Contacts of the helix formed by residues 136 - 151 (chain F) in PDB entry 4O9U
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 ALA 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132F LEU* 2.8 20.6 + - + +
133F SER 3.3 0.2 + - - -
135F GLN* 1.3 77.5 - - - +
137F THR* 1.3 61.2 + - - +
138F VAL 3.4 1.1 - - - -
139F ALA* 3.9 5.1 - - - +
140F GLY 3.1 21.0 + - - -
177F VAL* 3.7 21.3 - - + -
178F ALA* 3.1 31.8 - - + +
500F NAD 4.1 11.0 - - - +
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Residues in contact with THR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E PHE* 4.6 7.6 - - + -
158E LEU* 4.2 18.6 - - + -
160E THR* 5.3 7.8 - - + +
133F SER 3.1 10.3 + - - -
134F SER* 5.0 0.2 - - - -
136F ALA* 1.3 75.6 - - - +
138F VAL* 1.3 58.5 + - - +
139F ALA 3.2 0.2 - - - -
141F TYR* 3.1 30.8 + - - +
177F VAL* 3.1 26.9 + - - +
181F MET* 3.6 30.3 - - + +
325F MET* 4.7 12.1 - - + -
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E PHE* 3.7 17.9 - - + -
134F SER 3.2 23.5 + - - +
135F GLN* 4.8 0.4 - - - -
136F ALA 3.4 0.4 - - - -
137F THR* 1.3 76.0 - - - +
139F ALA* 1.3 59.8 + - - +
141F TYR* 4.4 2.6 - - - +
142F LEU* 3.6 23.7 + - - +
314F LEU 4.2 0.2 - - - +
315F PRO* 3.5 27.6 - - + -
318F LEU* 3.5 31.4 - - + -
322F ALA* 3.8 14.8 - - + -
325F MET* 3.7 22.4 - - + -
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Residues in contact with ALA 139 (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 GLN 4.3 13.2 + - - +
136F ALA* 3.6 8.8 + - - +
137F THR 3.2 0.6 - - - -
138F VAL* 1.3 78.5 - - - +
140F GLY* 1.3 53.8 + - - +
142F LEU 3.2 3.1 + - - -
143F ALA* 2.6 32.9 + - - +
178F ALA* 5.2 0.7 - - + -
284F LEU* 3.7 19.1 - - + -
314F LEU* 3.4 31.7 - - + +
315F PRO* 4.3 5.3 - - + +
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Residues in contact with GLY 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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136F ALA 3.1 14.0 + - - -
137F THR 3.3 1.1 + - - -
139F ALA* 1.3 74.1 - - - +
141F TYR* 1.3 64.1 + - - +
143F ALA* 3.0 16.6 + - - +
144F ALA 3.1 10.2 + - - -
178F ALA 3.3 26.5 - - - -
181F MET* 3.7 7.9 - - - -
182F ALA* 3.2 12.3 - - - -
284F LEU* 4.0 2.2 - - - +
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Residues in contact with TYR 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E ALA* 4.0 7.7 + - + +
153E ARG 3.8 0.9 + - - -
154E PHE* 3.6 27.4 - + + -
155E PHE* 2.9 37.1 + - - +
156E PRO* 3.2 29.6 - - + -
189E LEU* 4.7 3.6 - - + -
137F THR 3.1 17.3 + - - +
138F VAL 4.4 1.6 - - - +
140F GLY* 1.3 76.0 - - - +
142F LEU* 1.3 80.0 + - + +
144F ALA* 3.4 5.7 + - - +
145F ILE* 3.0 37.4 + - + +
181F MET* 3.7 23.2 + - + +
185F THR* 3.4 27.8 - - + -
318F LEU* 3.8 16.8 - - + -
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Residues in contact with LEU 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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148E ALA 3.9 14.8 - - - +
149E ARG* 5.2 5.4 - - - +
151E SER 5.2 0.2 - - - +
138F VAL 3.6 12.0 + - - +
139F ALA 3.2 9.5 + - - +
140F GLY 3.2 0.4 - - - -
141F TYR* 1.3 101.2 - - + +
143F ALA* 1.3 60.5 + - - +
144F ALA 3.2 0.9 - - - -
145F ILE* 3.6 6.7 - - + -
146F HIS* 3.0 41.3 + - + +
314F LEU* 3.3 37.7 - - + +
317F GLU* 3.8 26.2 - - + +
318F LEU* 3.8 19.7 - - + +
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Residues in contact with ALA 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 ALA 2.6 17.1 + - - +
140F GLY* 3.0 19.2 + - - +
142F LEU* 1.3 74.1 - - - +
144F ALA* 1.3 58.1 + - - +
147F ALA* 3.4 21.5 + - - +
182F ALA* 4.1 0.7 - - + -
253F ILE* 3.4 28.1 - - + +
282F VAL* 3.8 10.6 - - + +
284F LEU* 3.5 27.8 - - + -
314F LEU* 4.8 0.7 - - - -
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F GLY 3.1 7.3 + - - +
141F TYR 3.7 8.1 - - - +
143F ALA* 1.3 75.9 - - - +
145F ILE* 1.3 63.1 + - - +
147F ALA* 3.4 3.2 + - - +
148F ALA* 3.1 22.2 + - - +
155F PHE* 4.4 3.7 - - - -
182F ALA 3.7 21.3 - - - +
185F THR* 3.8 22.4 - - + -
186F ALA* 3.9 12.1 - - + +
189F LEU* 4.4 4.0 - - + +
253F ILE* 3.7 10.2 - - + +
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Residues in contact with ILE 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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145E ILE* 3.5 15.7 - - + +
148E ALA* 3.5 18.8 - - + +
149E ARG* 3.2 39.5 - - + +
189E LEU* 3.8 13.7 - - + -
141F TYR* 3.0 25.5 + - + +
142F LEU* 3.3 18.3 + - + +
144F ALA* 1.3 77.7 - - - +
146F HIS* 1.3 56.5 + - + +
148F ALA* 3.3 6.4 + - - +
149F ARG* 2.9 26.6 + - - +
185F THR* 3.7 22.9 - - + -
189F LEU* 5.2 3.8 - - + -
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Residues in contact with HIS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E ARG* 3.2 50.6 + - + -
142F LEU* 3.0 38.3 + - + +
143F ALA 4.4 3.4 - - - +
145F ILE* 1.3 75.4 - - + +
147F ALA* 1.3 59.7 - - - +
149F ARG* 3.9 10.1 - - - -
150F LEU* 3.0 38.9 + - + +
282F VAL* 4.4 7.6 - - + -
309F TYR* 3.9 34.6 - + + -
311F PRO* 5.6 0.7 - - + -
314F LEU* 4.7 7.9 - - + -
317F GLU* 3.0 28.2 + - - -
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Residues in contact with ALA 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 ALA 3.4 19.5 + - - +
144F ALA 3.4 7.2 - - - +
145F ILE 3.2 0.2 - - - -
146F HIS* 1.3 78.7 - - - +
148F ALA* 1.3 56.0 + - - +
151F SER* 3.0 29.8 + - - -
155F PHE* 4.0 7.3 - - + -
251F VAL* 3.7 28.8 - - + +
253F ILE* 4.1 5.4 - - + -
280F VAL* 4.0 9.0 - - - +
282F VAL* 3.8 14.7 - - + +
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Residues in contact with ALA 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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141E TYR* 3.9 10.5 + - - +
142E LEU* 4.3 5.4 - - - +
145E ILE* 3.6 29.3 - - + +
318E LEU* 4.7 0.5 - - - +
144F ALA 3.1 13.8 + - - +
145F ILE* 3.7 7.4 - - - +
147F ALA* 1.3 74.1 - - - +
149F ARG* 1.3 64.6 + - - +
151F SER* 3.3 17.9 + - - +
155F PHE* 3.5 25.3 - - + -
189F LEU* 4.2 7.9 - - + -
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Residues in contact with ARG 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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142E LEU* 4.1 11.8 - - - +
145E ILE* 3.3 14.1 - - + +
146E HIS* 3.3 38.8 + - + +
149E ARG* 2.8 65.2 - - + +
150E LEU* 5.6 0.6 - - - +
317E GLU* 5.1 9.0 + - - +
145F ILE 2.9 17.8 + - - +
146F HIS* 3.7 12.1 - - - +
147F ALA 3.4 0.2 - - - -
148F ALA* 1.3 79.8 - - - +
150F LEU* 1.3 80.9 + - - +
151F SER 3.7 4.7 - - - +
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Residues in contact with LEU 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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317E GLU 5.0 2.1 - - - +
146F HIS* 3.0 25.1 + - + +
149F ARG* 1.3 91.6 - - - +
151F SER* 1.3 64.8 + - - +
152F PRO* 3.4 8.7 - - - +
280F VAL* 4.0 22.3 - - + +
282F VAL* 5.1 1.3 - - + -
300F VAL* 4.0 28.0 - - + -
307F ARG* 4.0 44.7 + - + +
309F TYR* 3.9 38.1 - - + -
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Residues in contact with SER 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E GLU 4.1 2.3 - - - +
318E LEU* 3.1 18.5 - - - +
147F ALA 3.0 22.0 + - - -
148F ALA* 3.3 16.8 - - - +
149F ARG 3.3 4.2 - - - +
150F LEU* 1.3 77.6 - - - +
152F PRO* 1.3 63.9 - - - +
153F ARG* 3.1 32.5 + - - +
155F PHE* 4.1 9.5 - - - -
250F ASP* 5.4 1.4 + - - +
251F VAL* 4.9 4.8 - - - +
278F GLY 4.7 1.0 + - - -
280F VAL* 3.6 11.3 - - - +
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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
------------------------------------------------------------
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