Contacts of the helix formed by residues 139 - 153 (chain F) in PDB entry 7KHE
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 GLU 139 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137F TYR* 2.9 18.3 + - + -
138F PRO* 1.3 79.4 - - - +
140F ALA* 1.3 55.1 + - - +
141F ILE 3.6 0.2 - - - -
142F THR* 2.5 55.0 + - - +
143F TYR* 4.1 4.3 + - - +
276F MET* 4.9 14.0 - - + +
350F GLU* 3.8 27.2 - - + +
351F THR* 5.2 1.1 - - - +
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Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F VAL* 4.7 7.2 - - + +
137F TYR* 3.4 41.4 + - + +
139F GLU* 1.3 76.9 - - - +
141F ILE* 1.3 64.0 + - + +
142F THR 3.3 1.3 - - - -
143F TYR* 3.3 8.2 + - - +
144F LEU* 3.0 33.4 + - + +
269F LEU* 4.6 16.1 - - + +
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Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F ALA* 4.8 11.2 - - - +
137F TYR 4.1 17.9 - - - +
138F PRO* 4.2 11.4 + - + -
140F ALA* 1.3 77.0 - - + +
142F THR* 1.3 67.3 + - - +
144F LEU* 3.5 24.2 - - + -
145F LEU* 2.9 35.2 + - + +
224F LEU* 4.2 27.4 - - + -
228F TYR* 3.5 26.7 - - + -
249F ILE* 6.6 0.2 - - + -
252F LEU* 3.8 26.0 - - + -
256F PHE* 5.4 4.9 - - + -
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Residues in contact with THR 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F PRO 3.4 11.0 - - - +
139F GLU* 2.5 53.1 + - - +
141F ILE* 1.3 76.8 - - - +
143F TYR* 1.3 61.9 + - - +
145F LEU* 3.1 11.9 - - - +
146F GLU* 2.9 38.1 + - - +
228F TYR* 2.9 27.9 - - + +
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Residues in contact with TYR 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F GLU 4.5 3.6 - - - +
140F ALA* 3.3 9.1 + - - +
141F ILE 3.3 0.4 - - - -
142F THR* 1.3 81.6 + - - +
144F LEU* 1.3 71.1 + - + +
146F GLU* 3.8 6.9 - - + +
147F GLN* 2.5 70.2 + - + +
261F LEU* 6.4 0.7 - - + -
265F GLN* 5.0 10.3 - - + +
268F TYR* 3.6 33.5 - + - -
269F LEU* 3.4 33.9 - - + -
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F ALA* 3.0 23.1 + - + +
141F ILE* 3.2 29.6 + - + +
143F TYR* 1.3 80.3 - - + +
145F LEU* 1.3 60.0 + - - +
147F GLN* 3.2 2.0 + - - +
148F TYR* 2.8 29.7 + - - +
161F LEU* 4.8 3.0 - - - +
221F PHE* 4.8 12.6 - - + -
224F LEU* 4.9 4.5 - - + -
256F PHE* 3.2 39.0 - - + -
259F PHE* 5.5 1.8 - - + -
261F LEU* 4.3 15.7 - - + -
269F LEU* 3.5 31.2 - - + -
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Residues in contact with LEU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F ILE* 2.9 44.7 + - + +
142F THR* 3.1 13.5 - - - +
144F LEU* 1.3 74.0 - - - +
146F GLU* 1.3 93.9 + - + +
148F TYR* 4.2 6.5 - - - -
149F ASP* 2.9 30.1 + - - +
221F PHE* 5.1 6.0 - - + +
224F LEU* 5.5 4.9 - - + +
225F ARG* 3.2 53.2 - - + +
228F TYR* 4.3 20.4 - - + -
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Residues in contact with GLU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F THR* 2.9 30.5 + - - +
143F TYR* 3.8 9.2 - - + +
144F LEU 3.2 0.2 - - - -
145F LEU* 1.3 93.2 - - + +
147F GLN* 1.3 60.4 + - + +
149F ASP* 3.5 4.9 + - - +
150F ARG* 2.9 55.6 + - - +
225F ARG* 4.6 4.3 + - - -
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Residues in contact with GLN 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F TYR* 2.5 67.5 + - + +
144F LEU* 4.1 1.1 - - - +
146F GLU* 1.3 77.4 - - + +
148F TYR* 1.3 60.4 + - - +
150F ARG* 3.1 18.0 - - + +
151F VAL* 2.9 23.0 + - - +
156F ALA* 3.8 1.9 - - + +
160F ASP* 5.0 0.6 + - - +
161F LEU* 3.2 37.8 - - + +
265F GLN* 4.8 6.1 - - - +
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Residues in contact with TYR 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F LEU 2.8 17.8 + - - +
145F LEU* 3.8 5.2 - - - +
147F GLN* 1.3 73.5 - - - +
149F ASP* 1.3 65.8 + - - +
151F VAL* 2.9 14.6 + - + +
152F GLU* 2.9 58.6 + - + +
161F LEU* 3.4 17.2 - - + +
162F ILE* 4.2 10.5 - - + -
217F ALA* 2.9 10.6 - - + +
218F ARG* 2.9 35.1 + - - +
221F PHE* 3.3 65.1 - + + -
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Residues in contact with ASP 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F LEU* 2.9 8.5 + - - +
146F GLU* 3.7 8.2 - - - +
148F TYR* 1.3 79.2 - - - +
150F ARG* 1.3 65.0 + - - +
152F GLU* 2.8 9.9 + - - +
153F ALA* 2.6 38.7 + - + +
225F ARG* 2.2 43.2 + - - -
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Residues in contact with ARG 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F GLU* 2.9 56.5 + - - +
147F GLN* 3.1 23.6 - - + +
149F ASP* 1.3 77.4 - - - +
151F VAL* 1.3 55.2 + - - +
153F ALA* 4.7 0.9 - - - -
154F GLU 3.0 4.9 + - - -
155F GLU* 2.3 76.7 + - - +
156F ALA* 2.8 17.9 + - + -
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Residues in contact with VAL 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F GLN 2.9 16.5 + - - +
148F TYR* 2.9 19.3 + - + +
150F ARG* 1.3 76.6 - - - +
152F GLU* 1.3 69.7 + - - +
154F GLU* 3.3 13.7 + - - +
156F ALA* 3.3 20.3 - - + +
157F ARG* 2.9 30.5 + - - +
158F LEU* 3.5 35.8 - - + +
161F LEU* 3.3 17.7 - - + -
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Residues in contact with GLU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F TYR* 2.9 53.1 + - + +
149F ASP* 2.8 13.2 + - - +
151F VAL* 1.3 80.3 - - - +
153F ALA* 1.3 58.6 + - - +
154F GLU* 2.9 17.4 + - - +
158F LEU* 6.0 0.3 - - - +
218F ARG* 3.1 34.2 - - - +
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F ASP* 2.6 22.4 + - + +
150F ARG* 4.2 2.5 - - - +
152F GLU* 1.3 71.7 - - - +
154F GLU* 1.3 65.3 + - - +
155F GLU* 3.3 22.1 + - + +
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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