Contacts of the helix formed by residues 141 - 152 (chain F) in PDB entry 4OA5
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 141 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116F GLU* 5.1 0.9 + - - -
118F LEU* 4.2 13.9 - - - +
138F ASN* 3.1 20.4 + - - -
140F SER* 1.3 81.8 + - - +
142F TYR* 1.3 64.1 + - - +
143F LEU 3.3 2.7 - - - -
144F ALA* 3.0 21.0 + - - +
145F TYR* 3.0 43.8 + - - -
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Residues in contact with TYR 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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135F ILE* 3.4 31.7 + - + -
136F ASP* 3.8 8.3 + - - -
137F ALA 3.4 24.5 + - - -
138F ASN 3.5 9.6 - - - -
139F LYS* 3.2 25.9 + - + +
141F SER* 1.3 75.5 - - - +
143F LEU* 1.3 57.5 + - - +
145F TYR* 3.1 8.9 + + - +
146F LEU 2.8 24.9 + - - -
161F ALA* 3.8 14.6 - - + -
162F ASP 2.6 30.6 + - - -
163F ASN* 4.5 0.7 - - - +
164F THR* 4.3 0.9 - - + -
186F SER* 3.4 4.0 + - - +
187F MET* 3.4 32.8 - - + -
190F PHE* 3.4 36.0 - + + -
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Residues in contact with LEU 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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140F SER 5.8 0.2 - - - +
141F SER 3.3 0.2 - - - -
142F TYR* 1.3 77.8 - - - +
144F ALA* 1.3 58.0 + - - +
146F LEU* 3.3 12.5 + - + +
147F ASN* 2.9 52.1 + - - +
186F SER* 3.3 22.8 + - - +
189F ALA* 3.9 34.3 - - + +
190F PHE* 4.0 14.5 - - - +
193F GLU* 5.1 3.8 - - + -
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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
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118F LEU* 3.8 31.1 - - + +
141F SER* 3.0 15.6 + - - +
143F LEU* 1.3 77.6 - - - +
145F TYR* 1.3 59.9 + - - +
147F ASN* 3.3 11.0 + - - +
148F TRP* 3.0 25.8 + - - +
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Residues in contact with TYR 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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63F VAL* 3.8 16.1 - - + +
116F GLU* 4.1 5.7 + - - -
117F ALA* 3.4 33.0 - - + +
118F LEU* 3.9 19.5 - - + -
121F LEU* 3.7 17.3 - - + -
133F ILE* 4.4 8.7 - - + +
135F ILE* 3.7 40.6 - - + -
137F ALA* 5.0 2.6 - - + +
138F ASN* 2.5 36.2 + - - -
141F SER* 3.0 37.1 + - - -
142F TYR* 3.1 6.0 + + - +
144F ALA* 1.3 71.4 - - - +
146F LEU* 1.3 66.5 + - - +
148F TRP* 3.3 8.5 + - - +
149F ALA* 3.0 21.8 + - - +
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Residues in contact with LEU 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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135F ILE* 4.4 1.9 - - - +
142F TYR 2.8 13.2 + - - +
143F LEU* 3.5 14.4 - - + +
145F TYR* 1.3 79.5 - - - +
147F ASN* 1.3 57.2 + - - +
149F ALA* 3.0 4.7 + - - +
150F LYS* 2.9 41.8 + - + +
159F ILE* 3.9 25.4 - - + -
190F PHE* 3.7 31.9 - - + +
193F GLU* 3.5 34.1 - - + -
194F LEU* 3.8 25.4 - - + -
200F TYR* 4.5 1.6 - - - +
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Residues in contact with ASN 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 LEU* 2.9 43.4 + - - +
144F ALA* 3.3 9.7 + - - +
146F LEU* 1.3 73.2 - - - +
148F TRP* 1.3 63.7 + - - +
150F LYS* 3.5 39.5 + - - +
151F MET* 3.6 18.6 + - + +
193F GLU* 5.9 0.2 - - - +
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Residues in contact with TRP 148 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61F VAL* 4.0 8.5 - - + -
118F LEU* 5.8 2.7 - - + -
121F LEU* 3.1 66.8 + - + +
122F ASN* 4.8 2.0 - - - +
124F LEU* 4.3 8.7 - - + -
125F LYS* 4.3 6.0 - - + +
130F PHE* 3.9 22.4 - + - -
133F ILE* 4.0 21.3 - - + -
144F ALA 3.0 13.1 + - - +
145F TYR* 3.4 10.3 - - - +
147F ASN* 1.3 77.3 - - - +
149F ALA* 1.3 63.3 + - - +
151F MET* 3.1 11.0 + - + +
152F TYR* 3.0 74.9 + + + -
153F ILE* 4.3 15.0 - - + -
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Residues in contact with ALA 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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133F ILE* 3.9 20.2 - - + -
145F TYR 3.0 13.8 + - - +
146F LEU* 3.0 11.6 + - - +
148F TRP* 1.3 80.0 - - - +
150F LYS* 1.3 61.0 + - - +
153F ILE* 2.9 50.2 + - + +
159F ILE* 4.2 13.9 - - + -
216F LYS* 3.4 5.2 - - - -
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Residues in contact with LYS 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 LEU* 2.9 30.1 + - + +
147F ASN* 3.5 32.6 + - - +
148F TRP 3.3 0.2 - - - -
149F ALA* 1.3 75.5 - - - +
151F MET* 1.3 61.0 + - + +
193F GLU* 3.4 29.0 + - - +
199F LYS* 4.4 10.4 - - - +
200F TYR* 3.3 22.2 - - + +
216F LYS* 3.3 25.6 + - - +
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Residues in contact with MET 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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129F PRO* 5.7 1.6 - - - +
147F ASN* 3.6 20.1 + - + +
148F TRP* 3.1 11.4 + - + +
150F LYS* 1.3 82.9 - - + +
152F TYR* 1.3 100.5 + - + +
153F ILE 3.7 3.4 - - - +
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Residues in contact with TYR 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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125F LYS* 3.5 41.8 + - + +
128F ALA* 3.5 25.4 - - + -
129F PRO* 3.2 7.9 - - - +
130F PHE* 2.9 27.2 + - - -
148F TRP* 3.0 66.4 + + + +
151F MET* 1.3 114.2 - - + +
153F ILE* 1.3 64.6 + - - +
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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