Contacts of the helix formed by residues 152 - 161 (chain C) in PDB entry 5W4A
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 GLU 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C GLU* 1.3 95.3 + - + +
153C ASN* 1.3 69.0 + - - +
154C TYR* 3.3 6.8 + - + +
155C GLU* 3.3 11.0 + - + +
156C LYS* 3.0 22.8 + - - +
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Residues in contact with ASN 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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152C GLU* 1.3 76.9 + - - +
154C TYR* 1.3 57.5 + - - +
156C LYS* 3.2 11.5 + - - +
157C PHE* 2.8 31.4 + - - +
179C LEU 4.2 6.0 + - - +
180C GLY 4.1 12.3 + - - -
181C LEU* 3.6 28.2 - - + +
183C ASP* 5.9 2.9 - - - +
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Residues in contact with TYR 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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124A ASN* 4.9 4.5 + - - -
125A LEU* 5.0 5.5 - - - +
128A ARG* 3.0 49.1 + - - -
152C GLU* 3.3 5.1 - - + +
153C ASN* 1.3 78.4 - - - +
155C GLU* 1.3 60.2 + - - +
157C PHE* 3.4 5.9 + - - +
158C THR* 2.9 35.3 + - - -
183C ASP* 5.4 3.1 - - - +
185C ASP* 4.2 26.7 + - + -
186C THR* 3.7 29.2 - - + -
189C GLU* 4.6 1.8 + - - -
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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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146C LYS 5.2 0.3 - - - +
149C ASN 4.5 4.3 - - - +
150C SER* 3.4 22.3 + - - +
151C GLU* 3.0 24.3 + - - +
152C GLU* 3.3 13.1 + - + +
154C TYR* 1.3 78.1 - - + +
156C LYS* 1.3 67.1 + - - +
158C THR* 3.1 8.8 + - - -
159C GLU* 2.9 34.6 + - + +
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Residues in contact with LYS 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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82C LEU 5.0 0.6 + - - -
83C ALA 2.7 30.7 + - - -
84C LEU 3.9 11.1 + - - -
85C GLY* 4.0 7.3 - - - +
86C PRO* 5.7 0.6 - - - +
147C THR* 3.6 34.9 + - + +
148C ILE* 5.9 0.9 - - - +
150C SER* 3.6 15.8 - - - +
152C GLU 3.0 16.8 + - - +
153C ASN* 3.6 11.2 - - - +
155C GLU* 1.3 77.2 - - - +
157C PHE* 1.3 56.9 + - - +
159C GLU* 3.3 2.4 + - - +
160C LEU* 2.9 40.1 + - + +
179C LEU* 3.8 23.5 - - + +
181C LEU* 5.0 7.0 - - + -
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Residues in contact with PHE 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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128A ARG* 4.2 5.8 - - - -
153C ASN 2.8 20.3 + - - +
154C TYR* 3.6 6.7 - - - +
156C LYS* 1.3 73.0 - - - +
158C THR* 1.3 59.0 + - - +
160C LEU* 3.8 3.3 - - + -
161C SER* 2.9 51.9 + - - -
172C ALA* 6.3 0.4 - - + -
176C THR* 3.5 25.1 - - - -
181C LEU* 4.1 26.3 - - + +
186C THR* 3.6 27.4 - - + -
189C GLU* 3.4 33.9 - - + -
190C VAL* 3.7 25.8 - - + -
193C ILE* 3.9 17.0 - - + -
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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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128A ARG* 2.9 40.9 + - - +
146A LYS* 6.0 2.7 - - - +
154C TYR* 2.9 21.2 + - - -
155C GLU* 3.1 12.5 + - - -
157C PHE* 1.3 76.8 - - - +
159C GLU* 1.3 70.9 - - - +
161C SER* 3.4 16.7 - - - -
162C GLU* 3.8 12.1 + - - +
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Residues in contact with GLU 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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131C LYS* 5.6 0.2 + - - -
143C ILE* 3.7 8.5 - - - +
146C LYS* 3.5 47.1 - - + +
147C THR* 4.1 10.8 - - - +
150C SER* 3.6 14.6 - - - +
155C GLU* 2.9 29.7 + - + +
156C LYS 3.9 2.7 - - - +
158C THR* 1.3 82.0 - - - +
160C LEU* 1.3 64.9 + - - +
162C GLU* 3.0 31.6 + - - +
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Residues in contact with LEU 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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18C PHE* 5.7 2.2 - - + -
83C ALA* 5.1 1.3 - - + -
143C ILE* 4.5 3.4 - - + -
147C THR* 3.4 29.4 + - + +
156C LYS* 2.9 31.7 + - + +
157C PHE* 3.9 5.8 - - + +
159C GLU* 1.3 76.3 - - - +
161C SER* 1.3 57.3 + - - +
163C LEU* 2.9 43.4 + - + +
172C ALA* 3.9 10.1 - - + +
175C PHE* 3.7 44.9 - - + -
176C THR* 6.1 0.4 - - - +
179C LEU* 4.4 5.8 - - + -
181C LEU* 3.8 25.6 - - + -
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Residues in contact with SER 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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128A ARG* 5.6 0.6 + - - -
132A LEU* 4.1 19.0 - - - +
157C PHE* 2.9 48.8 + - - -
158C THR* 3.4 10.7 - - - -
159C GLU 3.2 0.4 - - - -
160C LEU* 1.3 77.7 - - - +
162C GLU* 1.3 63.3 + - - +
163C LEU 3.0 0.4 - - - -
164C CYS* 3.0 29.5 + - - +
165C GLY 4.3 0.5 + - - -
172C ALA* 4.8 0.7 - - - -
189C GLU* 5.1 1.0 + - - -
193C ILE* 3.9 8.1 - - - +
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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