Contacts of the helix formed by residues 117 - 138 (chain A) in PDB entry 2R5N
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 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A SER* 4.1 1.0 + - - -
115A PRO 3.5 0.2 + - - -
116A LEU* 1.3 73.4 - - - +
118A GLN* 1.3 62.9 + - - +
119A GLY 3.3 2.5 - - - -
120A ILE* 3.2 23.1 - - - +
121A ALA* 3.4 5.2 + - - +
157A CYS* 3.3 33.0 - - - +
160A GLU* 4.5 2.0 - - - -
162A ILE* 3.4 25.3 - - - +
163A SER 5.2 0.2 - - - -
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 6.0 1.6 - - + -
115A PRO* 3.3 15.3 + - + +
116A LEU 3.2 3.6 - - - +
117A GLY* 1.3 75.6 - - - +
119A GLY* 1.3 60.0 + - - +
121A ALA* 3.2 6.1 + - - +
122A ASN* 2.8 41.4 + - - +
162A ILE* 3.9 18.2 - - + -
412A PHE* 3.7 12.6 - - + -
416A ALA* 4.3 6.4 - - + +
419A ASN* 4.6 1.4 + - - -
443A ASN* 2.9 31.3 + - - +
444A ALA* 3.3 23.7 - - - +
447A MET* 3.4 17.8 - - + +
440B TYR* 3.1 23.8 + - - +
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Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 3.4 26.0 - - - +
63A SER* 3.2 17.2 + - - +
113A THR* 3.8 19.5 - - - +
115A PRO 4.5 2.2 + - - -
118A GLN* 1.3 76.3 - - - +
120A ILE* 1.3 57.2 + - - +
122A ASN* 3.0 6.2 + - - +
123A ALA* 2.9 24.9 + - - +
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Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 2.9 18.0 + - - +
117A GLY* 3.2 24.0 - - - +
119A GLY* 1.3 73.4 - - - +
121A ALA* 1.3 56.2 + - - +
123A ALA* 3.2 7.9 + - + +
124A VAL* 2.9 33.3 + - + +
151A ALA* 3.9 23.3 - - + -
153A MET* 4.0 37.0 - - + -
157A CYS* 4.9 0.9 - - + -
163A SER* 4.5 9.4 - - - -
166A VAL* 4.2 10.3 - - + -
167A CYS* 3.9 20.2 - - - -
178A LEU* 4.8 3.6 - - + -
180A ALA* 4.2 10.3 - - + -
210A TRP* 4.7 9.9 - - + -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY 3.4 2.2 + - - +
118A GLN 3.2 9.8 + - - +
120A ILE* 1.3 81.6 - - - +
122A ASN* 1.3 63.1 + - - +
124A VAL* 3.2 5.0 + - - +
125A GLY 3.0 17.5 + - - -
162A ILE* 3.8 11.2 - - + -
166A VAL* 3.6 31.4 - - + -
416A ALA* 3.4 29.2 - - + -
417A ILE* 3.6 7.8 - - - +
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Residues in contact with ASN 122 (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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61A VAL* 5.0 0.4 - - + -
111A THR* 2.8 34.8 + - + +
112A THR 4.4 5.2 - - - +
118A GLN* 2.8 32.0 + - - +
119A GLY* 3.0 8.4 + - - +
121A ALA* 1.3 73.5 - - - +
123A ALA* 1.3 57.7 + - - +
125A GLY 3.1 2.1 + - - -
126A MET* 2.8 35.9 + - + +
416A ALA* 2.9 34.5 + - - +
419A ASN* 3.8 15.2 - - - +
420A GLY* 3.3 16.6 - - - -
423A LEU* 4.7 1.6 - - - -
451A MET* 4.8 3.1 - - - +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 4.2 11.8 - - + +
119A GLY 2.9 12.3 + - - +
120A ILE* 3.4 9.6 - - + +
122A ASN* 1.3 74.4 - - - +
124A VAL* 1.3 59.9 + - - +
126A MET* 3.1 2.3 + - - +
127A ALA* 2.8 27.5 + - - +
149A THR* 3.4 28.6 - - + +
151A ALA* 3.9 24.9 - - + -
178A LEU* 4.1 8.5 - - + -
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Residues in contact with VAL 124 (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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120A ILE* 2.9 24.4 + - + +
121A ALA 3.2 7.6 + - - +
123A ALA* 1.3 74.4 - - - +
125A GLY* 1.3 57.8 + - - +
127A ALA* 3.2 2.3 + - - +
128A ILE* 2.9 39.8 + - + +
166A VAL* 3.8 32.1 - - + +
167A CYS* 4.9 2.2 - - - +
169A LEU* 5.5 0.4 - - + -
170A ALA* 4.1 6.3 - - + +
175A LEU* 4.0 11.4 - - + -
178A LEU* 3.8 25.6 - - + -
417A ILE* 3.9 24.0 - - + -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA 3.0 11.1 + - - -
122A ASN 3.1 2.9 + - - -
124A VAL* 1.3 75.8 - - - +
126A MET* 1.3 56.1 + - - +
128A ILE* 3.3 2.2 + - - +
129A ALA* 2.8 29.1 + - - +
417A ILE* 3.4 36.8 - - - +
420A GLY 4.0 7.0 - - - -
421A ILE* 3.5 7.6 - - - +
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Residues in contact with MET 126 (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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59A ARG* 3.9 23.8 - - + -
61A VAL* 3.7 31.6 - - + -
110A GLU* 3.9 30.3 - - + +
111A THR* 4.2 9.2 - - - -
122A ASN* 2.8 23.2 + - + +
123A ALA* 3.1 6.9 + - - +
125A GLY* 1.3 72.3 - - - +
127A ALA* 1.3 57.2 + - - +
129A ALA* 3.3 3.4 + - - +
130A GLU* 3.0 26.5 + - - +
149A THR* 3.8 12.8 + - + +
420A GLY 3.5 15.7 - - - +
423A LEU* 4.0 19.3 - - + -
424A HIS* 3.6 23.3 - - + -
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Residues in contact with ALA 127 (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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123A ALA 2.8 16.2 + - - +
124A VAL* 3.6 5.2 - - - +
126A MET* 1.3 72.6 - - - +
128A ILE* 1.3 66.6 + - - +
130A GLU* 3.4 6.0 + - - +
131A LYS* 3.0 24.6 + - - +
149A THR* 3.6 15.2 + - - +
175A LEU* 3.9 22.0 - - + +
177A LYS* 5.2 2.5 - - + -
178A LEU* 4.0 23.3 - - + +
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Residues in contact with ILE 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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124A VAL* 2.9 32.3 + - + +
125A GLY* 3.6 4.7 - - - +
127A ALA* 1.3 74.8 - - - +
129A ALA* 1.3 61.3 + - - +
131A LYS* 3.8 2.6 - - - +
132A THR* 2.7 35.9 + - - +
169A LEU* 5.0 4.0 - - + -
173A LEU* 3.8 24.2 - - + -
175A LEU* 3.8 20.2 - - + -
376A LEU* 4.3 7.9 - - + -
396A ILE* 3.8 24.5 - - + -
405A ILE* 4.0 17.7 - - + -
417A ILE* 3.9 26.7 - - + -
421A ILE* 4.4 2.5 - - + -
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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 GLY 2.8 17.6 + - - +
126A MET 3.5 1.1 - - - +
128A ILE* 1.3 78.7 - - - +
130A GLU* 1.3 57.5 + - - +
132A THR* 4.6 0.2 - - - -
133A LEU* 2.8 34.6 + - - +
376A LEU* 5.0 2.0 - - - -
421A ILE* 4.5 7.2 - - + -
424A HIS* 3.5 35.2 - - + +
427A PHE* 3.4 24.3 - - + -
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Residues in contact with GLU 130 (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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126A MET 3.0 15.0 + - - +
127A ALA* 3.4 7.5 + - - +
129A ALA* 1.3 75.4 - - - +
131A LYS* 1.3 67.3 + - - +
133A LEU* 4.5 0.2 - - - -
134A ALA* 2.9 33.3 + - - +
145A VAL* 3.6 8.8 - - + +
146A ASP* 3.4 6.2 + - - -
147A HIS* 3.0 63.7 + - + +
149A THR* 5.2 1.6 - - - +
177A LYS* 2.8 40.7 + - + +
424A HIS* 4.0 7.7 + - - -
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Residues in contact with LYS 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 ALA 3.0 17.8 + - - +
128A ILE* 3.8 4.3 - - - +
130A GLU* 1.3 85.7 + - - +
132A THR* 1.3 60.7 + - - +
134A ALA* 3.7 3.5 - - - +
135A ALA* 3.1 27.5 + - - +
173A LEU* 2.8 26.9 + - + +
174A LYS* 4.7 7.2 + - - +
175A LEU* 3.8 22.2 - - + -
396A ILE* 4.8 9.4 + - + +
400A ALA* 4.2 21.6 - - + +
678A EDO 3.2 24.2 + - - -
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Residues in contact with THR 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 ILE* 2.7 31.3 + - - +
131A LYS* 1.3 75.4 - - - +
133A LEU* 1.3 61.1 + - - +
135A ALA* 3.3 2.4 + - - +
136A GLN* 2.9 44.2 + - - +
376A LEU* 4.4 7.2 - - + +
396A ILE* 4.1 15.2 - - + +
400A ALA 3.5 16.5 + - - +
402A GLY 3.4 26.5 - - - +
427A PHE* 3.7 18.2 - - + -
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Residues in contact with LEU 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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55A ALA 6.0 0.2 - - - +
129A ALA 2.8 21.2 + - - +
130A GLU* 4.0 2.9 - - - +
132A THR* 1.3 74.7 - - - +
134A ALA* 1.3 55.9 + - - +
136A GLN* 3.3 1.9 + - - -
137A PHE* 2.9 65.0 + - + +
145A VAL* 4.1 10.5 - - + -
147A HIS* 5.8 0.9 - - + -
325A PHE* 3.7 16.6 - - + -
328A ARG* 3.8 9.2 - - + +
329A MET* 3.6 28.5 - - - -
424A HIS* 4.1 17.0 - - + -
425A GLY 4.4 2.5 - - - +
426A GLY* 4.2 9.4 - - - +
427A PHE* 3.6 20.6 - - + -
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Residues in contact with ALA 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 GLU* 2.9 24.0 + - - +
131A LYS* 3.7 6.1 - - - +
133A LEU* 1.3 76.9 - - - +
135A ALA* 1.3 59.4 + - - +
138A ASN* 2.9 51.8 + - - +
145A VAL* 3.6 23.2 - - + +
177A LYS* 5.5 2.2 - - - +
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Residues in contact with ALA 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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131A LYS 3.1 14.7 + - - +
132A THR 3.3 0.6 + - - +
134A ALA* 1.3 76.8 - - - +
136A GLN* 1.3 61.9 + - - +
138A ASN 4.7 2.4 - - - +
139A ARG* 4.7 4.2 + - - -
400A ALA* 3.4 43.7 - - + +
401A ALA* 3.5 13.6 - - + +
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Residues in contact with GLN 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 THR* 2.9 28.0 + - - +
133A LEU 3.8 3.8 - - - +
134A ALA 3.2 0.2 - - - -
135A ALA* 1.3 76.6 - - - +
137A PHE* 1.3 68.1 + - + +
139A ARG* 3.0 23.8 + - - -
328A ARG* 2.8 38.1 + - - +
373A PRO 4.6 7.4 + - - -
375A PHE 5.4 0.6 + - - -
401A ALA* 3.3 23.7 + - + +
402A GLY 3.0 26.9 + - - -
403A ASN* 4.8 4.2 - - - +
427A PHE* 4.0 8.0 - - - -
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Residues in contact with PHE 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 LEU* 2.9 43.0 + - + +
136A GLN* 1.3 86.0 - - + +
138A ASN* 1.3 68.4 + - - +
139A ARG* 3.4 6.5 + - - +
144A ILE* 4.1 13.7 - - + -
145A VAL* 4.6 2.7 - - + -
314A TYR* 2.7 42.2 + + - +
321A GLU* 3.3 28.5 - - + -
324A GLU* 4.1 7.6 - - + -
325A PHE* 3.5 36.1 - + + -
328A ARG* 3.5 37.5 - - + -
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Residues in contact with ASN 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 ALA* 2.9 35.9 + - - +
135A ALA 4.7 2.8 - - - +
137A PHE* 1.3 71.2 - - - +
139A ARG* 1.3 76.5 + - - +
142A HIS 3.5 3.8 - - - +
143A ASP* 3.6 29.4 + - - +
144A ILE* 3.0 8.7 + - - +
145A VAL* 2.9 48.0 + - - +
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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
------------------------------------------------------------
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