Contacts of the helix formed by residues 155 - 177 (chain Y) in PDB entry 5MG3
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 ALA 155 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D GLU* 2.8 14.9 + - - +
148Y LEU 5.8 0.2 - - - -
151Y ASN* 3.2 26.7 - - - +
152Y PRO* 4.8 1.6 - - + -
153Y GLY* 4.1 4.5 - - - +
154Y PHE* 1.4 72.7 - - - +
156Y PHE* 1.4 58.9 + - - +
157Y TYR 3.5 2.0 - - - -
158Y PHE* 3.2 17.9 + - + -
159Y THR* 2.8 34.8 + - - +
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Residues in contact with PHE 156 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D GLU* 4.2 21.3 - - - -
247D VAL* 4.3 20.9 - - + -
301D ASP* 6.2 0.2 - - - -
532G LEU 5.7 0.9 - - - -
534G LEU* 3.8 31.0 - - + -
42Y PRO* 3.5 12.7 - - + +
43Y GLY* 3.5 33.0 - - - -
44Y ILE* 4.0 19.7 - - + +
45Y ASP* 6.0 0.7 - - - +
154Y PHE* 3.4 28.9 + + - -
155Y ALA* 1.4 75.8 - - - +
157Y TYR* 1.4 62.7 + - + +
159Y THR* 3.1 11.4 + - - -
160Y ALA* 2.9 24.8 + - - +
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Residues in contact with TYR 157 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Y ILE* 5.5 10.3 - - + -
42Y PRO 5.8 0.9 - - - -
45Y ASP* 2.7 46.6 + - - -
48Y VAL* 5.3 0.9 - - - +
136Y ALA* 3.5 36.0 - - + +
142Y MET* 4.0 6.3 - - + -
143Y PRO* 4.1 11.8 - - + +
144Y GLY* 3.5 18.5 + - - -
145Y MET 3.6 4.3 + - - -
146Y GLN 4.5 0.5 + - - -
147Y GLY* 3.1 48.8 - - - -
148Y LEU 4.3 2.9 - - - +
149Y VAL* 4.0 9.9 - - + -
154Y PHE 5.1 1.4 + - - +
155Y ALA 3.5 0.2 - - - -
156Y PHE* 1.4 80.1 - - + +
158Y PHE* 1.4 55.7 + - - +
160Y ALA* 3.3 9.8 + - + +
161Y VAL* 3.0 31.5 + - - +
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Residues in contact with PHE 158 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LEU* 5.8 12.3 - - + -
431C PRO* 5.9 7.4 - - + -
148Y LEU 4.5 1.7 + - - +
149Y VAL* 3.2 35.6 - - - +
150Y ILE* 5.2 1.6 - - - -
151Y ASN 4.5 8.3 - - - +
152Y PRO* 6.1 1.1 - - + -
155Y ALA* 3.2 28.7 + - + +
157Y TYR* 1.4 73.0 - - - +
159Y THR* 1.3 55.2 - - - +
161Y VAL* 3.3 15.9 - - + +
162Y VAL* 2.8 59.7 + - + +
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Residues in contact with THR 159 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528G PHE* 6.3 0.2 - - + -
532G LEU* 3.9 25.4 - - + -
42Y PRO* 3.7 25.4 - - + -
155Y ALA* 2.8 25.0 + - - +
156Y PHE* 3.2 16.1 - - - -
158Y PHE* 1.3 76.2 - - - +
160Y ALA* 1.4 58.6 + - - +
162Y VAL* 4.2 6.6 - - + +
163Y SER* 2.7 35.5 + - - +
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Residues in contact with ALA 160 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Y ILE* 3.5 47.2 - - + +
42Y PRO* 4.7 2.9 + - - +
136Y ALA* 6.6 0.2 - - + -
156Y PHE 2.9 14.3 + - - +
157Y TYR* 3.3 11.0 + - + +
159Y THR* 1.4 71.3 - - - +
161Y VAL* 1.3 50.4 + - + +
163Y SER* 3.2 8.2 + - - -
164Y LEU* 2.8 44.6 + - + +
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Residues in contact with VAL 161 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LEU* 6.0 5.4 - - + -
129Y ILE* 5.3 4.7 - - + +
132Y SER* 3.7 36.8 - - - +
133Y ILE* 4.6 9.2 - - + +
136Y ALA* 4.2 4.5 - - + -
149Y VAL* 3.8 22.2 - - + -
157Y TYR 3.0 16.9 + - - +
158Y PHE* 3.3 19.3 - - + +
160Y ALA* 1.3 65.5 - - + +
162Y VAL* 1.4 65.7 + - + +
164Y LEU* 3.4 10.8 + - + +
165Y VAL* 3.1 29.4 + - + +
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Residues in contact with VAL 162 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LEU* 5.8 6.7 - - + -
528G PHE* 5.6 6.3 - - + -
158Y PHE* 2.8 58.9 + - + +
159Y THR* 4.2 6.3 - - + +
160Y ALA 3.5 0.4 - - - -
161Y VAL* 1.4 70.9 - - + +
163Y SER* 1.3 56.5 + - - +
165Y VAL* 3.4 3.4 + - - +
166Y THR* 2.8 47.4 + - - +
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Residues in contact with SER 163 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528G PHE* 3.4 38.2 - - - -
42Y PRO* 4.4 8.4 - - - +
77Y ILE* 3.6 29.5 - - - +
78Y PHE* 4.9 1.9 - - - -
159Y THR* 2.7 26.2 + - - +
160Y ALA* 3.4 6.3 - - - -
162Y VAL* 1.3 74.9 - - - +
164Y LEU* 1.4 54.1 + - - +
166Y THR* 4.6 0.2 - - - -
167Y GLY* 2.9 26.0 + - - -
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Residues in contact with LEU 164 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Y ILE* 5.7 0.7 - - + -
76Y SER 3.7 8.3 - - - +
77Y ILE* 3.4 16.1 - - - +
78Y PHE* 4.1 1.0 - - - +
79Y ALA* 3.4 32.1 - - + +
80Y LEU* 3.5 24.5 - - + +
132Y SER* 3.6 30.7 - - - +
135Y ILE* 5.2 6.7 - - + -
136Y ALA* 6.3 0.7 - - + -
160Y ALA* 2.8 34.8 + - + +
161Y VAL* 3.6 11.7 - - + +
163Y SER* 1.4 70.6 - - - +
165Y VAL* 1.4 60.4 + - - +
167Y GLY* 3.6 0.9 - - - -
168Y THR* 2.8 32.0 + - - -
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Residues in contact with VAL 165 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C CYS* 3.4 33.9 - - + -
427C LEU* 6.0 5.6 - - + -
125Y LEU* 4.2 0.8 - - + +
128Y ALA* 3.8 20.2 - - + +
129Y ILE* 4.0 16.4 - - + +
132Y SER* 3.3 23.6 - - - +
161Y VAL* 3.1 17.8 + - + +
162Y VAL* 4.2 3.1 - - - +
164Y LEU* 1.4 72.4 - - - +
166Y THR* 1.4 61.9 + - - +
168Y THR* 3.3 8.6 + - - -
169Y MET* 3.1 25.2 + - + +
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Residues in contact with THR 166 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528G PHE* 4.6 14.2 - - + -
162Y VAL* 2.8 32.7 + - - +
165Y VAL* 1.4 75.4 - - - +
167Y GLY* 1.3 55.9 + - - +
169Y MET* 3.1 16.9 + - + +
170Y PHE* 3.0 52.9 + - + -
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Residues in contact with GLY 167 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528G PHE* 5.8 1.0 - - - -
78Y PHE* 3.7 31.7 - - - -
163Y SER 2.9 19.4 + - - -
164Y LEU 3.6 2.5 - - - -
165Y VAL 3.2 0.2 - - - -
166Y THR* 1.3 76.6 - - - +
168Y THR* 1.4 50.5 - - - +
170Y PHE* 3.3 8.9 + - - +
171Y LEU* 2.8 34.2 + - - +
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Residues in contact with THR 168 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Y LEU* 3.5 19.9 - - - +
84Y PRO* 5.2 1.6 - - + +
124Y THR* 3.5 30.3 - - + -
125Y LEU* 3.3 22.4 - - + -
128Y ALA* 3.8 8.5 - - + +
164Y LEU 2.8 21.6 + - - -
165Y VAL* 3.3 10.3 + - - -
167Y GLY* 1.4 71.5 - - - +
169Y MET* 1.3 65.1 + - - +
170Y PHE 3.3 0.2 - - - -
171Y LEU* 4.4 9.9 - - + +
172Y MET* 3.1 33.6 + - + +
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Residues in contact with MET 169 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C GLY 3.8 11.4 - - - +
423C CYS* 3.6 39.3 - - + -
3Y LYS* 5.1 7.0 - - - -
6Y GLY 4.6 7.6 - - - +
7Y LEU* 3.4 26.4 - - + +
125Y LEU* 3.6 23.1 - - + -
165Y VAL* 3.1 18.8 + - + +
166Y THR* 3.1 25.5 + - + +
168Y THR* 1.3 77.4 - - - +
170Y PHE* 1.3 58.1 + - + +
173Y TRP* 3.1 24.1 + - - +
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Residues in contact with PHE 170 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521G ALA* 4.3 13.9 - - + -
524G ALA* 4.1 19.5 - - + -
525G THR* 3.1 47.8 - - + +
528G PHE* 3.9 23.8 - + - -
78Y PHE* 5.4 1.6 - + + -
166Y THR* 3.0 46.4 + - + -
167Y GLY* 3.3 8.5 + - - +
168Y THR 3.3 0.2 - - - -
169Y MET* 1.3 78.8 - - + +
171Y LEU* 1.3 57.0 + - - +
173Y TRP* 3.1 14.4 + + + +
174Y LEU* 3.0 32.9 + - - +
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Residues in contact with LEU 171 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Y PHE* 4.4 26.9 - - + -
78Y PHE* 6.1 8.9 - - + +
81Y GLY 4.1 20.9 - - - +
82Y ILE* 5.8 3.1 - - + -
85Y TYR* 6.4 1.3 - - + -
124Y THR* 6.3 0.7 - - + -
167Y GLY 2.8 19.5 + - - +
168Y THR* 4.3 8.7 - - + +
170Y PHE* 1.3 67.0 - - - +
172Y MET* 1.4 79.9 + - + +
174Y LEU* 3.4 27.6 + - + +
175Y GLY 3.4 8.5 + - - -
190Y ILE* 4.0 20.6 - - + +
193Y ALA* 4.5 21.5 - - + +
194Y GLY* 5.3 1.8 - - - +
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Residues in contact with MET 172 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y LEU* 3.9 23.3 - - + +
85Y TYR* 3.8 31.6 - - + -
121Y ARG* 3.6 43.0 + - + +
124Y THR* 3.8 13.7 - - + -
125Y LEU* 4.5 2.7 - - + -
168Y THR* 3.1 32.2 + - + +
169Y MET 3.9 1.1 - - - +
171Y LEU* 1.4 98.0 - - + +
173Y TRP* 1.3 60.8 + - - +
175Y GLY* 3.1 13.5 + - - -
176Y GLU* 3.9 14.5 + - - +
190Y ILE* 4.2 12.2 - - + +
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Residues in contact with TRP 173 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G MET* 3.3 31.0 - - + +
518G ARG* 3.8 25.4 - - + -
521G ALA* 4.0 20.6 - - + -
522G LEU* 4.1 17.7 - - + -
525G THR* 5.8 2.2 - - - -
7Y LEU* 3.3 26.4 + - - +
8Y ASP 2.7 36.1 + - - -
9Y PHE* 3.9 0.8 - - - +
10Y GLN* 3.5 15.7 - - - -
169Y MET 3.1 15.5 + - - +
170Y PHE* 3.1 18.7 + + + +
172Y MET* 1.3 73.5 - - - +
174Y LEU* 1.3 72.4 + - + +
175Y GLY 3.2 0.7 + - - -
176Y GLU* 3.3 4.3 + - - +
177Y GLN* 3.2 50.2 + - + +
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Residues in contact with LEU 174 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522G LEU* 5.1 6.5 - - + -
525G THR* 5.9 1.8 - - + -
28Y GLY 5.7 0.2 - - - -
29Y ALA* 3.9 37.4 - - + +
32Y VAL* 3.7 36.1 - - + -
33Y PHE* 4.9 2.2 - - + +
78Y PHE* 6.3 0.2 - - + -
170Y PHE* 3.0 19.1 + - + +
171Y LEU* 3.4 26.7 - - + +
173Y TRP* 1.3 91.6 - - + +
175Y GLY* 1.4 60.7 + - - +
177Y GLN* 2.8 34.3 + - + +
189Y ILE* 4.6 6.3 - - - +
190Y ILE* 6.0 0.2 - - + -
193Y ALA* 5.4 2.5 - - + -
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Residues in contact with GLY 175 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG* 6.3 0.2 - - - -
171Y LEU 3.4 4.4 + - - -
172Y MET 3.1 8.6 + - - -
174Y LEU* 1.4 80.6 - - - +
176Y GLU* 1.3 63.4 + - - +
178Y ILE* 3.2 19.2 - - - +
184Y GLY 4.9 0.2 - - - +
185Y ASN* 5.1 2.1 - - - +
189Y ILE* 3.6 23.8 - - - +
190Y ILE* 3.7 24.6 - - - +
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Residues in contact with GLU 176 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG* 2.6 49.1 + - - +
397C LEU* 4.4 6.4 - - + +
509G SER* 2.6 41.5 + - - +
7Y LEU 5.9 1.8 - - - +
9Y PHE* 3.9 16.3 - - + +
121Y ARG* 2.9 29.7 + - - +
172Y MET* 3.9 11.8 + - - +
173Y TRP* 3.3 6.7 + - - +
175Y GLY* 1.3 78.7 - - - +
177Y GLN* 1.4 59.0 + - - +
178Y ILE* 3.3 7.2 - - - -
179Y THR* 3.6 13.3 + - - -
185Y ASN* 4.9 1.8 - - - +
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Residues in contact with GLN 177 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522G LEU* 6.5 0.4 - - - -
9Y PHE* 4.3 3.3 - - - -
10Y GLN* 3.1 32.5 + - - +
25Y PHE* 3.3 52.6 + - - +
29Y ALA* 4.6 4.9 - - - +
173Y TRP* 3.2 49.6 + - + +
174Y LEU* 2.8 39.5 + - + +
175Y GLY 3.7 0.2 - - - -
176Y GLU* 1.4 73.0 - - - +
178Y ILE* 1.4 65.4 + - - +
179Y THR* 3.1 11.2 + - - -
180Y GLU* 4.0 0.9 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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