Contacts of the helix formed by residues 117 - 138 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER* 4.1 1.6 + - - -
116B LEU* 1.3 72.7 - - - +
118B GLN* 1.3 58.5 + - - +
119B GLY 3.4 2.2 - - - -
120B ILE* 3.1 24.1 - - - +
121B ALA* 3.4 5.7 + - - +
157B CYS* 3.3 33.0 - - - +
160B GLU* 4.4 2.2 - - - -
162B ILE* 3.5 26.2 - - - +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A TYR* 3.1 24.5 + - - +
112B THR 5.8 3.4 - - - +
113B THR* 5.1 1.1 - - + -
115B PRO* 3.3 15.7 + - + +
116B LEU 3.2 3.0 - - - +
117B GLY* 1.3 74.1 - - - +
119B GLY* 1.3 59.7 + - - +
121B ALA* 3.2 5.6 + - - +
122B ASN* 2.8 42.2 + - - +
162B ILE* 3.9 18.8 - - + -
412B PHE* 3.8 9.8 - - + -
416B ALA* 4.3 6.0 - - + +
419B ASN* 4.6 1.7 + - - -
443B ASN* 2.9 33.9 + - - +
444B ALA* 3.3 23.7 - - - +
447B MET* 3.4 16.8 - - + +
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Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.4 17.2 - - - +
63B SER* 3.3 14.3 + - - +
113B THR* 3.7 29.2 - - - +
115B PRO 4.5 2.0 + - - -
118B GLN* 1.3 76.4 - - - +
120B ILE* 1.3 56.8 + - - +
122B ASN* 3.0 8.0 + - - +
123B ALA 2.8 24.8 + - - -
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 2.9 19.1 + - - +
117B GLY* 3.1 26.5 - - - +
119B GLY* 1.3 72.2 - - - +
121B ALA* 1.3 56.1 + - - +
123B ALA* 3.2 8.4 + - + +
124B VAL* 2.8 34.8 + - + +
151B ALA* 4.0 22.7 - - + -
153B MET* 3.9 35.4 - - + -
157B CYS* 4.8 0.2 - - + -
163B SER* 4.6 9.2 - - - -
166B VAL* 4.3 9.9 - - + -
167B CYS* 3.9 24.0 - - - -
178B LEU* 4.7 4.0 - - + -
180B ALA* 4.3 10.8 - - + -
210B TRP* 4.7 5.4 - - + -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLY 3.4 8.9 + - - +
118B GLN 3.2 8.5 + - - +
119B GLY 3.2 0.4 - - - -
120B ILE* 1.3 80.4 - - - +
122B ASN* 1.3 63.6 + - - +
124B VAL* 3.1 5.5 + - - +
125B GLY 3.0 17.8 + - - -
162B ILE* 3.9 5.6 - - + -
166B VAL* 3.6 30.3 - - + -
416B ALA* 3.4 29.4 - - + -
417B ILE* 3.6 8.2 - - - -
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Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B VAL* 5.0 0.4 - - + -
111B THR* 2.8 33.9 + - + +
112B THR 4.4 5.7 - - - +
118B GLN* 2.8 35.0 + - - +
119B GLY* 3.3 8.2 - - - +
121B ALA* 1.3 71.8 - - - +
123B ALA* 1.3 57.9 + - - +
125B GLY 3.1 2.1 + - - -
126B MET* 2.8 37.8 + - + +
416B ALA* 3.0 28.5 + - - +
419B ASN* 3.8 14.5 - - - +
420B GLY* 3.3 16.6 - - - -
423B LEU* 4.7 2.5 - - + -
451B MET* 4.7 3.9 - - - +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 4.2 7.8 - - + +
119B GLY 2.8 11.7 + - - +
120B ILE* 3.4 9.4 - - + +
122B ASN* 1.3 74.6 - - - +
124B VAL* 1.3 65.5 + - - +
126B MET* 3.1 6.4 + - - +
127B ALA* 2.9 21.7 + - - +
149B THR* 3.4 26.7 - - + +
151B ALA* 4.0 25.1 - - + -
178B LEU* 4.2 8.3 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ILE* 2.8 25.9 + - + +
121B ALA 3.1 7.4 + - - +
123B ALA* 1.3 70.9 - - - +
125B GLY* 1.3 57.6 + - - +
127B ALA* 3.3 3.2 + - - +
128B ILE* 2.9 39.8 + - + +
166B VAL* 3.8 38.6 - - + +
167B CYS* 5.1 1.6 - - - -
169B LEU 5.5 0.2 - - - -
170B ALA* 4.0 7.0 - - + +
175B LEU* 4.1 10.5 - - + -
178B LEU* 3.8 26.2 - - + -
417B ILE* 3.8 20.0 - - + -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ALA 3.0 11.5 + - - -
122B ASN 3.1 2.7 + - - -
124B VAL* 1.3 77.5 - - - +
126B MET* 1.3 55.6 + - - +
128B ILE* 3.3 2.0 + - - +
129B ALA* 2.8 30.0 + - - +
417B ILE* 3.3 36.5 - - - +
420B GLY 3.9 6.7 - - - -
421B ILE* 3.6 7.1 - - - +
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.9 24.5 - - + -
61B VAL* 3.7 27.6 - - + -
110B GLU* 3.8 34.5 - - + +
111B THR* 4.2 4.9 - - - -
122B ASN* 2.8 22.4 + - + +
123B ALA* 3.1 7.1 + - - +
125B GLY* 1.3 72.5 - - - +
127B ALA* 1.3 56.9 + - - +
129B ALA* 3.4 0.8 + - - -
130B GLU* 3.0 25.8 + - - +
149B THR* 3.9 12.6 + - + +
420B GLY 3.5 14.6 - - - +
423B LEU* 4.1 23.8 - - + -
424B HIS* 3.5 25.2 - - + +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ALA 2.9 16.1 + - - +
124B VAL 3.7 4.0 - - - +
126B MET* 1.3 73.4 - - - +
128B ILE* 1.3 66.7 + - - +
130B GLU* 3.3 6.3 + - - +
131B LYS* 3.0 24.8 + - - +
149B THR* 3.6 15.2 + - - +
175B LEU* 4.0 15.9 - - + +
177B LYS* 5.2 3.4 - - + -
178B LEU* 4.0 28.5 - - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 2.9 30.7 + - + +
125B GLY* 3.6 4.7 - - - +
127B ALA* 1.3 76.6 - - - +
129B ALA* 1.3 61.6 + - - +
131B LYS* 3.4 2.9 + - - +
132B THR* 2.7 35.9 + - - +
169B LEU* 4.9 3.6 - - + -
173B LEU* 3.7 24.7 - - + -
175B LEU* 3.7 20.6 - - + -
376B LEU* 4.2 8.7 - - + -
396B ILE* 3.8 23.3 - - + -
405B ILE* 4.0 17.7 - - + -
417B ILE* 3.8 27.1 - - + -
421B ILE* 4.5 3.1 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLY 2.8 17.8 + - - +
126B MET 3.6 0.4 - - - +
128B ILE* 1.3 78.9 - - - +
130B GLU* 1.3 56.7 + - - +
132B THR* 4.6 0.2 - - - -
133B LEU* 2.8 34.6 + - - +
376B LEU* 5.0 2.5 - - - -
421B ILE* 4.5 7.4 - - + +
424B HIS* 3.5 33.9 - - + -
427B PHE* 3.3 25.9 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B MET 3.0 16.6 + - - +
127B ALA* 3.3 7.5 + - - +
129B ALA* 1.3 75.9 - - - +
131B LYS* 1.3 66.1 + - - +
133B LEU* 4.6 0.2 - - - -
134B ALA* 2.9 35.0 + - - +
145B VAL* 3.6 8.1 - - + +
146B ASP* 3.4 6.1 + - - -
147B HIS* 3.0 64.0 + - + +
149B THR* 5.1 1.6 - - - +
177B LYS* 2.7 41.4 + - - +
424B HIS* 4.0 8.0 + - - -
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ALA 3.0 17.1 + - - +
128B ILE* 3.8 3.6 - - - +
130B GLU* 1.3 85.1 + - - +
132B THR* 1.3 59.9 + - - +
134B ALA* 3.6 4.6 - - - +
135B ALA* 3.1 27.4 + - - +
173B LEU* 2.8 30.6 + - + +
174B LYS* 4.7 9.1 + - - +
175B LEU* 3.8 21.8 - - + -
396B ILE* 4.7 16.8 + - + +
397B ASN* 6.1 0.4 - - - +
400B ALA* 4.5 20.4 - - + +
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 2.7 32.2 + - - +
131B LYS* 1.3 76.5 - - - +
133B LEU* 1.3 60.0 + - - +
135B ALA* 3.2 2.8 + - - +
136B GLN* 2.9 43.7 + - - +
376B LEU* 4.4 6.8 - - + +
396B ILE* 4.2 15.9 - - + +
400B ALA 3.5 17.4 + - - +
402B GLY 3.4 25.8 - - - +
427B PHE* 3.7 17.5 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA 6.1 0.2 - - - +
129B ALA 2.8 22.5 + - - +
130B GLU* 4.0 2.0 - - - +
132B THR* 1.3 72.0 - - - +
134B ALA* 1.3 56.9 + - - +
136B GLN* 3.3 2.1 + - - -
137B PHE* 2.8 61.3 + - + +
145B VAL* 4.1 11.2 - - + -
147B HIS* 5.8 0.9 - - + -
325B PHE* 3.6 30.7 - - + -
328B ARG* 3.9 9.2 - - + +
329B MET* 3.6 20.4 - - - -
424B HIS* 4.1 16.6 - - + -
425B GLY 4.5 2.2 - - - +
426B GLY* 4.3 9.6 - - - +
427B PHE* 3.5 20.8 - - + -
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 2.9 24.4 + - - +
131B LYS* 3.6 5.8 - - - +
133B LEU* 1.3 76.5 - - - +
135B ALA* 1.3 57.5 + - - +
138B ASN* 2.9 53.5 + - - +
145B VAL* 3.7 22.1 - - + +
177B LYS* 5.4 2.9 - - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS 3.1 11.2 + - - +
132B THR 3.6 0.4 - - - +
134B ALA* 1.3 79.6 - - - +
136B GLN* 1.3 61.9 + - - +
138B ASN 4.6 2.6 - - - +
139B ARG* 4.6 4.5 + - - -
400B ALA* 3.4 45.1 - - + +
401B ALA* 3.5 12.6 - - + +
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B THR* 2.9 27.5 + - - +
133B LEU 3.7 3.6 - - - +
135B ALA* 1.3 77.8 - - - +
137B PHE* 1.3 68.9 + - + +
139B ARG* 2.9 23.9 + - - -
328B ARG* 2.8 38.2 + - - +
373B PRO 4.6 7.0 + - - -
375B PHE 5.4 0.4 + - - -
401B ALA* 3.2 22.9 + - + +
402B GLY 2.9 27.1 + - - -
403B ASN* 4.9 4.2 - - - +
427B PHE* 4.1 8.0 - - - -
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 2.8 47.0 + - + +
136B GLN* 1.3 82.3 - - + +
138B ASN* 1.3 68.1 + - - +
139B ARG* 3.4 6.9 + - - +
144B ILE* 4.2 13.9 - - + -
145B VAL* 4.7 2.2 - - + -
314B TYR* 2.7 43.5 + + - +
321B GLU* 3.2 29.6 - - + -
324B GLU* 4.1 7.9 - - + -
325B PHE* 3.5 34.1 - + + -
328B ARG* 3.5 37.5 - - + -
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Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA* 2.9 35.2 + - - +
135B ALA 4.6 2.9 - - - +
137B PHE* 1.3 71.0 - - - +
139B ARG* 1.3 76.4 + - - +
142B HIS 3.6 2.9 - - - -
143B ASP* 3.7 31.0 + - - +
144B ILE* 3.0 9.6 + - - +
145B VAL* 2.9 47.0 + - - +
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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