Contacts of the helix formed by residues 119 - 140 (chain A) in PDB entry 1GPU
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 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A SER* 4.3 0.4 + - - -
117A PRO 3.6 0.2 + - - -
118A LEU* 1.3 72.0 - - - +
120A GLN* 1.3 58.7 + - - +
121A GLY 3.5 1.3 - - - -
122A ILE* 3.3 12.6 - - - +
123A SER* 2.8 23.9 + - - -
159A CYS* 3.4 35.7 - - - +
162A GLU* 4.3 1.6 - - - -
164A ILE* 3.5 20.4 - - - +
165A SER* 4.5 0.4 + - - -
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR 4.9 2.2 - - - +
115A THR* 5.3 1.1 - - + -
117A PRO* 3.1 21.0 + - + +
118A LEU 3.3 0.4 - - - -
119A GLY* 1.3 75.0 - - - +
121A GLY* 1.3 56.6 + - - +
123A SER* 3.1 5.3 + - - -
124A ASN* 2.8 45.7 + - - +
164A ILE* 3.7 4.1 - - - +
419A HIS* 3.0 22.7 + - - -
423A ALA* 3.6 13.9 - - - +
426A ASN* 5.3 0.8 - - - +
451A GLY 3.5 9.4 - - - -
452A ALA* 3.5 31.9 - - - +
455A LEU* 3.6 27.7 - - + +
448B TYR* 2.9 20.0 + - - +
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.5 28.3 - - - +
66A SER* 3.3 12.6 + - - +
115A THR* 3.7 18.1 - - - +
117A PRO 4.8 0.8 + - - -
120A GLN* 1.3 76.5 - - - +
122A ILE* 1.3 62.4 + - - +
124A ASN* 3.0 8.7 + - - +
125A ALA* 2.9 19.4 + - - +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 2.8 19.1 + - - +
119A GLY* 3.3 18.4 - - - +
121A GLY* 1.3 71.2 - - - +
123A SER* 1.3 65.1 + - - +
125A ALA* 3.3 2.7 + - + +
126A VAL* 3.2 26.1 + - + +
153A VAL* 4.0 31.6 - - + -
155A LEU* 4.2 22.7 - - + -
159A CYS* 4.6 1.1 - - + -
165A SER* 3.7 24.0 - - - +
168A ALA* 5.7 0.7 - - + -
169A SER* 4.6 13.7 - - - +
180A LEU* 5.2 2.2 - - + -
182A ALA* 4.1 17.5 - - + -
207A TYR* 5.2 1.8 - - + +
212A TRP* 4.5 14.1 - - + -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY 2.8 17.8 + - - -
120A GLN 3.1 5.5 + - - -
122A ILE* 1.3 75.7 - - - +
124A ASN* 1.3 66.3 + - - +
126A VAL* 3.2 13.3 + - - +
127A GLY 3.3 7.4 + - - -
164A ILE* 3.4 20.2 + - - +
165A SER* 4.1 1.6 - - - -
168A ALA* 3.4 25.9 - - - +
420A ALA 4.9 2.2 - - - -
423A ALA* 3.4 26.2 - - - -
424A ILE* 3.6 10.2 - - - +
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Residues in contact with ASN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.5 42.8 - - + +
114A THR 4.3 7.4 - - - +
120A GLN* 2.8 32.7 + - - +
121A GLY* 3.3 8.3 - - - +
123A SER* 1.3 76.1 - - - +
125A ALA* 1.3 63.7 + - - +
127A GLY 3.0 11.1 + - - -
128A MET* 3.0 14.3 + - + +
423A ALA* 2.8 33.5 + - - +
426A ASN* 3.8 13.5 - - - +
427A GLY* 3.3 11.6 - - - -
455A LEU* 5.4 1.6 - - - +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 4.3 5.8 - - + +
121A GLY 2.9 9.7 + - - +
122A ILE 3.4 8.5 - - - +
123A SER 3.2 0.2 - - - -
124A ASN* 1.3 74.8 - - - +
126A VAL* 1.3 65.0 + - - +
128A MET* 3.1 7.6 + - - -
129A ALA* 2.9 22.0 + - - +
151A THR* 3.5 20.0 - - + +
153A VAL* 3.0 37.9 - - + -
180A LEU* 4.0 5.2 - - + -
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.2 20.0 + - + +
123A SER 3.2 8.0 + - - +
125A ALA* 1.3 77.2 - - - +
127A GLY* 1.3 62.4 + - - +
129A ALA* 3.3 3.6 + - - +
130A MET* 3.0 44.8 + - - +
168A ALA* 3.7 27.6 - - + +
169A SER* 4.9 1.1 - - - +
171A LEU 5.4 0.9 - - - -
172A ALA* 3.9 28.0 - - + +
175A LEU* 5.4 0.2 - - + -
177A LEU* 4.0 5.2 - - + -
180A LEU* 4.0 16.2 - - + -
212A TRP* 5.2 0.9 - - + -
424A ILE* 4.0 15.7 - - + -
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER 3.3 4.2 + - - -
124A ASN 3.0 8.4 + - - -
126A VAL* 1.3 77.7 - - - +
128A MET* 1.3 58.8 + - - +
130A MET* 3.2 2.7 + - - +
131A ALA* 2.9 25.5 + - - +
424A ILE* 3.6 34.9 - - - +
428A ILE* 3.4 18.0 - - - +
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Residues in contact with MET 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 4.2 26.2 - - - -
64A VAL* 3.7 25.8 - - + -
112A GLU* 3.6 32.3 - - + +
113A VAL* 3.6 26.2 - - + -
124A ASN* 3.0 15.1 + - + +
125A ALA* 3.1 10.7 + - - +
127A GLY* 1.3 75.7 - - - +
129A ALA* 1.3 57.9 + - - +
131A ALA* 3.3 6.0 + - - +
132A GLN* 3.0 28.1 + - - +
151A THR* 4.0 15.2 + - + +
427A GLY* 3.4 16.4 + - - +
430A ALA* 4.1 10.1 - - + -
431A PHE* 3.6 9.7 - - + +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ALA 2.9 15.4 + - - +
126A VAL 3.7 4.7 - - - +
128A MET* 1.3 73.3 - - - +
130A MET* 1.3 66.1 + - - +
132A GLN* 3.4 8.3 + - - +
133A ALA* 3.0 23.2 + - - +
151A THR* 3.7 15.4 + - - +
177A LEU* 4.1 15.9 - - + +
179A ASN* 5.1 4.7 - - + +
180A LEU* 4.0 28.3 - - + +
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Residues in contact with MET 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 3.0 28.5 + - - +
127A GLY* 3.2 6.9 + - - +
129A ALA* 1.3 75.2 - - - +
131A ALA* 1.3 64.0 + - - +
133A ALA* 3.3 3.8 + - - +
134A ASN* 3.0 21.7 + - - +
171A LEU* 5.1 0.7 - - + -
175A LEU* 3.6 25.1 - - + -
177A LEU* 3.7 16.8 - - + -
397A PHE* 3.6 30.8 - - + -
412A ILE* 3.6 41.1 - - + -
414A TYR* 4.9 0.9 - - + -
424A ILE* 3.7 27.4 - - + -
428A ILE* 4.8 5.4 - - + -
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY 2.9 16.1 + - - +
128A MET 3.6 1.8 - - - +
130A MET* 1.3 78.0 - - - +
132A GLN* 1.3 56.4 + - - +
134A ASN* 3.3 2.7 + - - -
135A LEU* 2.9 28.2 + - - +
428A ILE* 4.2 14.1 - - + +
431A PHE* 3.5 32.5 - - + -
435A TYR* 3.2 27.1 + - + -
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Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A MET 3.0 16.1 + - - +
129A ALA* 3.6 9.9 + - - +
131A ALA* 1.3 77.0 - - - +
133A ALA* 1.3 69.9 + - - +
135A LEU 3.3 0.2 + - - -
136A ALA* 3.0 24.8 + - - +
147A SER* 2.9 24.2 + - - +
148A ASP* 3.4 16.2 + - - -
149A ASN* 3.0 49.4 + - - +
151A THR* 5.1 0.9 - - - +
179A ASN* 4.0 18.0 + - - +
431A PHE* 3.8 16.5 - - + -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA 3.0 13.1 + - - +
130A MET* 3.3 8.9 + - - +
132A GLN* 1.3 86.8 - - - +
134A ASN* 1.3 57.5 + - - +
136A ALA* 3.9 3.6 - - - +
137A ALA* 3.0 29.8 + - - +
177A LEU* 4.7 4.7 - - + -
397A PHE* 4.0 4.3 - - + -
407A TYR* 3.7 37.9 - - + +
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Residues in contact with ASN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A MET 3.0 15.9 + - - +
131A ALA* 3.7 1.8 - - - +
133A ALA* 1.3 75.4 - - - +
135A LEU* 1.3 57.8 + - - +
137A ALA* 3.3 0.7 + - - +
138A THR* 2.7 47.2 + - - +
333A ARG* 5.0 2.9 + - - -
374A PRO 5.5 1.0 - - - +
377A ILE* 4.3 14.1 - - + +
397A PHE* 4.1 5.8 - - + -
407A TYR 3.1 19.8 + - - +
408A SER 3.5 10.3 + - - -
409A GLY 3.1 26.3 + - - -
410A ARG* 4.3 2.9 - - - +
435A TYR* 2.6 35.7 + - + +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.1 19.1 - - + +
131A ALA 2.9 16.8 + - - +
132A GLN 3.3 4.2 + - - +
134A ASN* 1.3 76.4 - - - +
136A ALA* 1.3 57.8 + - - +
138A THR* 4.5 0.4 - - - -
139A TYR* 2.9 61.5 + - + +
146A LEU* 5.7 2.5 - - + +
147A SER* 4.0 18.5 - - - +
330A LEU* 4.1 12.6 - - + -
333A ARG* 4.3 1.8 - - - +
431A PHE* 3.7 26.5 - - + -
433A ALA* 4.1 20.0 - - + -
435A TYR* 3.0 13.3 + - + +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLN* 3.0 24.2 + - - +
133A ALA* 3.9 4.5 - - - +
135A LEU* 1.3 77.2 - - - +
137A ALA* 1.3 59.3 + - - +
140A ASN* 2.9 57.8 + - - +
147A SER* 3.4 18.5 + - - +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ALA 3.0 19.2 + - - +
134A ASN 3.8 0.2 - - - +
136A ALA* 1.3 77.3 - - - +
138A THR* 1.3 59.7 + - - +
140A ASN 5.1 2.6 + - - +
407A TYR* 3.6 10.3 - - + +
408A SER* 3.6 37.6 - - - +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASN* 2.7 40.6 + - - +
137A ALA* 1.3 80.6 - - - +
139A TYR* 1.3 93.9 + - + +
140A ASN 5.1 1.0 - - - +
141A LYS* 5.3 2.8 + - - -
326A LEU* 4.4 14.5 - - + +
329A GLU* 4.8 3.4 - - - +
333A ARG* 5.0 2.9 - - - +
374A PRO* 6.1 2.5 - - + +
408A SER* 4.3 10.2 + - - -
410A ARG* 6.1 0.3 - - - +
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 2.9 46.3 + - + +
138A THR* 1.3 88.2 - - + +
140A ASN* 1.3 67.2 + - - +
141A LYS* 3.7 2.8 - - - +
146A LEU* 4.3 7.0 - - + -
147A SER* 6.4 0.2 - - - -
319A TYR* 2.7 41.3 + - - +
326A LEU* 3.9 32.3 - - + -
329A GLU* 2.6 31.7 + - + -
330A LEU* 4.1 29.4 - - + -
333A ARG* 2.8 46.3 + - - -
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU 4.9 0.2 - - - +
136A ALA* 2.9 32.4 + - - +
137A ALA 5.2 1.9 - - - +
138A THR 5.1 1.4 - - - +
139A TYR* 1.3 78.6 - - - +
141A LYS* 1.3 69.5 + - - +
144A PHE 3.5 4.9 - - - +
145A THR* 4.0 12.3 - - - +
146A LEU* 2.9 28.4 + - - +
147A SER* 2.9 33.9 + - - +
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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