Contacts of the helix formed by residues 136 - 145 (chain B) in PDB entry 1F15
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 VAL 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLY 5.2 9.2 - - - +
84B SER* 5.3 5.2 - - - +
85B TYR* 4.0 20.4 - - + -
135B SER* 1.3 73.5 - - - +
137B ALA* 1.3 75.6 + - + +
139B ILE* 3.5 20.6 - - + +
140B SER* 2.8 25.6 + - - +
188B TYR* 6.4 1.8 - - + -
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Residues in contact with ALA 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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134B LEU* 3.3 29.8 - - + -
135B SER 3.1 4.4 + - - -
136B VAL* 1.3 88.0 - - + +
138B ALA* 1.3 54.3 + - - +
139B ILE 2.8 0.2 + - - -
140B SER* 2.8 3.0 + - - -
141B ALA* 2.7 32.3 + - - +
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Residues in contact with ALA 138 (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 ASP* 3.8 22.4 - - + +
134B LEU* 4.1 14.0 - - + +
136B VAL 4.5 0.4 - - - +
137B ALA* 1.3 75.8 - - - +
139B ILE* 1.3 70.4 + - + +
141B ALA* 3.4 13.5 - - + -
142B MET* 2.8 39.3 + - + +
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Residues in contact with ILE 139 (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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85B TYR* 3.2 62.8 - - + +
128B VAL* 6.5 0.2 - - + -
134B LEU 5.1 3.8 - - - +
135B SER* 4.9 4.3 - - - +
136B VAL* 3.2 20.9 + - + +
137B ALA 2.8 4.6 + - - -
138B ALA* 1.3 84.6 - - + +
140B SER* 1.3 58.7 + - - +
142B MET* 2.7 35.0 + - + +
143B PHE* 3.6 25.5 + - + -
186B LEU* 3.7 26.2 - - + +
188B TYR* 4.9 2.0 - - + -
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Residues in contact with SER 140 (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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136B VAL* 2.8 21.1 + - - +
137B ALA* 3.6 2.7 - - - -
139B ILE* 1.3 75.7 - - - +
141B ALA* 1.3 62.0 + - - +
142B MET 3.2 0.2 - - - -
143B PHE* 3.5 28.6 + - - +
144B ALA* 3.8 6.8 + - - +
188B TYR* 4.3 22.9 - - - -
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Residues in contact with ALA 141 (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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137B ALA 2.7 12.0 + - - +
138B ALA* 3.4 23.8 - - + -
139B ILE 3.0 0.2 + - - -
140B SER* 1.3 74.0 - - - +
142B MET* 1.3 60.5 + - + +
144B ALA* 3.1 5.8 + - - +
145B ASP* 2.9 35.0 + - + +
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Residues in contact with MET 142 (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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124B THR* 4.9 5.5 + - + +
126B ARG* 2.7 65.3 + - - +
127B LYS 5.0 1.8 - - - +
128B VAL* 4.1 18.6 - - + -
133B ASP* 4.7 11.9 - - - +
138B ALA* 2.8 35.5 + - + +
139B ILE* 2.7 18.1 + - + +
141B ALA* 1.3 79.3 - - + +
143B PHE* 1.3 60.4 + - + +
145B ASP* 2.7 12.7 - - - +
146B GLY 4.6 0.7 + - - -
148B SER 4.4 5.9 - - - +
150B VAL* 4.8 0.9 - - - +
186B LEU* 3.8 25.6 - - + -
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Residues in contact with PHE 143 (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 TRP* 3.7 66.2 - + + -
123B VAL* 4.1 0.9 - - - -
124B THR* 3.3 26.9 - - - -
139B ILE* 3.7 23.1 - - + -
140B SER* 3.5 26.9 + - - +
141B ALA 3.1 0.6 - - - -
142B MET* 1.3 80.7 - - + +
144B ALA* 1.3 58.0 + - - +
146B GLY* 4.7 2.8 + - - -
150B VAL* 3.8 25.5 - - + +
186B LEU* 4.8 11.4 - - + -
188B TYR* 3.6 30.5 - + + -
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Residues in contact with ALA 144 (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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140B SER 3.8 6.5 + - - +
141B ALA* 3.1 7.4 + - - +
143B PHE* 1.3 78.0 - - + +
145B ASP* 1.3 57.9 + - - +
146B GLY* 2.9 12.4 + - - -
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Residues in contact with ASP 145 (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* 2.6 31.8 + - - -
141B ALA* 2.9 19.9 + - + +
142B MET* 2.7 27.2 - - - +
144B ALA* 1.3 75.4 - - - +
146B GLY* 1.3 64.6 + - - +
147B ALA* 3.1 11.8 + - - +
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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