Contacts of the helix formed by residues 149 - 173 (chain R) in PDB entry 6CMO
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 149 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R PRO* 4.1 17.8 - - - +
146R PHE* 4.9 4.2 - - - -
147R ARG 3.8 1.8 + - - -
148R PHE* 1.3 80.6 - - - +
150R GLU* 1.3 69.9 + - - -
151R ASN* 3.3 6.2 + - - -
152R HIS* 4.3 5.4 + - - +
153R ALA* 4.1 8.8 + - - +
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Residues in contact with GLU 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71R PRO* 5.1 11.9 - - + +
74R TYR* 5.7 8.5 - - + -
149R GLY* 1.3 77.4 - - - -
151R ASN* 1.3 64.7 + - - +
153R ALA* 3.2 8.8 + - - +
154R ILE* 2.9 41.1 + - + +
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Residues in contact with ASN 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149R GLY* 3.3 4.6 - - - -
150R GLU* 1.3 83.1 + - - +
152R HIS* 1.3 69.1 + - + +
154R ILE* 3.2 14.6 - - - +
155R MET* 2.9 45.6 + - + +
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Residues in contact with HIS 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130R VAL* 5.6 1.4 - - - +
146R PHE* 3.4 41.5 - + + -
149R GLY 4.3 5.4 + - - +
151R ASN* 1.3 80.5 - - + +
153R ALA* 1.3 60.3 + - - +
155R MET* 3.8 21.9 - - + +
156R GLY* 2.9 22.9 + - - -
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Residues in contact with ALA 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R PRO* 4.1 25.8 - - + +
74R TYR* 5.4 7.0 - - + -
75R ILE* 5.0 14.8 - - + +
134R GLU* 6.4 1.1 - - + -
149R GLY 4.1 9.1 + - - +
150R GLU* 3.2 16.5 + - - +
151R ASN 3.2 0.6 - - - -
152R HIS* 1.3 77.4 - - - +
154R ILE* 1.3 60.1 + - + +
156R GLY* 2.9 3.5 + - - -
157R VAL* 2.9 33.3 + - + +
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Residues in contact with ILE 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150R GLU* 2.9 26.3 + - + +
151R ASN* 3.2 23.1 - - - +
153R ALA* 1.3 74.9 - - + +
155R MET* 1.3 61.7 - - + +
157R VAL* 3.9 8.1 - - + +
158R ALA* 2.9 31.5 + - - +
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Residues in contact with MET 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151R ASN* 2.9 31.5 + - + +
152R HIS* 3.9 24.7 - - + +
154R ILE* 1.3 81.4 - - + +
156R GLY* 1.3 55.4 + - - +
158R ALA* 4.3 4.7 - - - +
159R PHE* 2.8 30.3 + - - +
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Residues in contact with GLY 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R ILE* 6.1 2.0 - - - -
130R VAL* 4.1 24.6 - - - +
152R HIS 2.9 17.1 + - - -
153R ALA* 2.9 5.1 + - - -
155R MET* 1.3 76.3 - - - +
157R VAL* 1.3 54.4 + - - +
159R PHE* 3.5 7.0 - - - +
160R THR* 2.7 37.9 + - - -
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Residues in contact with VAL 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R TYR* 5.1 10.1 - - + +
75R ILE* 4.9 14.1 - - + -
78R ASN* 3.4 35.0 - - + +
153R ALA 2.9 20.3 + - - +
154R ILE* 3.9 8.3 - - + +
155R MET 3.5 0.2 - - - -
156R GLY* 1.3 74.0 - - - +
158R ALA* 1.3 61.4 + - - +
160R THR* 3.1 6.6 + - - -
161R TRP* 3.0 46.6 + - + +
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Residues in contact with ALA 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154R ILE 2.9 18.6 + - - +
155R MET* 4.3 4.0 - - - +
157R VAL* 1.3 77.5 - - - +
159R PHE* 1.3 56.6 + - - +
161R TRP* 3.4 6.1 + - - +
162R VAL* 2.9 39.7 + - + +
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Residues in contact with PHE 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126R TRP* 3.9 28.3 - + - -
129R VAL* 6.1 1.1 - - + -
130R VAL* 5.5 10.1 - - + -
155R MET 2.8 24.2 + - - +
156R GLY* 3.5 8.3 - - - +
158R ALA* 1.3 76.6 - - - +
160R THR* 1.3 61.7 + - - +
162R VAL* 3.3 12.2 - - + +
163R MET* 3.0 63.9 + - + +
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Residues in contact with THR 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78R ASN* 5.2 5.3 + - - +
123R ILE* 4.2 27.1 - - + +
126R TRP* 3.9 23.8 - - + +
127R SER* 4.5 6.1 + - - +
130R VAL* 4.3 15.2 - - - +
156R GLY 2.7 21.0 + - - -
157R VAL* 3.1 10.8 + - - -
159R PHE* 1.3 80.7 - - - +
161R TRP* 1.3 66.6 + - + +
163R MET* 3.2 8.8 + - - +
164R ALA* 2.9 23.2 + - - +
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Residues in contact with TRP 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R ASN* 3.6 32.7 + - - +
82R ALA* 5.4 8.5 - - + +
123R ILE* 4.8 12.9 - - + +
157R VAL* 3.0 29.5 + - + +
158R ALA* 4.2 5.2 - - - +
160R THR* 1.3 86.8 - - + +
162R VAL* 1.3 62.6 + - + +
164R ALA* 3.1 10.2 + - + +
165R LEU* 2.9 30.9 + - + +
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Residues in contact with VAL 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158R ALA* 2.9 28.0 + - + +
159R PHE* 3.3 22.9 - - + +
161R TRP* 1.3 74.4 - - + +
163R MET* 1.3 63.7 + - + +
165R LEU* 3.8 13.7 - - + +
166R ALA* 2.9 26.3 + - - +
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Residues in contact with MET 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R TRP* 3.6 59.1 + - + +
159R PHE* 3.0 51.1 + - + +
160R THR 3.2 9.6 + - - +
162R VAL* 1.3 79.3 - - + +
164R ALA* 1.3 58.0 + - - +
166R ALA* 3.2 14.9 + - - +
167R CYS* 2.9 28.1 + - - +
211R HIS* 5.4 5.1 - - - -
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Residues in contact with ALA 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119R LEU* 3.4 24.5 - - + +
123R ILE* 3.7 28.5 - - + +
126R TRP* 6.1 0.2 - - - -
160R THR 2.9 8.6 + - - +
161R TRP* 3.1 18.1 + - + +
163R MET* 1.3 77.4 - - - +
165R LEU* 1.3 58.2 + - + +
167R CYS* 3.3 2.9 + - - -
168R ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119R LEU* 5.7 2.0 - - + -
161R TRP* 2.9 18.5 + - + +
162R VAL* 4.1 12.6 - - + +
163R MET 3.4 0.2 - - - -
164R ALA* 1.3 76.3 - - + +
166R ALA* 1.3 59.8 + - - +
168R ALA* 3.7 11.8 - - + +
169R ALA* 2.9 32.4 + - - +
172R LEU* 6.2 2.0 - - + -
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Residues in contact with ALA 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R VAL 2.9 19.8 + - - +
163R MET* 3.4 21.5 - - - +
164R ALA 3.2 0.4 - - - -
165R LEU* 1.3 77.9 - - - +
167R CYS* 1.3 60.0 + - - +
169R ALA* 4.3 2.8 - - - +
170R PRO* 3.5 18.5 - - - +
207R MET* 4.9 5.6 - - - +
211R HIS* 6.5 0.9 - - + -
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Residues in contact with CYS 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118R THR* 5.1 5.4 - - - -
119R LEU* 4.0 21.2 - - + +
122R GLU* 4.8 28.7 - - + -
126R TRP* 6.2 0.7 - - - +
163R MET 2.9 16.2 + - - +
164R ALA* 3.8 5.8 - - - +
165R LEU 3.3 0.2 - - - -
166R ALA* 1.3 76.9 - - - +
168R ALA* 1.3 59.4 + - - +
169R ALA 3.5 0.2 - - - -
170R PRO* 3.9 2.4 - - - +
171R PRO* 3.5 16.8 - - - +
178R TYR* 5.1 1.4 + - - -
207R MET* 5.2 13.8 - - - +
211R HIS* 5.4 13.7 - - + -
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Residues in contact with ALA 168 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115R PHE* 4.6 4.3 - - + -
119R LEU* 3.7 24.4 - - + +
164R ALA 2.9 17.4 + - - +
165R LEU* 3.4 14.6 + - + +
166R ALA 3.3 0.2 - - - -
167R CYS* 1.3 78.3 - - - +
169R ALA* 1.3 62.9 + - - +
170R PRO 3.5 0.4 - - - -
171R PRO* 3.3 4.5 - - - +
172R LEU* 3.2 45.1 + - + +
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Residues in contact with ALA 169 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165R LEU 2.9 18.7 + - - +
166R ALA* 4.3 3.8 - - - +
168R ALA* 1.3 77.6 - - - +
170R PRO* 1.3 64.4 - - + +
172R LEU* 4.8 2.5 - - - -
173R ALA* 2.9 37.2 + - + +
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Residues in contact with PRO 170 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166R ALA 3.5 17.0 - - - +
167R CYS 3.9 3.8 - - - +
169R ALA* 1.3 90.0 - - + +
171R PRO* 1.4 67.6 - - + +
174R GLY 3.6 0.3 + - - -
175R TRP* 2.8 41.3 + - + -
176R SER* 2.7 37.3 + - - +
203R PHE* 4.5 3.4 - - + -
207R MET* 4.7 19.3 - - + -
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Residues in contact with PRO 171 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167R CYS 3.5 15.5 - - - +
168R ALA* 3.3 13.0 - - - +
170R PRO* 1.4 92.5 - - + +
172R LEU* 1.3 61.8 + - + +
174R GLY* 4.2 4.4 + - - -
176R SER* 3.7 27.8 - - - +
177R ARG* 5.5 0.4 - - - -
178R TYR* 3.3 52.1 - - + +
207R MET* 6.4 0.2 - - + -
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Residues in contact with LEU 172 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115R PHE* 3.9 50.3 - - + -
165R LEU* 6.2 2.2 - - + -
168R ALA* 3.2 34.1 + - + +
169R ALA* 4.3 2.2 - - - +
171R PRO* 1.3 81.4 - - + +
173R ALA* 1.3 64.0 + - - +
174R GLY* 3.2 3.8 + - - -
178R TYR* 5.5 1.1 - - + -
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Residues in contact with ALA 173 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169R ALA* 2.9 22.6 + - + +
170R PRO* 5.1 0.7 - - + -
172R LEU* 1.3 76.0 - - - +
174R GLY* 1.3 58.4 + - - +
175R TRP* 3.6 6.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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