Contacts of the helix formed by residues 144 - 158 (chain E) in PDB entry 5OF4
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 144 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E THR* 3.2 19.1 - - - +
112E LYS 3.6 17.0 + - - -
113E ARG 4.0 3.4 - - - +
143E PRO* 1.3 80.9 - - - +
145E LEU* 1.3 60.7 + - - +
146E TYR* 3.7 13.9 + - - +
147E ASN* 2.8 31.0 + - - -
148E SER* 3.8 7.8 + - - -
171E PHE* 4.8 1.3 - - - -
177E CYS 3.3 21.7 + - - +
178E ASP* 4.1 3.1 - - - -
179E PRO* 4.3 1.4 - - - +
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Residues in contact with LEU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL* 5.6 0.7 - - + -
109E THR* 5.6 0.2 - - - -
144E SER* 1.3 70.5 - - - +
146E TYR* 1.3 58.8 + - - +
147E ASN 3.4 0.2 - - - -
148E SER* 3.3 11.0 + - - -
149E LEU* 3.0 33.8 + - + +
169E ILE* 3.6 43.3 - - + -
171E PHE* 4.5 15.3 - - + -
176E THR* 3.9 26.5 - - + +
178E ASP* 5.4 0.2 - - - +
182E ILE* 3.5 20.9 - - + -
186E ILE* 6.5 0.4 - - + -
207E VAL* 4.3 10.1 - - + -
208E CYS* 4.2 20.4 - - - -
211E LEU* 3.8 20.2 - - + -
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Residues in contact with TYR 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E SER* 3.3 3.7 + - - +
145E LEU* 1.3 75.7 - - - +
147E ASN* 1.3 74.0 + - - +
149E LEU 3.4 1.6 + - - -
150E SER* 2.9 35.6 + - - -
178E ASP* 3.6 23.2 - - + +
179E PRO* 4.6 11.4 - - + -
180E SER* 3.4 50.1 + - - -
181E ASN 4.3 5.8 - - - -
182E ILE* 3.5 15.8 - - + +
185E LEU* 3.5 39.7 - - + +
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Residues in contact with ASN 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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112E LYS 3.1 17.7 - - - +
113E ARG* 3.8 4.9 - - - -
114E ALA* 3.3 28.5 - - + +
144E SER* 2.8 23.0 + - - +
145E LEU 3.4 0.4 - - - -
146E TYR* 1.3 88.1 - - - +
148E SER* 1.3 57.5 + - - +
150E SER* 2.5 24.8 + - - +
151E ILE* 2.9 19.3 + - + +
179E PRO* 4.7 9.5 - - - +
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Residues in contact with SER 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL* 3.4 29.2 - - - +
107E ILE* 4.5 7.6 - - - +
109E THR* 2.6 29.5 + - - -
114E ALA* 3.3 13.1 - - - +
144E SER 3.8 3.0 + - - -
145E LEU* 3.3 14.3 + - - -
146E TYR 3.3 0.6 - - - -
147E ASN* 1.3 79.5 - - - +
149E LEU* 1.3 61.1 + - - +
151E ILE* 3.3 4.0 + - - +
152E ALA* 3.0 28.4 + - - +
169E ILE* 6.2 0.2 - - - -
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Residues in contact with LEU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E LEU* 3.0 30.1 + - + +
148E SER* 1.3 76.6 - - - +
150E SER* 1.3 60.2 + - - +
152E ALA* 3.9 7.4 - - + +
153E MET* 2.9 29.1 + - - +
167E VAL* 4.8 10.1 - - + -
169E ILE* 4.2 12.8 - - + -
182E ILE* 3.9 21.8 - - + -
185E LEU* 3.8 18.7 - - + +
186E ILE* 5.7 0.4 - - + -
189E LEU* 4.2 21.3 - - + +
194E ILE* 5.4 0.9 - - + -
196E VAL* 4.1 24.0 - - + -
211E LEU* 4.2 21.3 - - + -
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Residues in contact with SER 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 TYR* 2.9 24.8 + - - -
147E ASN* 2.5 31.6 + - - +
149E LEU* 1.3 77.4 - - - +
151E ILE* 1.3 59.9 + - - +
153E MET* 3.6 7.1 - - - +
154E GLN* 2.9 38.7 + - - +
185E LEU* 4.6 7.3 - - - +
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Residues in contact with ILE 151 (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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62E TYR* 5.9 0.4 - - + -
107E ILE* 3.7 24.7 - - + -
114E ALA* 3.3 44.4 - - + +
115E GLU 4.1 2.2 - - - +
116E LYS* 4.1 24.5 - - + +
147E ASN* 2.9 10.4 + - + +
148E SER* 3.8 4.3 - - - +
150E SER* 1.3 79.9 + - - +
152E ALA* 1.3 65.7 + - - +
154E GLN* 3.3 12.7 + - - +
155E THR* 3.0 39.7 + - - +
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Residues in contact with ALA 152 (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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62E TYR* 4.9 15.9 - - + -
107E ILE* 4.8 3.5 - - + +
148E SER 3.0 17.2 + - - +
149E LEU* 3.9 9.0 - - + +
151E ILE* 1.3 78.0 - - - +
153E MET* 1.3 59.1 + - - +
156E LEU* 2.9 34.2 + - + +
167E VAL* 4.2 31.0 - - + -
194E ILE* 4.4 9.0 - - + -
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Residues in contact with MET 153 (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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149E LEU 2.9 19.1 + - - +
150E SER* 3.6 7.6 - - - +
151E ILE 3.3 0.2 - - - -
152E ALA* 1.3 76.6 - - - +
154E GLN* 1.3 68.2 + - + +
156E LEU* 5.0 0.9 - - - -
157E LYS* 2.8 57.2 + - + +
185E LEU* 5.6 11.0 - - + -
188E THR* 5.0 12.3 - - + -
189E LEU* 4.0 26.0 - - + -
194E ILE* 5.1 3.5 - - - +
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Residues in contact with GLN 154 (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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150E SER* 2.9 24.9 + - - +
151E ILE* 3.3 14.6 + - - +
153E MET* 1.3 91.7 - - + +
155E THR* 1.3 67.1 + - - +
157E LYS* 3.6 2.1 + - - +
158E HIS* 3.1 27.9 + - - -
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Residues in contact with THR 155 (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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62E TYR* 3.3 31.5 + - + +
116E LYS* 4.2 23.6 + - - +
120E LEU* 5.3 3.4 - - + +
151E ILE* 3.0 24.5 + - - +
152E ALA 4.8 0.2 - - - -
154E GLN* 1.3 81.2 + - - +
156E LEU* 1.3 57.9 + - - +
158E HIS* 4.2 10.3 + - - +
159E MET* 4.1 13.5 - - - +
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Residues in contact with LEU 156 (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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60E HIS* 4.0 27.8 - - + +
62E TYR* 4.5 16.6 - - + -
120E LEU* 4.6 1.6 - - + -
152E ALA 2.9 17.4 + - - +
153E MET* 3.7 1.3 - - - -
155E THR* 1.3 76.0 - - - +
157E LYS* 1.3 62.8 + - - +
158E HIS 3.2 2.0 - - - -
159E MET* 3.7 29.0 + - + -
165E ARG* 2.8 61.4 + - + +
167E VAL* 4.3 12.3 - - + -
194E ILE* 3.9 25.6 - - + -
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Residues in contact with LYS 157 (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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153E MET* 2.8 36.3 + - + +
154E GLN* 4.0 6.7 - - - +
155E THR 3.5 0.6 - - - -
156E LEU* 1.3 79.7 - - - +
158E HIS* 1.3 80.0 + - + +
159E MET 3.6 6.4 + - - +
165E ARG* 4.3 7.2 + - - +
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Residues in contact with HIS 158 (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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154E GLN* 3.1 28.3 + - - -
155E THR* 4.5 7.9 - - - +
156E LEU* 3.2 1.4 - - - +
157E LYS* 1.3 99.9 - - - +
159E MET* 1.3 66.8 + - + +
160E PRO* 3.9 4.2 - - - +
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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