Contacts of the helix formed by residues 147 - 169 (chain L) in PDB entry 6GYS
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 ASP 147 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82L ALA* 5.0 2.5 - - + -
145L ASN 3.9 0.4 - - - -
146L ILE* 1.3 81.5 - - - +
148L THR* 1.3 63.0 + - - +
149L LYS* 3.1 28.5 + - - +
150L TYR* 3.1 35.4 + - + +
151L LEU* 3.9 3.5 + - - +
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Residues in contact with THR 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L ILE* 5.7 4.0 - - - +
130L ASN* 5.2 9.8 + - - -
146L ILE* 3.5 19.3 - - + +
147L ASP* 1.3 74.9 - - - +
149L LYS* 1.3 62.6 + - + +
151L LEU* 3.0 20.1 + - - +
152L GLU* 2.8 37.3 + - - +
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Residues in contact with LYS 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L ASP* 3.7 21.3 + - - +
148L THR* 1.3 78.2 - - + +
150L TYR* 1.3 63.7 + - - +
152L GLU* 3.2 27.6 - - - +
153L SER* 2.9 30.2 + - - -
368L THR* 6.2 1.8 - - - -
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Residues in contact with TYR 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L ALA* 3.6 40.6 - - + -
83L GLU* 4.5 6.0 - - - +
86L HIS* 3.4 32.9 + - + +
147L ASP* 3.1 28.3 + - - +
149L LYS* 1.3 76.9 - - - +
151L LEU* 1.3 63.9 + - + +
153L SER* 3.0 11.2 + - - -
154L VAL* 2.9 44.5 + - + +
367L PRO* 3.9 34.8 - - + -
368L THR 6.0 0.7 - - - -
369L TRP* 5.1 15.4 - + - -
395L PHE* 5.1 2.9 - - - -
400L PRO* 4.8 8.1 - - - +
403L PHE* 4.7 4.8 - + - -
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Residues in contact with LEU 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82L ALA* 4.0 6.3 - - + +
85L ILE* 3.9 31.4 - - + -
86L HIS* 4.8 3.1 - - + +
89L LEU* 5.3 4.3 - - + -
126L ILE* 4.6 22.4 - - + +
146L ILE* 3.7 38.1 - - + +
147L ASP 4.2 3.6 - - - +
148L THR* 3.0 17.8 + - - +
150L TYR* 1.3 96.3 - - + +
152L GLU* 1.3 56.1 + - - +
154L VAL* 3.2 10.9 + - + +
155L THR* 2.6 38.2 + - - -
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Residues in contact with GLU 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L THR* 2.8 25.2 + - - +
149L LYS* 3.2 30.8 + - - +
151L LEU* 1.3 76.8 - - - +
153L SER* 1.3 57.1 + - - +
155L THR* 3.2 8.7 + - - -
156L LYS* 2.8 40.7 + - - +
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Residues in contact with SER 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L LYS 2.9 15.4 + - - -
150L TYR* 3.0 13.4 + - - -
152L GLU* 1.3 74.2 - - - +
154L VAL* 1.3 60.4 + - - +
156L LYS* 3.3 12.6 + - - +
157L LEU* 2.9 30.3 + - - +
363L ASN 5.7 1.3 + - - -
364L LEU* 4.4 5.0 - - - +
365L VAL 5.3 4.3 - - - -
367L PRO* 6.0 4.3 - - - -
403L PHE* 4.2 16.8 - - - -
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Residues in contact with VAL 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L HIS* 3.5 36.6 - - + +
89L LEU* 4.9 11.9 - - + -
122L LEU* 5.1 5.2 - - + -
150L TYR* 2.9 37.4 + - + +
151L LEU* 3.4 12.6 - - + +
153L SER* 1.3 75.9 - - - +
155L THR* 1.3 62.6 + - - +
157L LEU* 3.2 5.7 + - - +
158L HIS* 3.0 48.6 + - + +
402L ASP* 3.9 1.8 - - - +
403L PHE* 4.3 11.7 - - + -
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Residues in contact with THR 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L ILE* 4.7 1.6 - - + +
122L LEU* 4.2 21.1 - - + -
123L LYS* 4.5 22.9 - - + -
126L ILE* 3.3 22.9 - - + +
151L LEU 2.6 21.9 + - - -
152L GLU* 3.4 10.1 - - - -
154L VAL* 1.3 76.9 - - - +
156L LYS* 1.3 53.9 + - - +
158L HIS* 3.5 1.6 + - - +
159L THR* 2.3 44.2 + - - +
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Residues in contact with LYS 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L GLU* 2.8 28.1 + - - +
153L SER* 3.7 10.4 + - - +
155L THR* 1.3 76.5 - - - +
157L LEU* 1.3 57.3 + - - +
159L THR* 3.3 10.2 - - + -
160L HIS* 2.8 29.9 + - + +
363L ASN* 4.6 36.8 + - + +
364L LEU* 4.3 17.0 - - + +
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Residues in contact with LEU 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L SER 2.9 17.3 + - - +
154L VAL 3.2 4.5 + - - +
156L LYS* 1.3 75.3 - - - +
158L HIS* 1.3 66.2 + - - +
160L HIS* 3.1 5.1 + - - +
161L TRP* 3.0 20.6 + - - +
364L LEU* 3.8 30.0 - - + +
402L ASP* 3.5 22.2 - - - +
403L PHE* 3.5 50.7 - - + +
406L ILE* 3.7 28.2 - - + +
407L MET* 4.6 9.6 - - + -
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Residues in contact with HIS 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L HIS* 4.7 1.6 + - - -
90L LEU* 6.0 0.6 - - - +
94L ILE* 3.7 29.5 - - + +
119L ILE* 4.3 6.3 - - + -
122L LEU* 4.3 21.7 - - + +
154L VAL* 3.0 42.0 + - + +
155L THR 4.0 3.1 - - - +
157L LEU* 1.3 74.1 - - - +
159L THR* 1.3 57.3 + - - +
161L TRP* 3.2 8.3 + - - +
162L ILE* 2.9 33.9 + - + +
402L ASP* 2.4 42.3 + - + -
406L ILE* 5.6 2.7 - - - +
412L PRO* 4.9 8.7 - - + +
413L TYR* 4.2 17.5 + - - +
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Residues in contact with THR 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L ILE* 3.6 22.4 - - + +
123L LYS* 5.6 1.6 - - - -
155L THR* 2.3 33.7 + - - +
156L LYS* 3.3 12.0 - - + -
158L HIS* 1.3 76.1 - - - +
160L HIS* 1.3 57.4 + - - +
162L ILE* 3.0 5.7 + - + +
163L ASP* 2.8 42.8 + - - +
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Residues in contact with HIS 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L LYS* 2.8 18.2 + - + +
157L LEU 3.1 5.4 + - - +
159L THR* 1.3 71.9 - - - +
161L TRP* 1.3 62.7 + + - +
163L ASP* 3.1 23.7 + - + +
164L SER* 2.9 29.4 + - - -
364L LEU* 3.6 29.1 - - + +
406L ILE* 4.6 13.9 - - + -
409L PHE* 5.5 8.9 - + - -
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Residues in contact with TRP 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L ASN* 5.2 1.0 - - - +
157L LEU 3.0 11.5 + - - +
158L HIS* 3.2 9.8 + - - +
160L HIS* 1.3 76.4 - + - +
162L ILE* 1.3 69.8 + - + +
164L SER* 2.3 50.0 + - - -
165L GLN* 2.9 18.9 + - + +
406L ILE* 3.5 36.8 - - + -
409L PHE* 4.0 32.8 - + - -
410L LYS 4.7 0.4 - - - -
411L SER* 4.3 11.5 + - - +
412L PRO* 3.9 20.5 - - + +
413L TYR* 4.3 16.9 - + - +
517L LEU* 6.1 0.2 - - + -
518L PRO* 3.6 41.3 - - + -
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Residues in contact with ILE 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L GLU* 6.1 3.8 - - + +
115L ASN* 3.4 31.9 - - + +
116L SER* 6.0 3.1 - - - -
119L ILE* 4.0 26.9 - - + -
158L HIS* 2.9 15.0 + - + +
159L THR* 3.0 9.4 + - + +
161L TRP* 1.3 79.8 - - + +
163L ASP* 1.3 53.7 + - - +
165L GLN* 3.3 24.6 + - + +
166L LYS* 2.7 41.5 + - + +
413L TYR* 4.5 7.9 - - - +
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Residues in contact with ASP 163 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159L THR* 2.8 26.9 + - - +
160L HIS* 3.1 33.8 + - + +
162L ILE* 1.3 76.8 - - - +
164L SER* 1.3 59.3 + - - +
166L LYS* 3.2 7.3 + - - +
167L ALA* 2.9 29.5 + - - +
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Residues in contact with SER 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L HIS* 2.9 17.1 + - - -
161L TRP* 2.3 60.1 + - - -
163L ASP* 1.3 76.1 - - - +
165L GLN* 1.3 57.5 + - - +
167L ALA* 3.4 6.8 + - - +
168L ILE* 3.0 31.3 + - - +
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Residues in contact with GLN 165 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107L GLU 4.9 1.8 + - - -
108L ASP* 4.3 5.9 + - - +
111L GLU* 3.0 22.6 + - - -
112L GLU* 3.4 35.9 - - + +
115L ASN* 2.4 33.6 + - - +
161L TRP* 2.9 18.0 + - + +
162L ILE* 3.4 15.1 - - + +
164L SER* 1.3 81.6 + - - +
166L LYS* 1.3 52.5 + - - +
168L ILE* 2.9 13.6 + - + +
169L THR* 2.5 42.0 + - - -
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Residues in contact with LYS 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L GLU* 4.1 17.5 - - - +
162L ILE* 2.7 26.8 + - + +
163L ASP* 3.6 9.4 - - - +
165L GLN* 1.3 73.4 - - - +
167L ALA* 1.3 60.7 + - - +
169L THR* 3.3 22.1 - - + +
173L THR* 3.5 12.9 - - + +
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Residues in contact with ALA 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L ASP 2.9 16.4 + - - +
164L SER* 3.8 7.2 - - - +
166L LYS* 1.3 76.4 - - - +
168L ILE* 1.3 57.1 + - + +
170L THR 3.7 2.9 - - - +
173L THR* 3.0 30.9 + - + -
174L ASN* 5.5 5.8 + - - +
181L LEU* 5.6 3.8 - - - +
520L PHE* 5.9 2.1 - - - -
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Residues in contact with ILE 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ASP* 3.7 8.2 - - - +
164L SER 3.0 14.6 + - - +
165L GLN* 2.9 23.5 + - + +
167L ALA* 1.3 75.8 - - - +
169L THR* 1.3 64.9 + - - +
170L THR* 3.1 8.9 + - - +
171L ASN* 5.4 2.4 - - - +
517L LEU* 5.5 0.4 - - + -
518L PRO* 5.4 2.5 - - + -
519L GLY* 3.6 21.1 - - - +
520L PHE* 3.6 66.6 - - + +
523L ILE* 5.3 3.5 - - + +
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Residues in contact with THR 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ASP* 2.6 39.1 + - - +
109L LEU* 3.7 6.1 - - - +
112L GLU* 2.4 41.9 + - - +
165L GLN* 2.5 19.2 + - - +
166L LYS* 3.3 28.3 - - + +
167L ALA 3.5 0.2 - - - -
168L ILE* 1.3 73.9 - - - +
170L THR* 1.3 70.7 + - - +
173L THR* 4.5 0.4 - - - +
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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