Contacts of the helix formed by residues 126 - 137 (chain B) in PDB entry 1R1P
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 SER 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TYR* 3.6 14.1 - - - -
124B PHE* 3.3 8.8 + - - +
125B PRO* 1.3 79.9 - - - +
127B LEU* 1.3 63.1 + - - +
128B ASN 3.5 2.9 + - - -
129B LYS* 3.0 17.1 + - - +
130B LEU* 3.1 17.7 + - - +
509B SO4 2.8 41.4 + - - -
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Residues in contact with LEU 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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91A PRO* 3.7 30.7 + - + +
92A GLY* 4.0 7.4 - - - +
61B PHE* 4.8 2.2 - - + -
84B ILE* 4.2 31.4 - - + -
94B PHE* 5.3 1.6 - - + -
109B VAL* 4.3 20.2 - - + -
117B TYR* 3.9 25.9 - - + -
126B SER* 1.3 69.7 - - - +
128B ASN* 1.3 67.8 + - - +
130B LEU* 3.2 14.6 + - + +
131B VAL* 2.9 28.4 + - - +
52C PHE* 3.8 32.3 - - + -
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 4.3 3.0 - - - -
126B SER* 3.2 2.7 + - - +
127B LEU* 1.3 80.7 - - - +
129B LYS* 1.3 63.3 + - + +
131B VAL* 3.4 6.9 + - - +
132B ASP* 3.0 23.0 + - - +
509B SO4 2.9 36.0 + - - +
51C SER* 3.7 16.5 - - - -
52C PHE* 2.9 59.2 + - - +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 3.6 18.8 - - + -
125B PRO* 3.8 27.3 - - + +
126B SER* 3.0 16.2 + - - +
128B ASN* 1.3 76.5 - - + +
130B LEU* 1.3 65.3 + - - +
132B ASP* 3.4 7.0 + - + +
133B TYR* 3.0 24.6 + - - +
509B SO4 3.6 26.9 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 3.9 18.8 - - + -
109B VAL* 4.7 3.1 - - + -
117B TYR* 3.7 24.7 - - + -
118B PHE* 3.7 26.7 - - - +
119B LEU* 3.9 27.6 - - + +
124B PHE* 3.5 24.6 - - + -
126B SER 3.1 12.5 + - - +
127B LEU* 3.6 18.4 - - + +
129B LYS* 1.3 77.1 - - - +
131B VAL* 1.3 69.2 + - + +
133B TYR* 3.3 3.5 + - - +
134B TYR* 3.2 33.4 + - + -
139B ILE* 5.7 0.4 - - + -
147B LEU* 5.7 0.7 - - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 4.0 18.8 - - + -
82B PHE* 3.8 27.1 - - + -
84B ILE* 4.0 26.9 - - + -
96B ILE* 5.5 0.7 - - + -
127B LEU 2.9 19.2 + - - +
128B ASN* 3.8 5.2 - - - +
130B LEU* 1.3 80.9 - - + +
132B ASP* 1.3 62.4 + - - +
134B TYR* 3.1 12.5 + - - -
135B ARG* 3.1 36.1 + - + +
147B LEU* 3.9 13.9 - - + +
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Residues in contact with ASP 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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128B ASN 3.0 17.4 + - - +
129B LYS* 3.7 9.2 - - + +
130B LEU 3.3 0.2 - - - -
131B VAL* 1.3 72.8 - - - +
133B TYR* 1.3 66.9 + - - +
135B ARG* 3.1 39.0 + - - +
136B THR* 3.9 6.2 + - - +
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Residues in contact with TYR 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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122B GLU* 3.8 28.5 + - + +
124B PHE* 3.3 39.0 - + + -
129B LYS 3.0 7.3 + - - +
130B LEU 3.5 3.6 - - - +
132B ASP* 1.3 76.7 - - - +
134B TYR* 1.3 91.0 + + - +
135B ARG 3.2 0.2 - - - -
136B THR* 3.3 8.8 + - - -
137B THR* 3.1 46.5 + - - +
501B SO4 2.6 26.1 + - - -
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Residues in contact with TYR 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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119B LEU* 3.5 27.7 + - + +
120B TRP* 3.5 22.1 + + - +
122B GLU* 4.7 0.7 + - - +
124B PHE* 4.1 17.3 - + - -
130B LEU* 3.2 22.3 + - + +
131B VAL 3.1 4.5 + - - -
133B TYR* 1.3 97.4 - + - +
135B ARG* 1.3 60.8 + - - +
136B THR 3.4 0.4 - - - -
137B THR* 3.2 23.2 - - + +
138B SER 3.7 9.9 - - - -
139B ILE* 3.5 22.7 - - + -
145B VAL 4.7 0.5 - - - +
146B PHE* 3.6 2.4 - - - -
147B LEU* 2.9 45.7 + - + -
501B SO4 2.7 38.1 + - - -
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Residues in contact with ARG 135 (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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60B TRP* 4.4 1.4 - - - +
82B PHE* 5.2 1.4 - - - -
131B VAL* 3.1 33.3 + - + +
132B ASP* 3.1 29.2 + - - +
134B TYR* 1.3 81.3 - - - +
136B THR* 1.3 66.5 + - + +
146B PHE* 3.5 17.6 - - - +
147B LEU* 3.6 24.4 + - + +
148B ARG* 4.4 1.8 - - - +
149B ASP* 2.9 49.7 + - - +
50C GLY 3.3 20.8 + - - +
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ASP 3.9 5.9 + - - +
133B TYR* 3.3 8.1 + - - -
135B ARG* 1.3 85.0 - - + +
137B THR* 1.3 64.9 + - - +
146B PHE* 3.5 15.6 - - - -
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Residues in contact with THR 137 (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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133B TYR* 3.1 52.8 + - + +
134B TYR* 3.2 26.0 - - - +
136B THR* 1.3 78.7 + - - +
138B SER* 1.3 74.5 + - - +
141B LYS* 6.3 0.4 - - - +
146B PHE* 3.7 4.5 - - - -
501B SO4 4.5 7.2 - - - +
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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