Contacts of the helix formed by residues 136 - 151 (chain F) in PDB entry 4F2N
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 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130F ILE* 4.4 0.3 - - - +
131F ALA* 3.7 16.1 + - - -
134F PHE* 3.2 7.6 + - - +
135F GLY* 1.3 77.8 - - - +
137F VAL* 1.3 65.1 + - - +
138F ASP* 3.6 10.3 + - - +
139F ASP* 3.0 29.1 + - - +
140F PHE* 3.1 21.3 + - - +
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Residues in contact with VAL 137 (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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122F MET* 3.9 30.1 - - + -
127F GLU* 3.7 41.1 - - + +
130F ILE* 4.2 14.4 - - + -
131F ALA* 4.4 2.8 - - + +
136F SER* 1.3 71.0 - - - +
138F ASP* 1.3 60.0 + - - +
140F PHE* 3.2 5.0 + - + +
141F MET* 2.9 48.5 + - + +
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Residues in contact with ASP 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F SER* 3.6 8.9 - - - +
137F VAL* 1.3 78.4 - - - +
139F ASP* 1.3 61.8 + - - +
141F MET* 3.2 13.4 + - - +
142F VAL* 3.0 34.8 + - + +
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Residues in contact with ASP 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F PHE* 3.3 24.7 - - - +
135F GLY* 4.7 2.6 - - - -
136F SER* 3.0 19.3 + - - +
138F ASP* 1.3 79.5 - - - +
140F PHE* 1.3 66.7 + - - +
142F VAL* 3.4 8.6 + - - +
143F SER* 3.0 27.4 + - - +
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Residues in contact with PHE 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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130F ILE* 3.4 35.0 - - + -
134F PHE* 3.7 33.9 - + + +
136F SER 3.1 8.8 + - - +
137F VAL* 3.4 9.6 - - + +
139F ASP* 1.3 76.7 - - - +
141F MET* 1.3 64.6 + - + +
143F SER* 3.2 3.7 + - - -
144F PHE* 2.8 48.2 + + + +
159F LEU* 3.7 37.5 - - + -
170F ILE* 3.8 19.3 - - + -
188F PHE* 5.0 2.5 - + - -
213F TRP* 3.6 27.1 - + - -
218F TRP* 4.3 11.2 - + - -
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Residues in contact with MET 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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122F MET* 4.9 1.1 - - + -
137F VAL* 2.9 38.5 + - + +
138F ASP* 3.2 12.1 + - - +
140F PHE* 1.3 81.1 - - + +
142F VAL* 1.3 57.4 + - + +
144F PHE* 3.4 1.0 + - - +
145F GLN* 2.9 39.7 + - - +
213F TRP* 3.6 58.7 - - + +
218F TRP* 3.9 23.3 - - + +
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Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F ASP* 3.0 23.4 + - + +
139F ASP* 3.9 9.6 - - - +
140F PHE 3.3 0.2 - - - -
141F MET* 1.3 77.9 - - + +
143F SER* 1.3 57.8 + - - +
145F GLN* 3.4 14.4 + - - +
146F GLN* 2.9 37.6 + - + +
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Residues in contact with SER 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F PHE* 5.1 7.1 - - - -
139F ASP* 3.0 17.1 + - - +
140F PHE* 3.7 4.9 - - - -
142F VAL* 1.3 77.8 - - - +
144F PHE* 1.3 58.6 + - - +
146F GLN* 3.8 11.4 + - - +
147F ALA* 3.0 28.9 + - - +
170F ILE* 3.7 17.3 - - - +
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Residues in contact with PHE 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 PHE* 2.8 39.3 + + + +
141F MET 3.8 4.0 - - - +
143F SER* 1.3 74.3 - - - +
145F GLN* 1.3 68.3 + - + +
147F ALA* 3.3 5.2 + - - +
148F GLY* 3.0 19.2 + - - -
157F THR* 3.4 43.8 - - + +
158F TRP 3.9 12.6 - - - -
159F LEU 4.0 0.7 - - - -
170F ILE* 3.7 12.7 - - + +
188F PHE* 3.5 33.0 - + - -
190F ALA* 3.6 22.0 - - + -
209F LEU* 4.5 9.0 - - + -
212F LEU* 5.4 1.6 - - + -
213F TRP* 3.5 24.7 - + + -
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Residues in contact with GLN 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 MET* 2.9 24.0 + - - +
142F VAL* 3.8 12.3 - - - +
144F PHE* 1.3 76.0 - - - +
146F GLN* 1.3 58.8 + - - +
148F GLY* 3.3 2.1 + - - -
149F VAL* 2.9 38.3 + - + +
206F ALA 5.3 2.7 + - - +
209F LEU* 3.8 26.5 - - + +
210F LYS* 3.7 32.7 - - - +
213F TRP* 2.7 36.3 + - + +
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Residues in contact with GLN 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 VAL* 2.9 26.1 + - + +
143F SER* 3.8 10.9 + - - +
144F PHE 3.3 0.2 - - - -
145F GLN* 1.3 77.8 - - - +
147F ALA* 1.3 56.8 + - - +
149F VAL* 3.4 5.0 + - - +
150F ASN* 3.0 54.5 + - - +
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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 SER 3.0 17.8 + - - +
144F PHE 3.6 4.7 - - - +
145F GLN 3.3 0.2 - - - -
146F GLN* 1.3 78.1 - - - +
148F GLY* 1.3 61.8 + - - +
150F ASN* 3.4 4.1 + - - +
151F ASN* 3.1 23.4 + - - +
157F THR* 3.8 9.4 - - + -
170F ILE* 3.8 13.7 - - + -
172F SER* 3.7 20.8 + - - +
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Residues in contact with GLY 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 PHE 3.0 12.9 + - - -
145F GLN 3.7 2.9 - - - -
147F ALA* 1.3 76.4 - - - +
149F VAL* 1.3 61.7 + - - +
151F ASN* 3.3 7.6 + - - +
157F THR* 3.2 21.0 + - - -
192F VAL* 4.1 6.3 - - - +
205F ARG* 3.0 23.2 + - - -
209F LEU* 3.7 18.4 - - - -
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Residues in contact with VAL 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 GLN* 2.9 27.3 + - + +
146F GLN* 3.9 5.6 - - - +
148F GLY* 1.3 73.2 - - - +
150F ASN* 1.3 70.6 + - - +
151F ASN 3.3 1.4 + - - +
205F ARG* 3.9 16.6 + - + +
206F ALA* 3.7 39.3 - - + +
209F LEU* 4.0 6.3 - - + -
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Residues in contact with ASN 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 GLN* 3.0 45.0 + - - +
147F ALA* 3.8 4.5 - - - +
148F GLY 3.3 0.2 - - - -
149F VAL* 1.3 87.1 - - - +
151F ASN* 1.3 59.0 + - - +
152F PHE* 3.0 12.9 + - - +
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Residues in contact with ASN 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 ALA 3.1 11.3 + - - +
148F GLY* 3.4 13.2 - - - +
149F VAL 3.3 2.6 - - - +
150F ASN* 1.3 74.4 - - - +
152F PHE* 1.3 68.3 + - - +
153F GLY 3.4 4.5 + - - +
154F SER 4.9 0.6 - - - +
155F GLY* 3.9 4.0 - - - -
156F TRP 3.2 25.9 + - - +
157F THR* 3.9 1.0 + - - -
172F SER* 3.9 16.3 - - - +
173F THR 3.1 29.2 + - - +
174F SER* 4.8 3.6 + - - -
192F VAL* 3.5 10.6 - - + +
205F ARG* 2.7 27.4 + - - +
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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