Contacts of the helix formed by residues 152 - 165 (chain C) in PDB entry 1ZRT
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 GLY 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C PHE* 5.2 0.7 - - - -
150C PRO 3.2 3.9 + - - -
151C TRP* 1.3 80.3 - - - +
153C GLN* 1.3 60.5 + - - -
154C MET 3.3 2.5 - - - -
155C SER* 3.3 5.5 + - - -
156C PHE 3.1 19.9 + - - -
279C ASN* 3.2 28.9 - - - -
281C VAL 3.3 8.5 - - - -
282C GLN* 4.4 1.1 - - - -
283C ALA* 3.3 8.8 - - - +
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Residues in contact with GLN 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 GLY* 1.3 70.9 - - - -
154C MET* 1.3 66.5 + - - +
156C PHE* 4.4 0.4 - - - +
157C TRP* 2.7 60.1 + - - +
278C ASP 3.1 15.5 + - - +
281C VAL* 2.8 38.6 + - + +
282C GLN 3.8 5.2 - - - +
283C ALA* 3.8 2.3 - - - +
284C ASN* 2.9 34.0 + - - +
287C SER* 2.9 25.7 + - - -
289C PRO* 3.7 21.9 - - + +
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Residues in contact with MET 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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147C TYR* 3.5 30.6 - - + +
152C GLY 3.3 0.4 - - - -
153C GLN* 1.3 78.6 - - - +
155C SER* 1.3 65.0 + - - +
157C TRP* 5.4 0.4 - - - -
158C GLY* 3.4 18.2 + - - -
276C HIS* 3.4 34.3 - - - +
278C ASP* 3.8 19.5 - - + +
279C ASN* 3.4 14.5 + - - +
289C PRO* 4.1 13.2 - - + -
291C HIS 4.6 2.7 - - - +
292C ILE* 3.7 32.8 - - + -
293C VAL 3.6 26.2 - - - +
503C SMA 3.7 14.6 - - - +
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Residues in contact with SER 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C TYR* 2.5 33.0 + - - -
148C VAL* 3.3 27.1 - - - +
150C PRO* 3.8 0.7 - - - +
151C TRP* 3.5 7.4 + - - -
152C GLY 3.3 20.6 + - - -
154C MET* 1.3 77.9 - - - +
156C PHE* 1.3 62.1 + - - +
158C GLY* 4.2 0.3 - - - -
159C ALA* 3.2 22.9 + - - +
279C ASN* 2.9 21.5 + - - -
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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
----------------------------------------------------------
151C TRP* 3.8 28.3 - + + -
152C GLY 3.1 13.2 + - - +
153C GLN 4.0 4.0 - - - +
154C MET 3.3 0.2 - - - -
155C SER* 1.3 80.3 - - - +
157C TRP* 1.3 97.2 + + + +
159C ALA* 3.3 8.1 - - - +
160C THR* 2.9 27.2 + - - -
186C VAL* 3.1 46.7 - - + -
283C ALA* 3.6 15.3 - - + -
284C ASN 3.8 5.8 - - - -
285C PRO* 3.5 35.7 - - + -
69R GLY 5.6 2.0 - - - -
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Residues in contact with TRP 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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153C GLN* 2.7 48.8 + - - +
154C MET 4.8 0.4 - - - +
156C PHE* 1.3 95.1 - + - +
158C GLY* 1.3 54.3 + - - +
159C ALA 3.2 0.2 - - - -
160C THR* 2.8 32.5 + - + -
161C VAL* 2.7 39.1 + - - +
284C ASN 3.1 16.7 + - - -
285C PRO 3.8 18.2 - - - -
286C LEU 4.9 0.2 - - - -
287C SER 3.0 8.9 + - - -
288C THR* 3.4 35.6 - - + +
289C PRO* 3.5 15.3 - - + -
292C ILE* 3.7 21.1 - - + -
70R LYS* 6.5 0.2 - - + -
71R PRO* 5.1 4.0 - - + -
137R GLY 4.0 8.3 - - - -
138R CYS* 4.0 20.4 - - + -
139R VAL* 4.6 8.5 - - + -
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Residues in contact with GLY 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PHE* 4.0 7.9 - - - -
154C MET 3.4 13.8 + - - -
155C SER 4.2 0.9 - - - -
157C TRP* 1.3 77.1 - - - +
159C ALA* 1.3 55.4 + - - +
161C VAL* 4.1 2.9 - - - -
162C ILE* 2.8 38.7 + - - +
503C SMA 3.9 30.5 - - - -
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Residues in contact with ALA 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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144C PHE* 4.1 10.7 - - - -
148C VAL* 4.0 22.4 - - + -
151C TRP* 5.2 1.8 - - + -
155C SER 3.2 15.4 + - - +
156C PHE* 3.3 12.1 - - - +
157C TRP 3.2 0.6 - - - -
158C GLY* 1.3 75.9 - - - +
160C THR* 1.3 52.0 + - - +
163C THR* 2.4 39.3 + - - +
186C VAL* 3.8 17.1 - - + +
190C THR* 5.9 0.2 - - + -
194C PHE* 4.6 7.4 - - + -
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Residues in contact with THR 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 16.3 + - - -
157C TRP* 2.8 31.5 + - + -
159C ALA* 1.3 74.1 - - - +
161C VAL* 1.3 67.3 + - - +
163C THR* 3.6 4.1 + - - -
164C GLY* 3.4 12.6 + - - -
186C VAL* 3.4 26.1 - - + +
70R LYS* 6.4 1.3 - - + -
132R VAL* 5.6 3.6 - - + -
136R LEU 3.1 14.6 - - - +
137R GLY* 4.1 22.7 - - - +
138R CYS 5.5 0.2 - - - -
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Residues in contact with VAL 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 TRP 2.7 23.0 + - - +
158C GLY* 3.7 6.5 - - - +
160C THR* 1.3 73.4 - - - +
162C ILE* 1.3 59.5 - - + +
164C GLY* 2.9 17.7 + - - -
165C LEU* 2.9 15.7 + - + +
292C ILE* 5.1 0.2 - - + -
503C SMA 3.2 51.8 - - + +
136R LEU* 3.6 27.7 - - + +
138R CYS* 3.8 26.7 - - - -
155R CYS* 4.5 0.4 - - - -
156R HIS* 3.8 4.3 - - + -
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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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144C PHE* 3.5 38.8 - - + -
158C GLY* 2.8 19.2 + - - +
161C VAL* 1.3 78.2 - - + +
163C THR* 1.3 64.1 + - - +
165C LEU* 3.3 24.0 - - + +
166C PHE* 3.1 24.3 - - - -
298C PHE* 5.0 1.6 - - + -
503C SMA 3.5 81.0 - - + +
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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
----------------------------------------------------------
144C PHE* 4.9 1.5 - - + -
159C ALA 2.4 31.4 + - - +
160C THR* 3.6 5.0 + - - -
162C ILE* 1.3 81.9 - - - +
164C GLY* 1.3 55.5 + - - +
165C LEU 3.4 0.2 - - - -
166C PHE* 3.2 27.7 + - - +
177C GLN* 2.8 29.1 + - - +
180C LEU* 4.1 24.3 - - + +
181C LEU* 3.5 25.6 - - + +
186C VAL* 5.3 0.2 - - + -
190C THR* 5.1 0.2 - - + -
194C PHE* 4.2 22.2 - - + -
503C SMA 4.3 4.0 - - + -
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Residues in contact with GLY 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 THR 3.4 9.4 + - - -
161C VAL 2.9 9.0 + - - -
163C THR* 1.3 78.7 + - - +
165C LEU* 1.3 55.0 - - - +
166C PHE 3.1 1.6 - - - -
167C GLY* 2.8 23.7 + - - -
168C ALA* 3.3 4.7 + - - -
177C GLN* 3.4 16.1 - - - +
329C LYS* 5.2 2.3 - - - -
135R HIS 5.2 0.2 - - - +
136R LEU* 3.5 19.7 - - - +
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Residues in contact with LEU 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 VAL* 2.9 13.3 + - + +
162C ILE* 3.3 39.7 - - + +
164C GLY* 1.3 74.2 - - - +
166C PHE* 1.3 60.4 + - + +
168C ALA* 3.3 20.9 - - - +
169C ILE* 3.8 7.4 - - - +
305C LEU* 3.8 17.3 - - + -
333C VAL* 3.7 40.1 - - + +
336C MET* 4.1 10.3 - - + -
337C PHE* 5.6 7.5 - - + -
503C SMA 3.9 29.6 - - + +
136R LEU* 3.4 14.5 - - + +
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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