Contacts of the helix formed by residues 150 - 159 (chain F) in PDB entry 1RFU
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 ASN 150 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117F GLY 2.5 29.5 - - - +
118F ASP* 3.9 5.9 - - - -
119F GLN* 2.7 35.2 - - - +
127F TYR* 4.9 0.2 + - - -
149F PRO* 1.3 74.1 - - - +
151F GLN* 1.3 68.2 + - - +
152F PHE 2.8 0.2 + - - -
153F GLU* 2.7 33.1 + - + +
154F ALA* 2.5 25.3 + - - +
186F THR* 4.3 3.8 - - - -
5402F ADP 3.5 35.3 + - - -
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Residues in contact with GLN 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 GLN* 3.6 12.9 - - - +
150F ASN* 1.3 81.1 - - - +
152F PHE* 1.3 61.5 + - - +
154F ALA* 3.0 3.5 + - - +
155F GLU* 2.5 53.0 + - - +
162F ILE* 4.0 26.1 + - + +
185F ILE* 3.8 12.6 - - + +
187F SER 3.1 26.2 + - - +
188F SER* 2.8 31.1 - - - -
189F ASN* 3.0 34.9 + - - +
190F LEU* 5.6 2.0 - - - +
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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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117F GLY* 3.5 38.6 - - - -
118F ASP 3.6 3.6 - - - -
119F GLN* 3.0 27.7 - - + +
124F GLY* 3.6 28.7 - - - -
125F ALA* 3.5 29.4 - - - -
126F MET* 3.7 16.8 - - + -
150F ASN* 2.8 3.3 + - - +
151F GLN* 1.3 78.4 - - - +
153F GLU* 1.3 68.6 + - + +
155F GLU* 3.0 21.8 + - + +
156F LEU* 2.7 40.0 + - + +
161F LYS* 5.7 5.4 - - - -
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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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113F ASP* 4.7 2.6 - - - +
114F PRO* 2.8 29.9 - - + +
115F VAL* 3.1 8.7 - - - +
116F MET* 2.6 32.7 + - + +
117F GLY 3.3 24.1 + - - +
127F TYR* 4.6 2.3 + - - -
148F THR 4.6 2.1 - - - +
149F PRO* 3.9 2.6 - - - +
150F ASN* 2.7 44.0 + - + +
152F PHE* 1.3 77.6 - - + +
154F ALA* 1.3 54.0 + - - +
156F LEU* 2.8 14.2 + - - +
157F LEU* 2.7 38.6 + - - +
5401F PLP 5.3 0.9 + - - -
5402F ADP 5.1 3.9 + - - -
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Residues in contact with ALA 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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149F PRO* 3.9 12.6 - - + +
150F ASN 2.5 21.0 + - - +
151F GLN* 3.2 6.3 - - + +
153F GLU* 1.3 73.1 - - - +
155F GLU* 1.3 65.3 + - + +
157F LEU* 3.2 7.5 + - - +
158F THR* 3.0 24.2 + - - +
162F ILE* 5.9 2.7 - - + -
171F VAL* 3.8 13.8 - - + +
175F LEU* 4.7 2.0 - - + -
185F ILE* 3.5 30.5 - - + -
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Residues in contact with GLU 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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151F GLN* 2.5 54.3 + - - +
152F PHE* 3.3 17.9 - - + +
154F ALA* 1.3 71.8 - - - +
156F LEU* 1.3 66.5 + - + +
157F LEU 2.9 0.7 + - - -
158F THR* 3.5 4.9 + - - -
159F GLY* 2.8 21.7 + - - -
160F ARG 3.2 25.5 + - - +
161F LYS* 3.2 28.6 + - - +
162F ILE* 3.1 34.5 + - + +
171F VAL* 5.0 0.2 - - - +
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Residues in contact with LEU 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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116F MET* 3.6 34.1 - - + -
126F MET* 3.9 24.7 - - + -
133F LEU* 3.5 40.0 - - + +
137F ARG* 4.5 3.1 + - - -
152F PHE* 2.7 35.9 + - + +
153F GLU* 2.8 15.5 + - - +
155F GLU* 1.3 78.6 - - - +
157F LEU* 1.3 59.9 + - - +
159F GLY* 3.6 7.8 + - - -
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Residues in contact with LEU 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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114F PRO* 4.0 26.7 - - + -
116F MET* 3.8 18.8 - - + -
133F LEU* 4.3 3.6 - - + -
136F TYR* 4.2 6.7 - - + -
137F ARG* 3.2 48.7 - - + +
141F VAL* 4.0 26.0 - - + -
147F ILE* 5.3 3.4 - - + -
149F PRO* 4.5 3.4 - - + -
153F GLU 2.7 19.3 + - - +
154F ALA* 3.7 9.6 - - - +
155F GLU 2.9 1.2 + - - -
156F LEU* 1.3 70.6 - - - +
158F THR* 1.3 59.1 + - - +
159F GLY 2.9 10.6 + - - -
175F LEU* 4.1 23.1 - - + -
178F MET* 4.3 8.5 - - + +
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Residues in contact with THR 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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154F ALA 3.0 7.2 + - - -
155F GLU* 3.5 3.8 + - - -
157F LEU* 1.3 76.2 - - - +
159F GLY* 1.3 55.7 + - - +
160F ARG* 3.0 19.1 + - - +
171F VAL* 3.0 48.7 - - + +
174F MET* 3.5 37.1 - - + +
175F LEU* 3.4 25.4 - - + +
178F MET* 4.3 7.9 - - - -
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Residues in contact with GLY 159 (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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137F ARG* 5.8 2.7 - - - -
155F GLU 2.8 9.7 + - - -
156F LEU* 4.0 7.2 - - - -
157F LEU 2.9 7.5 + - - -
158F THR* 1.3 76.9 - - - +
160F ARG* 1.3 61.1 + - - +
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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