Contacts of the helix formed by residues 136 - 150 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E ILE 4.2 0.5 - - - +
131E ALA* 3.5 17.4 + - - +
134E PHE* 3.3 6.5 + - - +
135E GLY* 1.3 77.8 - - - +
137E VAL* 1.3 61.9 - - - +
138E ASP* 3.4 7.8 + - - +
139E ASP* 2.6 36.1 + - - +
140E PHE* 3.1 21.3 + - - +
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Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E MET* 4.0 15.5 - - + -
127E GLU* 3.7 43.7 - - + +
130E ILE* 4.0 17.0 - - + -
131E ALA* 4.2 4.9 - - + +
136E SER* 1.3 72.8 - - - +
138E ASP* 1.3 62.7 + - - +
140E PHE* 3.3 3.7 + - + +
141E MET* 3.0 54.2 + - + +
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Residues in contact with ASP 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E SER* 3.3 7.8 + - - +
137E VAL* 1.3 82.1 - - - +
139E ASP* 1.3 55.7 + - - +
141E MET* 3.2 16.1 + - - +
142E VAL* 3.0 37.0 + - + +
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Residues in contact with ASP 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E PHE* 3.3 22.9 - - - +
135E GLY* 4.4 2.6 - - - -
136E SER* 2.6 29.6 + - - +
138E ASP* 1.3 72.9 - - - +
140E PHE* 1.3 67.0 + - - +
142E VAL* 3.6 4.8 + - - +
143E SER* 2.8 32.3 + - - +
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Residues in contact with PHE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ILE* 3.5 29.6 - - + -
134E PHE* 3.8 35.5 - + + +
136E SER 3.1 4.4 + - - +
137E VAL* 3.3 9.2 + - + +
139E ASP* 1.3 79.8 - - - +
141E MET* 1.3 66.9 + - + +
143E SER* 3.3 2.6 + - - -
144E PHE* 2.9 47.9 + + + +
159E LEU* 3.6 38.6 - - + -
170E ILE* 3.9 17.0 - - + -
188E PHE* 5.1 2.0 - + - -
213E TRP* 3.7 28.0 - + - -
218E TRP* 4.1 13.7 - + - -
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Residues in contact with MET 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E MET* 4.3 3.8 - - + -
137E VAL* 3.0 39.8 + - + +
138E ASP* 3.2 15.7 + - - +
140E PHE* 1.3 84.3 - - + +
142E VAL* 1.3 60.1 + - + +
144E PHE 3.3 0.3 + - - -
145E GLN* 2.9 38.8 + - - +
213E TRP* 3.6 49.2 - - + +
218E TRP* 4.0 27.8 - - + +
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E ASP* 3.0 23.4 + - + +
139E ASP* 4.1 4.3 - - - +
141E MET* 1.3 77.3 - - + +
143E SER* 1.3 57.4 + - - +
145E GLN* 3.3 16.7 + - + +
146E GLN* 2.9 31.5 + - + +
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Residues in contact with SER 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E PHE* 5.4 3.7 - - - -
139E ASP* 2.8 24.8 + - - +
140E PHE* 3.7 4.7 - - - -
142E VAL* 1.3 73.7 - - - +
144E PHE* 1.3 61.2 + - - +
146E GLN* 3.9 5.5 - - - +
147E ALA* 3.0 28.8 + - - +
170E ILE* 3.7 15.5 - - - +
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Residues in contact with PHE 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PHE* 2.9 39.7 + + + +
141E MET 3.7 3.1 - - - +
143E SER* 1.3 75.1 - - - +
145E GLN* 1.3 69.1 + - - +
147E ALA* 3.2 3.3 + - - +
148E GLY* 2.9 19.8 + - - -
157E THR* 3.4 46.2 - - + +
158E TRP 3.9 13.5 - - - -
159E LEU 4.0 0.7 - - - -
170E ILE* 3.6 12.9 - - + +
188E PHE* 3.5 33.9 - + - -
190E ALA* 3.6 22.4 - - + -
209E LEU* 4.3 9.9 - - + -
212E LEU* 5.4 1.6 - - + -
213E TRP* 3.5 23.6 - + + -
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Residues in contact with GLN 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E MET* 2.9 27.1 + - - +
142E VAL* 3.6 14.8 + - - +
144E PHE* 1.3 77.8 - - - +
146E GLN* 1.3 58.6 + - - +
148E GLY 3.2 1.7 + - - -
149E VAL* 2.9 35.5 + - + +
206E ALA 5.1 1.9 + - - +
209E LEU* 3.6 25.6 - - + +
210E LYS* 3.9 23.3 - - - +
213E TRP* 2.7 36.6 + - + +
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Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E VAL* 2.9 20.7 + - + +
143E SER* 3.9 6.3 - - - +
144E PHE 3.2 0.2 - - - -
145E GLN* 1.3 78.3 - - - +
147E ALA* 1.3 57.5 + - - +
149E VAL* 3.3 6.6 + - + +
150E ASN* 2.9 49.3 + - - +
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E SER 3.0 18.7 + - - +
144E PHE 3.6 4.7 - - - +
146E GLN* 1.3 78.6 - - - +
148E GLY* 1.3 56.6 + - - +
150E ASN* 3.5 5.0 + - - +
151E ASN* 3.1 27.9 + - - +
157E THR* 3.9 3.4 - - + -
170E ILE* 3.8 24.2 - - + -
172E SER* 3.7 14.0 + - - +
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Residues in contact with GLY 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PHE 2.9 13.1 + - - -
145E GLN 3.7 2.7 - - - -
147E ALA* 1.3 74.6 - - - +
149E VAL* 1.3 60.3 + - - +
151E ASN* 3.4 6.4 + - - +
157E THR* 3.3 20.3 + - - -
192E VAL* 4.1 6.6 - - - +
205E ARG* 2.9 27.1 + - - -
209E LEU* 3.6 18.6 - - - -
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Residues in contact with VAL 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E GLN* 2.9 22.8 + - + +
146E GLN* 3.7 7.2 - - + +
148E GLY* 1.3 75.8 - - - +
150E ASN* 1.3 72.4 + - - +
151E ASN 3.3 1.4 + - - +
152E PHE* 5.8 0.2 - - - -
205E ARG* 3.8 18.5 + - + +
206E ALA* 3.8 37.9 - - + +
209E LEU* 3.6 6.3 - - + +
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Residues in contact with ASN 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLN* 2.9 46.0 + - - +
147E ALA* 3.7 5.6 - - - +
149E VAL* 1.3 88.1 - - - +
151E ASN* 1.3 58.2 + - - +
152E PHE* 3.0 12.7 + - - +
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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