Contacts of the helix formed by residues 150 - 159 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C GLY 2.7 27.7 - - - +
118C ASP* 3.8 7.1 - - - -
119C GLN* 3.3 29.8 + - - +
127C TYR* 5.4 0.2 + - - -
149C PRO* 1.3 74.4 - - - +
151C GLN* 1.3 56.7 + - - +
152C PHE* 4.1 4.8 - - - +
153C GLU* 2.7 34.3 + - + +
154C ALA* 2.5 36.4 + - - +
185C ILE* 4.4 0.4 - - - -
186C THR* 4.2 3.8 + - - -
2402C ADP 3.6 35.0 + - - -
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLN* 3.0 27.4 - - - +
150C ASN* 1.3 74.0 - - - +
152C PHE* 1.3 54.4 + - - +
154C ALA* 3.4 2.9 - - - +
155C GLU* 2.6 61.6 + - - +
162C ILE* 3.7 29.7 + - + +
185C ILE* 3.8 11.8 - - + +
187C SER 3.1 13.2 + - - +
188C SER* 2.9 28.6 - - - -
189C ASN* 3.0 37.1 + - - +
190C LEU* 4.8 1.7 + - - +
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Residues in contact with PHE 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLY* 3.6 29.4 - - - -
118C ASP 3.7 3.6 - - - -
119C GLN* 3.6 25.4 - - + +
124C GLY* 3.4 29.6 - - - -
125C ALA* 3.6 35.9 - - - -
126C MET* 3.6 17.0 - - + -
150C ASN* 3.0 4.9 - - - +
151C GLN* 1.3 79.7 - - - +
153C GLU* 1.3 66.5 + - - +
155C GLU* 2.9 22.8 + - + +
156C LEU* 2.8 39.8 + - + +
161C LYS* 5.5 5.6 - - - -
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASP* 4.7 2.4 - - - +
114C PRO* 2.9 24.8 - - + +
115C VAL* 3.1 7.9 - - - +
116C MET* 2.7 33.3 + - + +
117C GLY 3.5 24.3 + - - +
127C TYR* 4.6 0.7 + - - -
148C THR 4.5 2.3 - - - +
149C PRO* 3.8 7.6 - - + +
150C ASN* 2.7 42.0 + - + +
152C PHE* 1.3 79.0 - - + +
154C ALA* 1.3 51.6 + - - +
156C LEU* 2.8 14.4 + - - +
157C LEU* 2.8 38.0 + - - +
2402C ADP 4.9 4.9 + - - -
2403C ZN 4.3 5.5 - - - -
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C PRO* 3.9 12.9 - - + +
150C ASN 2.5 22.8 + - - +
151C GLN* 3.4 5.8 - - + +
153C GLU* 1.3 71.8 - - - +
155C GLU* 1.3 63.4 + - + +
157C LEU* 3.3 7.2 + - - +
158C THR* 2.9 26.1 + - - +
162C ILE* 5.8 2.2 - - + -
171C VAL* 3.8 13.5 - - + +
175C LEU* 4.6 2.2 - - + +
185C ILE* 3.5 30.5 - - + -
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C GLN* 2.6 62.4 + - - +
152C PHE* 3.2 16.6 - - - +
154C ALA* 1.3 72.7 - - - +
156C LEU* 1.3 54.8 + - - +
157C LEU 3.1 0.7 + - - -
158C THR* 3.4 4.9 + - - -
159C GLY* 2.7 32.7 + - - -
160C ARG 3.2 25.3 + - - +
161C LYS* 3.3 29.7 + - - +
162C ILE* 2.9 34.1 + - + +
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Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C MET* 3.4 36.1 - - + -
126C MET* 3.6 29.4 - - + -
133C LEU* 3.4 36.7 - - + +
137C ARG* 4.4 4.0 + - - -
152C PHE* 2.8 37.1 + - + +
153C GLU* 2.8 13.9 + - - +
155C GLU* 1.3 77.2 - - - +
157C LEU* 1.3 57.5 + - - +
159C GLY* 3.6 8.3 + - - -
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PRO* 3.9 28.3 - - + -
116C MET* 3.7 20.0 - - + -
133C LEU* 4.3 3.1 - - + -
136C TYR* 4.1 15.9 - - + -
137C ARG* 3.2 38.2 - - + +
141C VAL* 3.9 27.4 - - + -
147C ILE* 5.2 3.1 - - + -
149C PRO* 4.4 8.1 - - + -
153C GLU 2.8 20.7 + - - +
154C ALA* 3.8 3.6 - - - +
155C GLU 3.1 0.2 + - - -
156C LEU* 1.3 69.6 - - - +
158C THR* 1.3 59.6 + - - +
159C GLY 2.9 8.5 + - - -
175C LEU* 4.2 23.8 - - + -
178C MET* 4.4 7.7 - - - +
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Residues in contact with THR 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ALA 2.9 12.9 + - - -
155C GLU* 3.4 3.6 + - - -
157C LEU* 1.3 74.6 - - - +
159C GLY* 1.3 55.6 + - - +
160C ARG* 3.0 20.8 + - - +
171C VAL* 3.1 42.9 - - + +
174C MET* 3.3 36.3 - - + +
175C LEU* 3.6 25.1 - - + +
178C MET* 4.6 6.3 - - - -
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Residues in contact with GLY 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ARG* 5.9 2.5 - - - -
155C GLU 2.7 10.3 + - - -
156C LEU* 4.0 8.5 - - - -
157C LEU 2.9 6.8 + - - -
158C THR* 1.3 75.7 - - - +
160C ARG* 1.3 61.2 + - - +
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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