRO* 1.3 56.6 - - - -
128B VAL* 2.8 79.1 + - + +
129B ALA* 3.0 7.8 + - - +
132B ILE* 5.4 0.2 - - - +
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Residues in contact with PRO 127 (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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123B PRO 3.5 6.7 - - - +
124B PHE 4.1 4.9 - - - +
125B ARG 2.5 24.0 - - - +
126B ARG* 1.3 73.6 - - - +
128B VAL* 1.3 61.9 + - + +
129B ALA 2.4 19.9 + - - -
130B THR* 2.5 25.2 + - + +
131B THR* 2.7 31.4 + - + -
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Residues in contact with VAL 128 (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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126B ARG* 2.8 53.3 + - + +
127B PRO* 1.3 85.0 - - + +
129B ALA* 1.3 55.9 + - - +
131B THR* 4.1 7.0 + - - -
132B ILE* 2.8 24.4 - - - +
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Residues in contact with ALA 129 (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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105A TYR* 2.9 22.1 + - + +
115B GLU* 3.5 11.2 - - + +
123B PRO* 3.1 29.8 - - + -
126B ARG* 3.0 13.7 + - - +
127B PRO 2.4 4.8 + - - -
128B VAL* 1.3 75.3 - - - +
130B THR* 1.3 68.5 + - - +
132B ILE* 2.8 23.2 - - - +
133B PHE* 2.9 5.7 + - - +
201B CLA 5.0 0.7 - - - +
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Residues in contact with THR 130 (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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105A TYR* 3.2 12.6 + - - -
123B PRO 3.3 13.0 + - - -
124B PHE* 3.6 18.9 + - + +
127B PRO* 2.5 21.7 + - + -
129B ALA* 1.3 72.7 - - - +
131B THR* 1.3 59.9 + - + +
133B PHE* 2.4 32.2 + - + +
134B LEU* 2.6 43.0 + - + -
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Residues in contact with THR 131 (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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127B PRO* 2.7 35.2 + - + +
128B VAL* 4.1 6.2 - - - -
130B THR* 1.3 77.8 - - + +
132B ILE* 1.3 79.0 + - - +
133B PHE 2.8 1.7 + - - -
134B LEU* 2.9 14.7 - - - +
135B PHE* 2.9 21.1 - - - +
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Residues in contact with ILE 132 (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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115B GLU* 3.7 17.7 - - - +
126B ARG* 5.4 0.4 - - - +
128B VAL 2.8 27.4 - - - +
129B ALA* 2.8 23.3 - - - +
131B THR* 1.3 82.6 + - - +
133B PHE* 1.3 51.6 + - - +
135B PHE* 3.4 26.0 - - + -
136B GLY* 2.5 32.8 + - - -
201B CLA 3.2 16.6 - - + +
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Residues in contact with PHE 133 (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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102A PHE* 4.1 20.9 - + - -
105A TYR* 3.4 28.3 - + + -
106A LEU* 3.3 37.0 - - + -
129B ALA 2.9 10.3 + - - +
130B THR* 2.4 26.0 + - + +
132B ILE* 1.3 65.8 - - - +
134B LEU* 1.3 76.2 + - + -
135B PHE 2.3 19.8 + - - -
136B GLY 2.9 6.6 + - - -
137B THR* 2.4 48.3 + - + +
201B CLA 3.5 30.7 - - + -
15E PHE* 4.3 12.6 - + - -
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Residues in contact with LEU 134 (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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106A LEU* 5.6 0.4 - - + -
130B THR* 2.6 41.8 + - + +
131B THR* 2.9 10.5 - - - +
133B PHE* 1.3 88.7 - - + +
135B PHE* 1.3 59.3 + - - +
137B THR* 3.6 6.1 - - - +
138B LEU* 3.4 24.0 - - + +
15E PHE* 5.2 3.6 - - + -
19E ALA* 3.5 29.8 - - + -
20E VAL* 3.6 29.6 - - + -
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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