Contacts of the helix formed by residues 136 - 151 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ILE* 4.4 0.2 - - - +
131A ALA* 3.6 17.7 + - - +
134A PHE* 3.4 5.7 + - - +
135A GLY* 1.3 77.8 - - - +
137A VAL* 1.3 63.7 + - - +
138A ASP* 3.4 8.0 + - - +
139A ASP* 2.7 34.6 + - - +
140A PHE* 3.1 21.1 + - - +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A MET* 4.0 27.6 - - + -
127A GLU* 3.8 40.8 - - + +
130A ILE* 3.9 16.4 - - + -
131A ALA* 4.2 4.4 - - + +
136A SER* 1.3 70.4 - - - +
138A ASP* 1.3 63.2 + - - +
140A PHE* 3.1 3.6 + - + +
141A MET* 2.9 46.3 + - + +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 3.3 7.4 + - - +
137A VAL* 1.3 80.6 - - - +
139A ASP* 1.3 62.7 + - - +
141A MET* 3.2 16.0 + - - +
142A VAL* 3.1 31.6 + - + +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.7 20.6 - - - +
135A GLY* 4.3 3.3 - - - -
136A SER* 2.7 35.0 + - - +
138A ASP* 1.3 74.2 - - - +
140A PHE* 1.3 65.8 + - - +
142A VAL* 3.5 5.6 + - - +
143A SER* 3.0 30.1 + - - +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 3.4 35.4 - - + -
134A PHE* 3.8 36.7 - + + +
136A SER 3.1 7.6 + - - +
137A VAL* 3.1 4.9 + - + +
139A ASP* 1.3 77.4 - - - +
141A MET* 1.3 67.9 + - + +
143A SER* 3.3 3.0 + - - -
144A PHE* 2.9 59.6 + + + +
159A LEU* 3.7 36.6 - - + -
170A ILE* 4.0 7.0 - - + -
188A PHE* 5.1 2.0 - + - -
213A TRP* 3.7 26.0 - + - -
218A TRP* 4.1 13.9 - + - -
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Residues in contact with MET 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A MET* 4.6 2.5 - - + -
137A VAL* 2.9 37.8 + - + +
138A ASP* 3.2 16.1 + - - +
140A PHE* 1.3 87.9 - - + +
142A VAL* 1.3 57.5 + - + +
144A PHE 3.3 0.2 + - - -
145A GLN* 2.9 38.5 + - - +
213A TRP* 3.6 46.4 - - + +
218A TRP* 3.9 29.4 - - + +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP* 3.1 19.8 + - + +
139A ASP* 4.0 5.6 - - - +
141A MET* 1.3 76.5 - - + +
143A SER* 1.3 58.1 + - - +
145A GLN* 3.3 14.8 + - - +
146A GLN* 2.9 47.3 + - + +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 5.2 4.5 - - - -
139A ASP* 3.0 20.3 + - - +
140A PHE* 3.7 4.9 - - - -
142A VAL* 1.3 76.9 - - - +
144A PHE* 1.3 58.2 + - - +
146A GLN* 3.5 8.1 + - - +
147A ALA* 3.0 28.8 + - - +
170A ILE* 3.8 17.1 - - - +
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 2.9 45.4 + + + +
141A MET 3.7 3.8 - - - +
143A SER* 1.3 73.7 - - - +
145A GLN* 1.3 68.9 + - + +
147A ALA* 3.2 3.5 + - - +
148A GLY* 3.0 19.8 + - - -
157A THR* 3.4 45.1 - - + +
158A TRP 3.9 15.3 - - - -
159A LEU 4.0 0.2 - - - -
170A ILE* 3.6 11.3 - - + +
188A PHE* 3.6 33.9 - + - -
190A ALA* 3.7 20.9 - - + -
209A LEU* 4.4 10.3 - - + -
212A LEU* 5.4 1.1 - - + -
213A TRP* 3.5 18.8 - + + -
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Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A MET* 2.9 24.7 + - - +
142A VAL* 3.7 13.7 + - - +
144A PHE* 1.3 78.2 - - - +
146A GLN* 1.3 57.2 + - + +
148A GLY* 3.2 2.4 + - - -
149A VAL* 2.9 36.4 + - + +
206A ALA 5.0 2.2 + - - +
209A LEU* 3.6 25.4 - - + +
210A LYS* 3.8 33.4 + - - +
213A TRP* 2.7 36.1 + - + +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A VAL* 2.9 35.5 + - + +
143A SER* 3.7 7.2 - - - +
145A GLN* 1.3 76.9 - - + +
147A ALA* 1.3 58.6 + - - +
149A VAL* 3.3 9.1 + - - +
150A ASN* 2.9 49.8 + - - +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER 3.0 17.1 + - - +
144A PHE 3.2 4.4 + - - +
146A GLN* 1.3 75.8 - - - +
148A GLY* 1.3 58.5 + - - +
150A ASN* 3.4 4.9 + - - -
151A ASN* 3.0 29.6 + - - +
157A THR* 3.9 4.5 - - + -
170A ILE* 3.8 24.2 - - + -
172A SER* 3.8 13.1 + - - +
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE 3.0 12.7 + - - -
145A GLN 3.6 2.9 - - - -
147A ALA* 1.3 74.3 - - - +
149A VAL* 1.3 60.8 + - - +
150A ASN 3.3 0.7 + - - -
151A ASN* 3.3 5.4 + - - +
157A THR* 3.3 21.6 + - - -
192A VAL* 4.1 5.5 - - - +
205A ARG* 2.9 27.1 + - - -
209A LEU* 3.6 17.9 - - - -
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLN* 2.9 24.3 + - + +
146A GLN* 3.7 11.7 - - - +
148A GLY* 1.3 76.7 - - - +
150A ASN* 1.3 69.7 + - - +
151A ASN 3.4 1.1 + - - +
152A PHE* 5.8 0.2 - - - -
205A ARG* 3.7 18.3 + - + +
206A ALA* 3.7 39.3 - - + +
209A LEU* 4.0 7.2 - - + -
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Residues in contact with ASN 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLN* 2.9 39.0 + - - +
147A ALA* 3.7 4.9 - - - +
149A VAL* 1.3 84.7 - - - +
151A ASN* 1.3 59.5 + - - +
152A PHE* 3.0 13.2 + - - +
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Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ALA 3.0 16.2 + - - +
148A GLY 3.3 10.0 + - - +
149A VAL 3.4 0.6 - - - -
150A ASN* 1.3 72.6 - - - +
152A PHE* 1.3 69.4 + - - +
153A GLY 3.4 4.7 + - - +
154A SER 4.9 0.2 - - - +
155A GLY* 3.9 3.0 - - - -
156A TRP 3.1 25.5 + - - +
157A THR* 3.5 9.8 + - - +
172A SER* 3.7 15.2 - - - +
173A THR 3.1 29.0 + - - +
174A SER* 4.8 4.0 - - - -
192A VAL* 3.6 7.0 - - + +
205A ARG* 2.7 27.0 + - - +
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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