Contacts of the helix formed by residues 146 - 161 (chain C) in PDB entry 5XVO
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 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C ASP* 3.2 16.9 + - - +
144C PRO 3.2 7.1 - - - +
145C ALA* 1.3 81.8 - - - +
147C ARG* 1.3 65.0 + - - +
148C GLU* 3.2 3.5 - - - +
149C GLY* 3.0 32.2 + - - -
150C HIS* 3.1 17.5 + - - +
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Residues in contact with ARG 147 (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 ILE* 4.6 2.0 - - + -
135C MET* 3.0 55.6 - - + +
138C GLU* 3.6 34.6 + - + +
139C LEU* 3.7 15.0 - - + -
143C ASP* 2.8 15.6 + - - +
145C ALA* 3.5 31.3 + - + +
146C ASN* 1.3 74.8 - - - +
148C GLU* 1.3 60.1 + - - +
150C HIS* 3.8 16.9 + - - +
151C ALA* 2.8 33.1 + - - +
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Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C TRP* 3.9 15.1 - - - -
109C ILE* 3.1 42.6 - - + +
112C LYS* 3.4 27.4 + - - +
113C ILE* 4.1 13.9 - - + +
116C GLN* 4.7 1.6 + - - -
139C LEU* 4.7 0.2 - - - +
143C ASP* 2.8 14.9 + - - +
146C ASN* 4.5 2.8 - - - +
147C ARG* 1.3 78.3 - - - +
149C GLY* 1.3 59.1 + - - +
151C ALA* 3.5 2.6 - - - +
152C ALA* 2.9 28.4 + - + +
203C LYS* 5.3 2.1 + - - -
219C GLU* 3.4 10.7 - - - +
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Residues in contact with GLY 149 (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 ASN* 3.0 27.5 + - - -
148C GLU* 1.3 78.1 - - - +
150C HIS* 1.3 64.1 + - - +
152C ALA* 3.8 6.0 - - - +
153C ARG* 3.1 24.6 + - - +
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Residues in contact with HIS 150 (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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135C MET* 3.0 33.2 - - + +
146C ASN* 3.1 16.9 + - - +
147C ARG* 3.8 13.7 + - - +
149C GLY* 1.3 73.4 - - - +
151C ALA* 1.3 66.7 + - - +
153C ARG* 3.4 5.6 + - + +
154C SER* 3.1 26.2 + - - -
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Residues in contact with ALA 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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113C ILE* 4.3 17.9 - - + -
116C GLN* 4.2 10.1 - - - +
132C LEU* 4.1 16.8 - - + +
135C MET* 3.6 21.4 - - + -
147C ARG 2.8 18.6 + - - +
148C GLU 3.5 5.2 - - - +
150C HIS* 1.3 78.9 - - - +
152C ALA* 1.3 56.5 + - - +
154C SER* 3.6 2.7 - - - -
155C TYR* 2.9 31.3 + - - +
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Residues in contact with ALA 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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112C LYS* 4.8 10.1 - - - +
116C GLN* 4.0 17.9 - - - +
148C GLU* 2.9 17.0 + - + +
149C GLY* 3.8 7.6 - - - +
151C ALA* 1.3 74.4 - - - +
153C ARG* 1.3 66.6 + - - +
155C TYR* 3.3 2.6 + - - +
156C PHE* 2.9 42.8 + - + -
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Residues in contact with ARG 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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149C GLY 3.1 17.6 + - - +
150C HIS* 3.8 6.1 - - + +
151C ALA 3.4 0.2 - - - -
152C ALA* 1.3 77.4 - - - +
154C SER* 1.3 55.5 + - - +
156C PHE* 3.5 4.3 + - - +
157C ASN* 2.5 67.5 + - - +
162C ASN 5.2 2.6 + - - -
164C PHE 4.2 3.9 + - - -
165C THR* 3.6 34.6 - - - +
166C ARG 5.2 0.2 - - - +
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Residues in contact with SER 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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128C LYS* 5.1 5.7 - - - +
131C ALA* 5.7 2.4 - - - +
132C LEU* 4.0 15.4 - - - +
135C MET* 5.2 2.9 - - - -
150C HIS* 3.1 21.9 + - - -
151C ALA* 3.6 5.8 - - - -
153C ARG* 1.3 76.4 - - - +
155C TYR* 1.3 61.3 + - - +
157C ASN* 3.2 7.8 + - - +
158C THR* 2.8 37.3 + - - -
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Residues in contact with TYR 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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116C GLN* 3.3 59.7 - - + -
119C HIS* 2.8 28.9 + - - +
120C LEU* 3.8 23.5 - - + +
132C LEU* 4.2 5.7 - - + +
151C ALA 2.9 20.2 + - - +
152C ALA* 3.4 4.9 - - - +
154C SER* 1.3 76.3 + - - +
156C PHE* 1.3 91.1 + + - +
158C THR* 3.5 3.2 - - - -
159C LEU* 3.1 39.1 + - + +
223C PRO* 4.3 3.3 - - - +
226C ASP* 2.8 33.5 + - - +
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Residues in contact with PHE 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 GLN* 4.9 3.1 - - - -
152C ALA* 2.9 39.4 + - + +
153C ARG* 4.1 4.0 - - - +
155C TYR* 1.3 98.3 - + - +
157C ASN* 1.3 61.9 + - - +
159C LEU* 4.4 1.8 - - + +
160C PHE* 2.9 57.1 + + - +
161C GLY 4.3 0.5 - - - +
164C PHE* 4.0 23.1 - + + -
166C ARG* 4.0 26.0 - - + -
176C LEU* 3.9 18.6 - - + -
180C TYR* 3.7 22.7 - + - -
226C ASP* 4.3 6.3 - - - -
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Residues in contact with ASN 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ARG* 2.5 57.3 + - - +
154C SER* 3.6 6.7 + - - +
156C PHE* 1.3 76.5 - - - +
158C THR* 1.3 60.2 + - - +
161C GLY* 2.6 44.3 + - - +
162C ASN* 3.3 31.1 + - - +
164C PHE 3.4 23.4 + - - -
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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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120C LEU* 3.8 15.6 - - + +
125C TYR* 3.5 53.1 + - + -
128C LYS* 4.0 27.6 - - + +
154C SER* 2.8 25.3 + - - -
155C TYR* 3.5 5.5 - - - -
157C ASN* 1.3 80.6 - - - +
159C LEU* 1.3 59.6 + - - +
161C GLY 4.4 1.2 + - - -
162C ASN* 5.5 0.2 - - - -
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Residues in contact with LEU 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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119C HIS* 3.7 20.0 - - + +
120C LEU* 3.8 20.4 - - + -
123C ARG* 4.2 18.4 - - + -
125C TYR* 4.6 7.4 + - + -
155C TYR* 3.1 49.5 + - + +
156C PHE 3.9 0.4 - - - +
158C THR* 1.3 82.6 - - - +
160C PHE* 1.3 86.6 - - + +
161C GLY 3.6 0.4 + - - -
226C ASP* 5.1 2.0 - - + -
230C TYR* 3.4 40.5 + - + -
233C ARG* 4.9 2.9 + - - -
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Residues in contact with PHE 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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156C PHE* 2.9 46.7 + + - +
159C LEU* 1.3 90.8 - - + +
161C GLY* 1.3 63.9 + - - +
163C ASP* 5.8 1.2 - - - +
164C PHE* 3.6 37.5 + + + +
172C ILE* 3.7 42.2 - - + -
176C LEU* 4.6 4.7 - - + -
226C ASP* 5.1 2.7 - - + -
229C ILE* 4.5 6.7 - - + -
230C TYR* 3.9 33.7 - + + -
233C ARG* 4.1 18.2 - - + +
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Residues in contact with GLY 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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157C ASN* 2.6 31.1 + - - +
158C THR 4.4 1.4 + - - -
159C LEU 3.6 1.4 - - - -
160C PHE* 1.3 74.6 - - - +
162C ASN* 1.3 64.8 + - - -
163C ASP* 3.2 3.4 - - - -
164C PHE* 3.2 15.6 + - - +
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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