Contacts of the helix formed by residues 136 - 150 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ILE* 4.6 0.2 - - - -
131B ALA* 3.9 16.5 - - - +
134B PHE* 3.3 6.4 + - - +
135B GLY* 1.3 78.9 - - - +
137B VAL* 1.3 64.1 + - - +
138B ASP* 3.4 9.5 + - - +
139B ASP* 3.1 29.5 + - - +
140B PHE* 3.1 21.8 + - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET* 3.9 34.3 - - + -
127B GLU* 3.9 27.1 - - + +
130B ILE* 4.0 20.6 - - + -
131B ALA* 4.7 2.3 - - + +
136B SER* 1.3 73.4 - - - +
138B ASP* 1.3 61.8 + - - +
140B PHE* 3.2 4.8 + - + +
141B MET* 2.8 55.8 + - + +
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B SER* 3.3 8.8 + - - +
137B VAL* 1.3 79.8 - - - +
139B ASP* 1.3 59.2 + - - +
141B MET* 3.3 15.2 + - - +
142B VAL* 3.0 36.5 + - + +
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 3.4 24.2 - - - +
135B GLY* 4.2 4.0 - - - -
136B SER* 3.1 24.6 + - - +
138B ASP* 1.3 73.0 - - - +
140B PHE* 1.3 65.7 + - - +
142B VAL* 3.5 7.4 + - - +
143B SER* 3.0 29.2 + - - +
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 3.5 34.3 - - + -
134B PHE* 3.7 31.2 - + + +
136B SER 3.1 7.4 + - - +
137B VAL* 3.2 9.4 + - + +
139B ASP* 1.3 75.3 - - - +
141B MET* 1.3 62.4 + - + +
143B SER* 3.2 4.1 + - - -
144B PHE* 2.8 51.2 + + + +
159B LEU* 3.6 38.4 - - + -
170B ILE* 3.8 21.5 - - + -
188B PHE* 5.0 1.8 - + - -
213B TRP* 3.7 25.8 - + - -
218B TRP* 4.2 13.0 - + - -
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Residues in contact with MET 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET* 5.0 0.7 - - + -
137B VAL* 2.8 40.7 + - + +
138B ASP* 3.3 14.6 + - - +
140B PHE* 1.3 78.5 - - + +
142B VAL* 1.3 59.3 + - + +
144B PHE* 3.7 0.7 - - - +
145B GLN* 2.9 40.8 + - - +
213B TRP* 3.6 60.3 - - + +
218B TRP* 3.9 24.2 - - + +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASP* 3.0 22.7 + - + +
139B ASP* 3.9 8.1 - - - +
141B MET* 1.3 75.4 - - + +
143B SER* 1.3 64.3 + - - +
145B GLN* 3.4 12.5 + - - +
146B GLN* 3.1 31.0 + - + +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 5.2 5.8 - - - -
139B ASP* 3.0 19.2 + - - +
140B PHE* 3.5 5.4 - - - -
142B VAL* 1.3 78.9 - - - +
144B PHE* 1.3 58.0 + - - +
146B GLN* 3.4 10.7 + - - +
147B ALA* 3.0 28.9 + - - +
170B ILE* 3.7 16.5 - - - +
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B PHE* 2.8 47.2 + + + +
141B MET 3.7 3.1 - - - +
143B SER* 1.3 73.0 - - - +
145B GLN* 1.3 67.2 + - + +
147B ALA* 3.3 3.6 + - - +
148B GLY* 3.1 18.7 + - - -
157B THR* 3.4 45.2 - - + +
158B TRP 3.8 15.9 - - - -
159B LEU 4.0 0.2 - - - -
170B ILE* 3.8 15.5 - - + +
188B PHE* 3.5 30.7 - + - -
190B ALA* 3.7 21.3 - - + -
209B LEU* 4.6 8.5 - - + +
212B LEU* 5.5 1.6 - - + -
213B TRP* 3.4 23.1 - + + -
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B MET* 2.9 25.4 + - - +
142B VAL* 3.8 10.6 + - - +
144B PHE* 1.3 78.4 - - + +
146B GLN* 1.3 56.2 - - - +
148B GLY 3.3 0.7 + - - -
149B VAL* 2.9 36.4 + - + +
206B ALA 5.1 2.7 + - - +
209B LEU* 3.6 28.4 - - + +
210B LYS* 3.9 22.0 - - - +
213B TRP* 2.7 35.6 + - + +
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B VAL* 3.1 26.4 + - + +
143B SER* 3.6 9.6 - - - +
145B GLN* 1.3 74.1 - - - +
147B ALA* 1.3 65.9 + - - +
149B VAL* 3.3 6.1 + - - +
150B ASN* 3.0 47.9 + - - +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER 3.0 17.9 + - - +
144B PHE 3.3 4.2 + - - +
146B GLN* 1.3 78.0 - - - +
148B GLY* 1.3 63.3 + - - +
150B ASN* 3.4 6.5 + - - +
151B ASN* 3.1 23.7 + - - +
157B THR* 4.1 1.6 - - + -
170B ILE* 3.9 20.2 - - + -
172B SER* 3.6 19.3 + - - +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PHE 3.1 12.9 + - - -
145B GLN 3.8 2.7 - - - -
146B GLN 3.3 0.2 - - - -
147B ALA* 1.3 74.5 - - - +
149B VAL* 1.3 59.9 + - - +
151B ASN* 3.4 7.0 + - - +
157B THR* 3.2 21.8 + - - -
192B VAL* 4.2 5.2 - - - +
205B ARG* 2.9 27.4 + - - -
209B LEU* 3.7 17.5 - - - -
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLN* 2.9 24.8 + - + +
146B GLN* 3.3 7.4 + - - +
148B GLY* 1.3 76.9 - - - +
150B ASN* 1.3 72.0 + - - +
151B ASN 3.4 1.4 + - - +
205B ARG* 3.8 17.0 + - + +
206B ALA* 3.8 38.1 - - + +
209B LEU* 3.6 5.6 - - + +
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Residues in contact with ASN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLN* 3.0 43.7 + - - +
147B ALA* 3.7 6.5 - - - +
149B VAL* 1.3 85.0 - - - +
151B ASN* 1.3 60.3 + - - +
152B PHE* 3.0 11.6 + - - +
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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