Contacts of the helix formed by residues 153 - 167 (chain C) in PDB entry 1M6X
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 SER 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C GLY 3.5 1.7 + - - -
152C GLU* 1.3 73.8 - - - +
154C ILE* 1.3 66.4 + - - +
155C TRP* 3.6 7.8 + - - +
156C GLU* 2.8 39.0 + - - +
157C ILE* 2.8 26.1 + - - +
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Residues in contact with ILE 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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148C LEU* 3.8 30.7 - - + -
153C SER* 1.3 73.7 - - - +
155C TRP* 1.3 55.9 + - + +
157C ILE* 3.1 10.2 + - + +
158C THR* 2.7 36.9 + - - +
186C PHE* 3.7 35.4 - - + -
310C LEU* 4.0 26.5 - - + +
313C SER* 4.5 5.8 - - - -
314C PHE* 4.2 30.3 - - + -
317C MET* 5.6 9.0 - - + -
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Residues in contact with TRP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C SER* 3.3 7.4 + - - +
154C ILE* 1.3 79.4 - - + +
156C GLU* 1.3 63.3 + - + +
158C THR* 3.1 16.9 + - + -
159C GLU* 3.0 24.3 + - - +
183C LEU* 4.7 0.9 - - + -
186C PHE* 4.0 24.8 - + - -
187C ILE* 4.2 13.0 - - + -
235C ALA* 5.3 4.5 - - + -
239C ILE* 3.9 35.9 - - + -
241C PRO* 6.0 1.1 - - + -
314C PHE* 4.5 28.5 - + - -
357C LEU 5.2 0.4 + - - -
358C VAL* 3.1 35.5 + - + +
360C ARG* 3.3 58.7 - - + +
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Residues in contact with GLU 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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151C GLY 4.2 2.3 - - - +
152C GLU* 3.2 22.5 - - + +
153C SER* 2.8 44.0 + - - +
155C TRP* 1.3 77.7 - - + +
157C ILE* 1.3 62.0 + - - +
159C GLU* 3.4 9.0 + - - +
160C LYS* 3.1 28.8 + - - +
293C TYR* 4.9 0.9 - - - -
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Residues in contact with ILE 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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147C LEU* 3.6 43.3 - - + +
148C LEU* 4.8 2.9 - - - -
152C GLU* 3.9 23.1 - - + +
153C SER 2.8 21.7 + - - +
154C ILE* 3.3 20.2 - - + +
156C GLU* 1.3 76.4 - - - +
158C THR* 1.3 65.3 + - - +
160C LYS* 3.2 3.3 + - - +
161C ILE* 3.0 41.3 + - + +
293C TYR* 3.6 24.2 - - + +
310C LEU* 4.4 11.0 - - + -
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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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154C ILE* 2.7 31.0 + - - +
155C TRP* 3.3 19.7 - - + -
157C ILE* 1.3 78.2 - - - +
159C GLU* 1.3 58.6 + - - +
161C ILE 3.3 0.2 + - - -
162C LEU* 2.8 34.6 + - + +
182C PHE* 3.4 33.5 - - + -
183C LEU* 4.5 12.6 - - + -
186C PHE* 4.0 27.6 - - + -
239C ILE* 5.4 0.9 - - + -
310C LEU* 4.7 4.6 - - - +
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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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155C TRP 3.0 12.4 + - - +
156C GLU* 3.7 10.7 - - - +
157C ILE 3.3 0.2 - - - -
158C THR* 1.3 75.1 - - - +
160C LYS* 1.3 60.4 + - - +
162C LEU* 3.3 7.2 + - - +
163C ASN* 2.8 52.3 + - - +
238C ARG* 2.5 57.7 + - - +
239C ILE* 4.1 28.9 - - + +
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Residues in contact with LYS 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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152C GLU* 2.5 29.7 + - - +
156C GLU* 3.1 13.8 + - - +
157C ILE 3.2 8.7 + - - +
159C GLU* 1.3 76.9 - - - +
161C ILE* 1.3 67.8 + - - +
163C ASN* 2.9 9.5 + - - +
164C SER* 2.9 21.4 + - - -
292C PRO* 4.7 8.2 - - + +
293C TYR* 3.2 28.7 - - + +
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Residues in contact with ILE 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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147C LEU* 6.3 0.9 - - + -
157C ILE* 3.0 33.7 + - + +
158C THR 3.7 5.8 - - - +
160C LYS* 1.3 75.5 - - - +
162C LEU* 1.3 63.9 + - - +
164C SER* 2.6 27.6 + - - +
165C PHE* 3.4 15.3 - - + -
182C PHE* 3.7 39.5 - - + -
287C LEU* 4.2 16.4 - - + -
292C PRO* 4.1 5.2 - - + -
293C TYR* 3.9 16.8 - - + -
296C PHE* 3.8 26.2 - - + -
306C ILE* 4.6 2.0 - - + -
310C LEU* 4.3 8.1 - - + -
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Residues in contact with LEU 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* 2.8 20.3 + - + +
159C GLU* 3.4 4.9 - - - +
161C ILE* 1.3 78.5 - - - +
163C ASN* 1.3 62.3 + - - +
165C PHE* 3.4 14.7 + - - -
179C GLN* 3.0 65.7 + - + +
182C PHE* 3.8 17.0 - - + -
183C LEU* 4.5 8.5 - - + -
239C ILE* 3.7 31.6 - - + -
244C TYR* 3.3 35.7 - - + +
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Residues in contact with ASN 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 GLU* 2.8 44.9 + - - +
160C LYS* 2.9 7.8 + - - +
162C LEU* 1.3 73.8 - - - +
164C SER* 1.3 58.2 + - - +
165C PHE 2.9 5.4 - - - -
166C GLU* 2.8 38.9 + - + +
167C TYR* 4.3 2.4 + - - -
179C GLN* 5.0 3.6 - - - +
239C ILE* 5.5 1.6 - - - +
244C TYR* 4.9 6.7 + - - -
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Residues in contact with SER 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 LYS 2.9 7.3 + - - -
161C ILE 2.6 19.7 + - - -
163C ASN* 1.3 75.0 - - - +
165C PHE* 1.3 66.0 + - - +
167C TYR 4.9 0.2 - - - -
168C THR* 3.0 29.7 + - - +
287C LEU* 4.9 0.3 - - - +
290C ASN* 3.6 12.8 - - - +
292C PRO* 3.6 40.0 - - - +
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Residues in contact with PHE 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 ILE* 3.4 37.5 - - + -
162C LEU* 3.4 13.2 + - - +
163C ASN 2.9 0.8 - - - -
164C SER* 1.3 78.7 - - - +
166C GLU* 1.3 67.4 + - - +
167C TYR 2.8 5.7 + - - -
168C THR* 3.5 4.3 - - - -
169C SER* 2.9 32.1 + - - +
175C LYS* 3.6 2.7 - - + +
178C TYR* 3.5 37.5 - + + -
179C GLN* 4.0 17.5 - - + -
182C PHE* 4.7 6.1 - - + -
283C TYR* 3.6 28.5 - + - -
286C ALA* 4.2 2.0 - - + -
287C LEU* 3.9 38.6 - - + -
290C ASN* 3.9 12.6 - - - -
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Residues in contact with GLU 166 (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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163C ASN* 2.8 28.2 + - + +
165C PHE* 1.3 75.8 - - - +
167C TYR* 1.3 99.8 + - + +
169C SER* 5.4 0.3 - - - -
175C LYS* 3.1 42.7 + - - +
179C GLN* 3.7 17.3 + - - +
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Residues in contact with TYR 167 (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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163C ASN 4.3 2.9 + - - -
164C SER 4.8 0.6 + - - -
165C PHE 2.8 1.0 + - - -
166C GLU* 1.3 114.2 + - + +
168C THR* 1.3 69.3 + - + +
169C SER 3.2 11.6 + - - +
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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