Contacts of the helix formed by residues 148 - 158 (chain F) in PDB entry 5G04
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 LEU 148 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F CYS* 4.1 20.4 - - + +
116F PHE* 3.7 46.4 - - + +
119F SER* 5.2 4.0 - - - -
141F SER* 5.6 3.4 - - - +
142F LEU* 3.7 13.8 - - + +
145F ASN* 4.9 4.9 - - - +
146F PRO* 2.7 20.0 + - - +
147F PHE* 1.3 84.0 - - + +
149F TRP* 1.3 64.6 + - - +
150F SER 3.4 0.2 - - - -
151F PRO* 3.2 32.7 - - + +
152F PHE* 4.0 1.2 + - - +
167F THR* 5.2 3.0 - - - +
466F LEU* 6.4 0.4 - - - -
11H ALA* 5.1 5.6 - - + +
15H ALA* 5.1 5.4 - - + -
23H ASP* 4.1 18.4 - - - +
27H LEU* 5.1 5.2 - - + -
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Residues in contact with TRP 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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147F PHE 3.7 3.9 + - - +
148F LEU* 1.3 73.1 - - - +
150F SER* 1.3 61.4 + - - +
152F PHE* 3.3 34.3 + + + +
153F GLU* 2.8 69.0 + - + +
167F THR* 4.5 8.1 - - + -
466F LEU* 3.9 28.5 - - + +
469F MET* 4.4 5.2 - - + -
470F GLY* 3.5 32.1 - - - -
473F TYR* 3.8 28.3 - + + -
500F TRP* 3.8 18.4 - + - -
23H ASP* 3.9 10.6 - - + +
26H PHE* 3.2 45.5 - + + -
27H LEU* 5.7 1.7 - - + +
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Residues in contact with SER 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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119F SER* 4.1 8.5 + - - -
138F TYR* 5.3 0.4 - - - -
149F TRP* 1.3 75.8 - - - +
151F PRO* 1.3 65.6 - - - +
153F GLU* 3.8 13.4 - - - +
154F SER* 2.6 35.9 + - - -
20H ALA* 5.4 1.0 - - - +
22H ARG* 4.9 8.1 - - - -
23H ASP* 2.6 40.2 + - - +
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Residues in contact with PRO 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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119F SER* 4.2 11.2 - - - +
138F TYR* 3.8 26.6 - - + -
141F SER* 4.2 14.8 - - - +
142F LEU* 3.8 23.1 - - + +
148F LEU* 3.2 40.4 - - + +
150F SER* 1.3 99.1 - - - +
152F PHE* 1.3 55.1 + - - +
154F SER* 3.8 1.2 - - - -
155F LEU* 2.9 31.7 + - - +
23H ASP* 4.1 0.9 - - - +
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Residues in contact with PHE 152 (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 LEU* 3.6 25.9 - - + +
148F LEU 4.2 3.8 - - - +
149F TRP* 3.3 46.1 + + + +
151F PRO* 1.3 81.2 - - - +
153F GLU* 1.3 57.8 + - - +
155F LEU* 3.2 4.9 + - - +
156F CYS* 3.0 39.3 + - - +
162F PRO* 3.4 42.6 - - + -
163F ASP 4.4 9.9 - - - -
164F PRO* 5.3 3.6 - - + -
166F GLN* 5.0 3.8 - - + -
167F THR* 4.3 22.0 - - + -
470F GLY* 3.8 26.0 - - - -
473F TYR* 4.9 1.3 - - + -
474F LEU* 4.5 7.6 - - + -
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Residues in contact with GLU 153 (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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149F TRP* 2.8 55.6 + - + +
150F SER* 3.8 13.4 - - - +
152F PHE* 1.3 73.2 - - - +
154F SER* 1.4 60.7 + - - +
156F CYS* 3.0 24.6 - - - -
157F GLU* 3.2 20.9 + - - +
473F TYR* 3.7 33.7 + - + +
500F TRP* 4.4 7.8 + - - -
504F GLN* 5.5 0.2 + - - -
22H ARG* 4.3 28.4 + - - +
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Residues in contact with SER 154 (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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123F HIS* 5.3 4.0 + - - -
138F TYR* 3.6 30.8 + - - -
150F SER* 2.6 24.8 + - - -
151F PRO 3.8 0.7 - - - -
153F GLU* 1.4 74.1 - - - +
155F LEU* 1.3 66.5 + - - +
157F GLU* 3.3 10.8 + - - +
158F ILE* 3.1 29.3 + - - +
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Residues in contact with LEU 155 (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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135F SER* 4.0 24.7 - - - +
138F TYR* 4.3 5.1 - - + -
139F GLN* 3.7 36.8 - - + +
142F LEU* 4.0 17.7 - - + -
151F PRO 2.9 17.9 + - - +
152F PHE 3.3 5.8 - - - +
154F SER* 1.3 77.9 - - - +
156F CYS* 1.3 60.7 + - - +
158F ILE* 3.4 16.4 + - - +
160F GLU* 2.8 39.0 - - + +
162F PRO* 3.8 28.0 - - + -
166F GLN* 4.3 0.2 - - - +
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Residues in contact with CYS 156 (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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152F PHE* 3.0 25.4 + - + +
153F GLU* 3.0 29.4 - - - -
155F LEU* 1.3 74.3 - - - +
157F GLU* 1.3 57.8 + - - +
158F ILE 2.6 18.2 - - - +
159F GLY 5.0 0.2 - - - +
160F GLU 3.4 9.5 - - - +
161F LYS* 5.1 3.8 - - - +
162F PRO* 3.8 18.6 - - + -
473F TYR* 3.8 26.0 - - - -
474F LEU* 4.3 21.1 - - + +
477F CYS* 4.4 7.5 - - + +
478F SER 5.7 0.3 + - - -
633F ARG* 3.6 9.2 + - - -
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Residues in contact with GLU 157 (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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153F GLU* 3.2 22.7 + - - +
154F SER* 3.3 12.1 + - - +
156F CYS* 1.3 71.2 - - - +
158F ILE* 1.3 66.2 + - + +
473F TYR* 3.5 17.9 + - + +
477F CYS* 3.5 27.4 - - - -
631F ASN* 4.2 23.1 + - - +
633F ARG* 3.2 26.2 + - - +
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Residues in contact with ILE 158 (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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126F CYS* 3.3 34.8 - - + -
131F LEU* 3.5 38.4 - - + -
135F SER* 3.6 19.7 - - - +
138F TYR* 3.8 15.9 - - + +
154F SER* 3.1 18.9 + - - +
155F LEU* 3.5 9.6 - - - +
156F CYS 2.6 24.8 - - - +
157F GLU* 1.3 78.8 - - + +
159F GLY* 1.3 77.2 + - - +
160F GLU* 3.1 9.2 + - + +
633F ARG* 3.7 5.5 + - - +
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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