Contacts of the helix formed by residues 151 - 165 (chain C) in PDB entry 5AQF
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 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C GLY 5.2 1.6 + - - -
149C TYR 3.4 3.9 + - - +
150C PHE* 1.3 76.3 - - - +
152C ASP* 1.3 64.8 + - - +
153C SER* 3.1 12.6 + - - -
154C GLN* 2.9 42.9 + - - +
155C ARG* 3.1 24.3 + - - +
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Residues in contact with ASP 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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151C ASN* 1.3 75.3 - - - +
153C SER* 1.3 57.0 + - - +
155C ARG* 3.5 11.0 + - - +
156C GLN* 2.9 30.9 + - - +
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Residues in contact with SER 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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75C GLY* 2.7 27.3 + - - -
77C ARG* 6.1 0.5 - - - -
151C ASN* 3.1 10.8 + - - -
152C ASP* 1.3 75.3 - - - +
154C GLN* 1.3 60.4 + - - +
156C GLN* 3.8 4.9 - - - +
157C ALA* 2.9 31.9 + - - +
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Residues in contact with GLN 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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74C ILE* 3.3 17.9 + - - +
75C GLY* 3.8 15.5 - - - +
76C ARG* 3.1 44.5 + - + +
149C TYR* 4.1 4.2 - - - +
150C PHE* 3.4 43.6 - - + -
151C ASN* 2.9 45.5 + - - +
153C SER* 1.3 74.6 - - - +
155C ARG* 1.4 61.0 + - - +
157C ALA* 3.7 1.7 + - - +
158C THR* 2.9 29.5 + - - -
1384C GOL 3.8 1.0 + - - -
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Residues in contact with ARG 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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146C VAL* 3.5 20.2 - - + +
147C PRO 3.4 7.3 + - - -
148C ALA 3.0 24.2 + - - -
150C PHE* 2.9 27.9 + - + -
151C ASN 3.1 18.7 + - - +
152C ASP* 3.7 11.0 - - - +
154C GLN* 1.4 74.4 - - - +
156C GLN* 1.4 57.4 + - - +
158C THR* 3.2 7.8 + - - -
159C LYS* 3.0 27.1 + - - +
172C ILE* 4.5 20.9 + - + +
174C ASN* 2.9 35.3 + - - +
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Residues in contact with GLN 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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152C ASP 2.9 19.6 + - - +
153C SER* 3.8 5.6 - - - +
155C ARG* 1.4 76.2 - - - +
157C ALA* 1.3 56.0 + - - +
159C LYS* 3.2 17.0 + - - +
160C ASP* 2.8 65.0 + - - +
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Residues in contact with ALA 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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74C ILE* 3.6 11.8 - - + +
75C GLY* 3.6 26.7 - - - +
117C GLU* 3.4 23.8 - - - +
153C SER 2.9 19.0 + - - +
154C GLN 4.0 1.1 - - - +
156C GLN* 1.3 75.7 - - - +
158C THR* 1.4 57.0 + - - +
160C ASP* 3.5 9.8 + - - +
161C ALA* 3.0 22.3 + - - +
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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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11C LEU* 4.2 14.9 - - + +
74C ILE* 3.9 15.7 - - - +
124C LEU* 4.4 2.1 - - - +
144C VAL* 3.9 25.5 - - + +
145C THR 4.6 0.7 - - - +
146C VAL* 3.6 22.0 - - + -
150C PHE* 3.7 16.8 - - - -
154C GLN 2.9 15.5 + - - -
155C ARG 3.2 8.5 + - - -
157C ALA* 1.4 71.1 - - - +
159C LYS* 1.4 65.4 + - - +
161C ALA* 3.2 5.1 + - - +
162C GLY* 3.1 17.7 + - - -
169C VAL* 5.5 0.3 - - - +
172C ILE* 4.0 5.3 - - + +
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Residues in contact with LYS 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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155C ARG 3.0 12.3 + - - +
156C GLN* 3.2 24.4 + - - +
158C THR* 1.4 74.6 - - - +
160C ASP* 1.4 56.5 + - - +
162C GLY* 3.1 5.4 + - - -
163C THR* 3.0 32.2 + - - +
169C VAL* 4.3 19.6 - - + +
172C ILE* 4.1 23.5 - - + +
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Residues in contact with ASP 160 (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 GLU* 4.6 14.5 - - + +
156C GLN* 2.8 50.0 + - - +
157C ALA* 3.6 10.6 - - - +
159C LYS* 1.4 73.1 - - - +
161C ALA* 1.4 58.6 + - - +
163C THR* 3.2 9.8 + - - -
164C ILE* 2.9 40.9 + - + +
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Residues in contact with ALA 161 (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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11C LEU* 5.3 0.4 - - + -
74C ILE* 4.4 0.2 - - + -
117C GLU* 3.3 28.0 - - - +
120C SER* 3.9 11.9 - - - -
121C SER* 3.2 21.9 - - - +
124C LEU* 3.7 11.7 - - + -
157C ALA 3.0 14.1 + - - +
158C THR* 3.2 13.2 + - - +
160C ASP* 1.4 73.4 - - - +
162C GLY* 1.3 56.8 - - - +
164C ILE* 4.4 0.7 - - - -
165C ALA* 3.0 26.0 + - - +
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Residues in contact with GLY 162 (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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124C LEU* 3.5 16.3 - - - +
144C VAL* 5.6 0.2 - - - -
158C THR 3.1 7.4 + - - -
159C LYS 3.1 8.2 + - - -
161C ALA* 1.3 75.8 - - - +
163C THR* 1.4 54.0 + - - +
165C ALA* 3.3 8.4 + - - +
167C LEU* 2.9 41.1 + - - +
169C VAL* 3.9 16.8 - - - -
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Residues in contact with THR 163 (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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159C LYS* 3.0 17.3 + - - +
160C ASP* 3.5 13.4 + - - -
162C GLY* 1.4 71.6 - - - +
164C ILE* 1.4 60.9 + - + +
166C GLY* 3.0 19.6 + - - -
167C LEU 3.9 10.0 + - - +
169C VAL* 4.7 1.6 - - - +
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Residues in contact with ILE 164 (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 GLU* 4.1 30.5 - - + +
118C GLU* 4.7 14.4 - - + -
121C SER* 3.5 22.0 - - - +
160C ASP* 2.9 33.6 + - + +
163C THR* 1.4 73.0 - - + +
165C ALA* 1.3 56.8 + - - +
166C GLY* 3.1 4.9 + - - -
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Residues in contact with ALA 165 (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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121C SER* 3.4 21.7 - - - +
124C LEU* 3.8 17.5 - - + -
125C THR* 3.5 20.2 + - - +
128C LYS* 3.6 19.8 - - - +
161C ALA 3.0 18.2 + - - +
162C GLY* 3.5 6.3 - - - +
163C THR 3.2 0.4 - - - -
164C ILE* 1.3 73.2 - - - +
166C GLY* 1.3 59.0 + - - +
167C LEU* 3.3 5.9 + - + +
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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