Contacts of the helix formed by residues 154 - 165 (chain C) in PDB entry 3Q29
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 154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C SO4 3.8 11.3 + - - +
151C ASN* 3.7 24.3 + - - +
152C LEU 4.6 2.0 - - - -
153C GLN* 1.3 79.9 + - - +
155C PRO* 1.3 69.4 - - - +
156C TYR 3.1 2.6 + - - -
157C PHE* 3.1 26.0 + - + +
158C THR* 3.9 5.4 + - - -
345C ARG* 3.2 24.9 + - - +
348C VAL* 5.9 1.1 - - - -
1D GLC 3.7 18.4 - - - +
2D GLC 2.7 37.9 + - - +
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Residues in contact with PRO 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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153C GLN 4.1 0.4 - - - +
154C GLU* 1.3 86.9 - - - +
156C TYR* 1.3 63.3 + - - +
157C PHE 3.1 0.2 - - - -
158C THR* 3.8 8.5 - - - +
159C TRP* 2.8 28.6 + - + +
162C ILE* 5.8 0.3 - - - +
341C TRP* 3.7 23.1 - - + +
344C VAL* 3.6 28.7 - - + +
345C ARG* 3.7 37.9 - - + +
348C VAL* 4.4 6.9 - - + -
2D GLC 3.1 16.4 - - - +
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Residues in contact with TYR 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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112C GLU* 4.5 8.7 + - - +
113C ALA* 4.4 5.0 - - - -
114C LEU* 3.4 48.2 + - + +
155C PRO* 1.3 78.7 - - - +
157C PHE* 1.3 72.8 + + + +
159C TRP* 3.8 5.1 + - - +
160C PRO* 3.4 9.5 - - - +
231C TRP* 4.0 22.2 - + - -
259C PHE* 4.0 39.7 + - + -
261C GLY* 5.0 2.1 + - - -
331C MET* 4.9 6.3 - - + -
341C TRP* 4.2 10.0 - + - -
1D GLC 3.7 37.7 + - - -
2D GLC 3.1 38.9 + - - +
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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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114C LEU* 3.7 20.9 - - + +
130C TRP* 5.9 0.7 - - - -
150C PHE* 3.5 19.5 - + + -
151C ASN* 3.2 54.5 - - + +
154C GLU* 3.1 12.2 + - + +
155C PRO 3.1 0.4 - - - -
156C TYR* 1.3 86.1 - + - +
158C THR* 1.3 58.5 + - - +
159C TRP 3.5 0.2 - - - -
160C PRO* 3.2 14.8 - - - +
161C LEU* 6.0 0.3 - - - +
211C TYR* 3.9 23.8 - + - -
227C ILE* 3.4 34.1 - - + +
228C ASN* 3.9 15.0 - - - -
231C TRP* 4.7 3.1 - + - -
1D GLC 3.6 29.8 - - - -
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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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150C PHE* 4.2 13.8 - - - -
151C ASN 4.7 1.0 + - - -
152C LEU* 4.2 8.0 - - - +
154C GLU 3.9 5.1 + - - -
155C PRO* 3.2 7.5 + - - -
157C PHE* 1.3 75.1 - - - +
159C TRP* 1.3 66.2 + - - +
160C PRO* 3.1 4.0 - - - -
161C LEU* 3.1 18.9 + - + +
162C ILE* 3.3 31.6 + - + -
193C LEU* 4.9 0.2 - - + -
196C LEU* 3.7 33.2 - - + +
348C VAL* 3.8 24.0 - - + +
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Residues in contact with TRP 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 PRO 2.8 18.2 + - - +
156C TYR* 3.9 4.9 - - - +
158C THR* 1.3 77.5 - - - +
160C PRO* 1.3 69.2 - - + +
161C LEU 3.0 0.2 + - - -
162C ILE* 3.0 24.8 + - + +
163C ALA* 2.8 39.1 + - + +
167C GLY 4.6 1.1 - - - -
168C TYR* 3.6 32.5 - - - -
169C ALA 3.5 18.2 - - - -
183C GLY 4.7 0.9 - - - -
184C VAL* 4.2 11.7 - - + -
257C LYS 3.5 15.1 + - - -
259C PHE* 3.3 53.1 - + + +
329C GLU* 5.8 2.8 - - - +
340C PHE* 3.7 21.8 - + - -
341C TRP* 5.2 2.0 - + + -
344C VAL* 4.5 20.2 - - + -
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Residues in contact with PRO 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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114C LEU* 4.0 15.9 - - + -
130C TRP* 5.6 4.0 - - + -
156C TYR 3.4 8.5 - - - +
157C PHE 3.2 15.9 - - - +
158C THR 3.1 6.3 - - - -
159C TRP* 1.3 93.1 - - + +
161C LEU* 1.3 58.8 + - - +
164C ALA 3.3 9.5 + - - -
227C ILE* 5.3 3.6 - - + -
248C LEU* 3.9 25.1 - - + -
256C SER* 3.5 10.5 - - - +
257C LYS* 2.9 32.4 + - - +
258C PRO* 3.9 19.5 - - + -
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Residues in contact with LEU 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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130C TRP* 3.9 51.4 - - + -
150C PHE* 6.0 0.2 - - + -
158C THR* 3.1 11.3 + - + +
159C TRP 3.0 0.4 - - - -
160C PRO* 1.3 77.9 - - - +
162C ILE* 1.3 66.3 + - + +
164C ALA* 3.5 14.6 + - - +
165C ASP 4.6 0.3 + - - -
192C GLY* 3.4 30.6 - - - +
195C PHE* 4.3 4.0 - - + -
196C LEU* 3.9 29.8 - - + +
251C PHE* 3.7 34.1 - - + -
256C SER* 4.5 3.4 - - - -
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Residues in contact with ILE 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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158C THR* 3.3 34.0 + - + +
159C TRP* 3.0 36.4 + - + +
161C LEU* 1.3 78.7 - - - +
163C ALA* 1.3 60.9 + - - +
164C ALA 3.5 0.2 + - - -
165C ASP 4.2 0.7 + - - -
167C GLY* 3.6 5.4 + - - -
184C VAL* 5.9 0.9 - - + -
188C GLY 3.7 5.4 - - - +
189C ALA* 3.6 40.4 - - + +
192C GLY* 4.2 6.7 - - - +
193C LEU* 4.2 28.7 - - + +
344C VAL* 4.9 4.7 - - + -
348C VAL* 4.1 17.7 - - + -
362C LEU* 5.7 5.8 - - + -
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Residues in contact with ALA 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 TRP* 2.8 39.0 + - + +
162C ILE* 1.3 78.2 - - - +
164C ALA* 1.3 66.6 + - - +
165C ASP 3.3 0.4 - - - -
166C GLY* 3.0 12.8 + - - -
167C GLY* 3.2 26.6 + - - +
257C LYS* 3.8 31.5 - - + -
329C GLU* 6.3 0.9 - - + -
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Residues in contact with ALA 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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160C PRO 3.3 13.9 + - - +
161C LEU* 3.5 15.0 - - - +
162C ILE 3.3 1.6 - - - -
163C ALA* 1.3 78.8 - - - +
165C ASP* 1.3 57.9 + - - +
166C GLY 3.5 1.7 + - - -
251C PHE* 3.7 26.0 - - + -
254C GLN* 3.2 22.5 - - - +
255C PRO* 3.5 24.5 - - - +
256C SER* 4.1 4.7 - - - -
257C LYS* 4.3 5.5 - - - +
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Residues in contact with ASP 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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161C LEU 4.6 0.4 + - - -
162C ILE 4.2 3.4 + - - -
163C ALA 3.3 0.6 - - - -
164C ALA* 1.3 76.6 - - - +
166C GLY* 1.3 55.9 + - - +
187C ALA* 4.9 1.0 - - - +
188C GLY* 3.2 32.1 + - - +
191C ALA* 4.3 1.4 - - - +
251C PHE* 4.2 18.0 - - + -
252C LYS* 3.1 35.5 - - + +
254C GLN* 3.6 23.4 + - + +
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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