Contacts of the helix formed by residues 138 - 154 (chain M) in PDB entry 5X6E
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 138 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134M PHE 4.7 0.9 - - - -
137M ASN* 1.3 82.2 - - - +
139M LYS* 1.3 60.0 + - - -
140M LEU* 3.0 11.5 - - - +
141M GLY 2.9 16.4 + - - +
142M SER* 3.2 9.1 + - - -
139N LYS* 5.6 4.5 - - - -
16O A 5.0 1.1 - - - -
17O T 3.6 9.0 - - - -
18P G 5.6 8.2 - - - -
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Residues in contact with LYS 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M PHE 6.0 1.1 - - - -
138M GLY* 1.3 71.9 - - - -
140M LEU* 1.3 59.5 + - - +
142M SER* 3.6 15.3 - - - +
143M ILE* 3.2 26.9 + - - +
179M GLY* 3.9 32.0 + - - +
180M ILE* 3.7 18.1 - - + +
189M ILE* 4.3 4.9 - - + +
135N SER* 3.4 28.4 + - - +
136N ILE 5.4 1.0 + - - -
138N GLY* 4.4 15.9 - - - +
17O T 2.7 25.0 + - - +
18O G 3.1 30.2 + - - +
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Residues in contact with LEU 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M ASN* 6.0 0.2 - - + -
138M GLY* 3.0 6.5 - - - +
139M LYS* 1.3 76.9 - - - +
141M GLY* 1.3 66.2 + - - +
143M ILE* 3.0 14.4 + - - +
144M CYS* 3.2 23.3 + - - -
189M ILE* 4.6 24.2 - - + -
192M LYS* 5.2 17.3 - - + -
213M TYR* 6.1 0.4 - - - +
217M TYR* 5.0 19.7 - - + +
16O A 3.2 42.8 - - - +
17O T 3.3 13.7 - - - +
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Residues in contact with GLY 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ASP 4.4 13.7 - - - +
134M PHE* 4.7 2.1 - - - -
137M ASN* 3.9 23.1 - - - +
138M GLY 2.9 9.8 + - - -
140M LEU* 1.3 78.5 - - - +
142M SER* 1.3 61.3 + - - +
144M CYS* 3.7 1.7 + - - +
145M GLY* 3.1 19.9 + - - -
217M TYR* 4.2 19.0 - - - +
218M ALA* 5.0 0.9 - - - +
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Residues in contact with SER 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M PHE* 3.2 56.3 + - - +
138M GLY 3.2 7.5 + - - -
139M LYS* 3.6 24.2 - - - +
140M LEU 3.1 0.4 - - - -
141M GLY* 1.3 77.0 - - - +
143M ILE* 1.3 56.8 + - - +
145M GLY 3.3 0.9 + - - -
146M GLN* 2.9 26.9 + - - +
178M SER* 3.6 16.8 - - - -
179M GLY 4.6 1.5 + - - -
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Residues in contact with ILE 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M LYS 3.2 15.7 - - - +
140M LEU* 3.0 7.9 + - - +
142M SER* 1.3 75.7 - - - +
144M CYS* 1.3 57.4 + - - +
146M GLN* 3.2 6.9 + - + +
147M LEU* 2.8 42.8 + - + +
174M LEU* 4.6 14.5 - - + +
178M SER* 3.4 24.5 - - - +
180M ILE* 3.6 16.8 - - + -
186M VAL* 4.5 15.9 - - + -
189M ILE* 4.3 11.0 - - + -
190M ILE* 4.2 9.9 - - + -
193M LEU* 3.7 26.9 - - + -
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Residues in contact with CYS 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M LEU* 3.2 21.2 + - - +
141M GLY 4.1 1.6 - - - +
143M ILE* 1.3 79.2 - - - +
145M GLY* 1.3 57.3 - - - +
147M LEU* 3.7 2.1 - - - +
148M LEU* 2.8 30.7 + - - +
193M LEU* 4.6 19.5 - - - -
213M TYR* 4.8 9.6 - - - -
214M LEU* 3.7 33.0 - - + +
217M TYR* 4.0 33.7 - - + -
218M ALA* 4.7 2.0 - - - -
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Residues in contact with GLY 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M PHE* 4.1 13.9 - - - -
141M GLY 3.1 14.5 + - - -
142M SER 3.6 3.4 - - - -
143M ILE 3.2 0.2 - - - -
144M CYS* 1.3 73.6 - - - +
146M GLN* 1.3 63.9 + - - +
148M LEU* 3.2 4.5 + - - +
149M ILE* 3.2 26.0 + - - +
218M ALA* 3.7 23.4 - - - +
221M LEU* 4.5 4.8 - - - +
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Residues in contact with GLN 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M TYR* 5.1 2.6 - - - -
130M LYS* 3.5 18.7 + - - -
134M PHE* 4.0 6.7 - - + -
142M SER 2.9 16.3 + - - +
143M ILE* 3.2 6.9 + - + +
145M GLY* 1.3 75.2 - - - +
147M LEU* 1.3 63.6 + - - +
149M ILE* 3.1 24.6 + - - +
150M LEU* 3.0 41.0 + - + +
174M LEU* 5.1 9.9 - - + +
177M SER* 2.2 40.9 + - - +
178M SER* 5.3 4.0 - - - +
301M GSH 3.7 17.8 + - - -
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Residues in contact with LEU 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M ILE* 2.8 38.1 + - + +
144M CYS* 3.7 5.8 - - - +
146M GLN* 1.3 76.3 - - - +
148M LEU* 1.3 49.7 + - - +
150M LEU* 3.4 16.3 + - + +
151M THR* 2.3 43.4 + - - +
164M ILE* 5.4 9.6 - - + +
169M LEU* 5.8 0.9 - - + -
174M LEU* 4.7 17.5 - - + -
190M ILE* 5.4 4.0 - - + -
193M LEU* 4.8 11.0 - - + -
199M ILE* 4.7 25.4 - - + -
206M PHE* 5.2 13.0 - - + -
208M VAL* 5.6 0.7 - - + -
214M LEU* 4.3 20.9 - - + -
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Residues in contact with LEU 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M CYS 2.8 16.1 + - - +
145M GLY* 3.4 6.7 - - - +
146M GLN 3.2 0.2 - - - -
147M LEU* 1.3 75.8 - - - +
149M ILE* 1.3 63.4 + - - +
151M THR* 3.4 7.2 + - - -
152M TYR* 3.3 55.9 + - + -
211M LEU* 4.9 4.9 - - + -
214M LEU* 3.5 30.9 - - + +
215M LYS* 3.7 15.0 - - + -
218M ALA* 3.3 27.1 - - + +
221M LEU* 4.5 4.7 - - + -
222M ASP* 4.0 22.2 - - + +
225M PHE* 4.5 8.1 - - + -
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Residues in contact with ILE 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M TYR* 3.2 27.6 - - + +
130M LYS* 3.9 10.1 - - + -
145M GLY 3.2 14.1 + - - +
146M GLN* 3.1 20.6 + - - +
148M LEU* 1.3 76.5 - - - +
150M LEU* 1.3 62.6 + - - +
151M THR 3.2 1.0 + - - -
152M TYR* 3.3 9.4 + - - +
153M VAL* 3.3 20.6 + - + +
221M LEU* 3.6 29.8 - - + -
225M PHE* 4.1 22.9 - - + -
301M GSH 3.3 37.9 - - - +
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Residues in contact with LEU 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M TYR* 5.0 9.0 - - + -
146M GLN* 3.0 45.0 + - + +
147M LEU* 3.8 14.8 - - + +
149M ILE* 1.3 74.6 - - - +
151M THR* 1.3 61.7 + - - +
154M TYR* 3.1 60.1 + - + +
155M GLY* 3.3 2.9 + - - -
164M ILE* 4.1 16.2 - - + +
166M LEU* 4.3 13.5 - - + -
169M LEU* 4.4 12.1 - - + -
174M LEU* 4.1 21.8 - - + -
301M GSH 4.2 3.6 - - - +
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Residues in contact with THR 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M LEU* 2.3 32.0 + - - +
148M LEU* 3.5 10.2 - - - -
149M ILE 3.1 0.4 - - - -
150M LEU* 1.3 77.9 - - - +
152M TYR* 1.3 57.4 + - + +
155M GLY* 3.1 24.9 - - - +
162M ILE* 4.3 4.3 - - + -
164M ILE* 4.9 3.8 - - - +
208M VAL* 3.7 35.5 - - + +
211M LEU* 3.6 24.5 - - + -
214M LEU* 4.2 5.2 - - - +
236M LEU* 3.5 21.5 - - + +
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Residues in contact with TYR 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148M LEU* 3.3 44.6 + - + +
149M ILE 3.3 2.6 + - - +
151M THR* 1.3 84.2 - - - +
153M VAL* 1.3 63.6 + - - +
155M GLY 3.9 6.4 + - - +
211M LEU* 3.9 20.0 - - + +
215M LYS* 4.5 1.2 - - - +
222M ASP* 2.6 24.4 + - - -
225M PHE* 3.6 29.8 - + + -
232M THR* 3.5 29.8 - - - +
233M TRP* 3.4 32.8 + + - -
235M LYS* 5.8 1.6 - - - +
236M LEU* 4.3 24.1 - - + +
237M ASN* 3.0 21.9 + - - -
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Residues in contact with VAL 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M LYS* 3.8 40.8 - - + +
149M ILE* 3.3 23.8 - - + +
152M TYR* 1.3 78.6 - - - +
154M TYR* 1.3 88.4 + - + +
155M GLY 3.7 2.8 + - - +
225M PHE* 4.9 9.9 - - + -
232M THR* 5.1 16.7 - - + +
301M GSH 4.8 20.4 - - + +
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Residues in contact with TYR 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M ILE* 4.1 17.6 - - + +
62M TYR* 3.4 29.1 - + - +
63M TYR 4.5 0.2 - - - -
64M LYS* 3.4 47.3 - - + +
150M LEU* 3.1 53.5 + - + +
153M VAL* 1.3 95.4 - - + +
155M GLY* 1.3 59.1 + - - +
164M ILE* 4.5 4.3 - - + -
165M THR* 2.9 51.7 + - - +
166M LEU* 4.3 20.2 - - + -
301M GSH 4.1 10.9 + - - -
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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