Contacts of the helix formed by residues 120 - 142 (chain A) in PDB entry 2DFM
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 PRO 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.9 16.4 - - + -
117A LEU* 5.6 1.1 - - + -
118A THR 3.5 7.4 - - - +
119A ILE* 1.3 97.5 - - + +
121A ILE* 1.3 60.6 + - - +
122A LEU* 3.1 12.6 - - + +
123A TYR* 2.9 48.1 + - + +
124A VAL* 3.2 7.6 + - - +
317A PRO* 5.9 0.4 - - + -
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE 3.4 3.8 + - - +
120A PRO* 1.3 68.8 - - - +
122A LEU* 1.3 72.6 + - + +
124A VAL* 2.9 8.0 + - + +
125A LYS* 2.8 49.0 + - + +
217A LEU* 4.1 25.6 - - + -
275A THR* 5.7 0.7 - - - -
276A PRO* 4.1 30.3 - - + -
305A PHE* 3.9 17.3 - - + -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 4.4 9.6 - - + -
121A ILE* 1.3 88.0 - - + +
123A TYR* 1.3 66.0 + - + +
125A LYS* 3.3 11.8 + - - +
126A VAL* 2.9 33.2 + - + +
308A GLU* 3.5 24.9 - - - +
309A LEU* 4.9 0.6 - - - +
315A GLN* 4.5 15.5 - - - +
316A LEU* 6.3 1.1 - - + -
317A PRO* 4.4 26.9 - - + -
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Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 6.2 0.9 - + - -
119A ILE* 3.4 22.7 - - + -
120A PRO* 2.9 42.6 + - + +
122A LEU* 1.3 75.7 - - + +
124A VAL* 1.3 59.3 + - - +
126A VAL* 3.2 6.1 + - + +
127A TYR* 2.7 56.7 + + + -
157A PRO 5.7 3.8 - - - -
160A ALA* 5.3 14.8 - - + -
316A LEU* 5.4 4.3 - - + -
317A PRO* 3.0 47.9 - - + +
318A ASN* 4.9 2.1 + - - +
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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
----------------------------------------------------------
119A ILE* 3.3 32.8 - - + +
120A PRO 3.2 7.8 + - - +
121A ILE* 2.9 15.0 + - + +
123A TYR* 1.3 76.4 - - - +
125A LYS* 1.3 58.4 + - - +
127A TYR* 4.0 0.5 - - - +
128A MET* 2.9 31.9 + - + +
213A LEU* 3.3 32.3 - - + -
216A LEU* 4.1 22.7 - - + +
217A LEU* 4.2 18.2 - - + -
305A PHE* 4.3 7.4 - - + -
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 2.8 37.8 + - - +
122A LEU* 3.6 9.0 - - - +
124A VAL* 1.3 74.1 - - - +
126A VAL* 1.3 66.0 + - - +
129A TYR* 2.9 24.1 + - - +
276A PRO* 6.1 2.0 - - - +
278A GLU* 5.6 3.8 + - - -
305A PHE* 2.8 61.8 + - + +
306A PHE* 3.2 8.9 - - + -
308A GLU* 3.4 43.6 + - + +
309A LEU* 3.9 19.3 - - + -
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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 LEU* 2.9 21.0 + - + +
123A TYR* 3.2 9.2 + - + +
125A LYS* 1.3 76.3 - - - +
127A TYR* 1.3 65.4 + - + +
129A TYR* 3.9 1.0 - - - +
130A GLN* 3.1 46.4 + - + +
160A ALA* 3.5 15.7 - - + +
309A LEU* 4.0 18.4 - - + -
316A LEU* 4.5 10.1 - - + -
322A LEU* 3.6 33.4 - - + -
325A LEU* 5.5 2.6 - - + +
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Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 4.6 11.2 - - + -
108A VAL* 4.9 11.1 - - + +
119A ILE* 3.5 18.2 - - + +
123A TYR* 2.7 62.2 + + + +
124A VAL* 4.0 4.7 - - - +
126A VAL* 1.3 80.9 - - + +
128A MET* 1.3 64.9 + - + +
130A GLN* 3.3 0.3 + - - +
131A LEU* 3.0 17.9 + - - +
153A LEU* 6.0 0.9 - - + -
155A VAL* 3.5 41.9 - - + +
157A PRO* 5.9 1.2 - - - +
160A ALA* 4.6 14.4 - - - -
162A LEU* 3.1 38.3 - - + +
216A LEU* 4.4 15.5 - - + -
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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
----------------------------------------------------------
124A VAL* 2.9 24.3 + - + +
125A LYS* 4.9 0.2 - - - -
127A TYR* 1.3 79.4 - - - +
129A TYR* 1.3 64.3 + - - +
131A LEU* 3.0 13.5 + - + +
132A PHE* 2.9 52.9 + - + -
153A LEU* 5.9 1.3 - - - -
209A ALA* 3.3 29.2 - - + +
212A VAL* 4.1 14.4 - - - -
213A LEU* 3.4 47.8 - - + -
216A LEU* 4.7 6.7 - - - -
305A PHE* 5.3 0.2 - - + -
306A PHE* 3.8 17.0 - - + -
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Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS 2.9 19.9 + - - +
126A VAL 3.9 2.7 - - - +
128A MET* 1.3 75.3 - - - +
130A GLN* 1.3 65.3 + - - +
132A PHE* 3.2 6.9 + - - +
133A ARG* 3.0 32.9 + - + +
301A CYS* 3.3 39.1 - - + +
306A PHE* 3.3 30.7 - + + -
309A LEU* 3.4 11.9 - - + -
310A ARG* 4.3 9.8 + - - -
325A LEU* 3.2 51.5 + - + -
326A PHE* 4.7 3.0 - + - -
328A PHE* 3.0 30.0 - + - -
343A LEU* 4.4 6.9 + - - +
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Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 2.7 33.6 - - - +
126A VAL* 3.1 29.1 + - - +
127A TYR* 3.8 3.6 - - - +
128A MET 3.2 0.4 - - - -
129A TYR* 1.3 79.2 - - - +
131A LEU* 1.3 62.9 + - - +
133A ARG* 3.1 4.1 + - - +
134A SER* 3.0 25.8 + - - -
160A ALA 2.7 28.9 + - - -
161A VAL* 3.4 8.8 - - - +
162A LEU* 2.7 35.5 + - + +
323A PRO* 4.6 6.7 - - - +
325A LEU* 4.1 22.6 - - + +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR 3.0 14.5 + - - +
128A MET* 3.0 21.5 + - + +
130A GLN* 1.3 77.0 - - - +
132A PHE* 1.3 54.5 + - - +
134A SER* 3.2 4.8 + - - -
135A LEU* 2.7 60.7 + - + +
148A ILE* 4.2 13.7 - - + -
153A LEU* 3.4 42.4 - - + -
162A LEU* 4.5 9.8 - - + +
164A LEU* 4.3 13.0 - - + -
209A ALA* 3.8 30.3 - - + -
212A VAL* 4.9 2.5 - - + -
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Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 2.9 58.6 + - + -
129A TYR* 3.6 2.0 - - - +
131A LEU* 1.3 74.4 - - + +
133A ARG* 1.3 54.6 + - - +
135A LEU* 3.2 9.5 + - + -
136A ALA* 2.7 33.3 + - - +
206A VAL* 4.8 5.2 - - + -
209A ALA* 3.9 17.9 - - + -
282A LEU* 4.5 3.1 - - + -
286A LEU* 3.5 35.9 - - + -
297A PRO* 3.4 24.3 - - + +
300A ALA* 3.6 28.0 - - + -
301A CYS* 3.3 22.2 - - - -
306A PHE* 4.2 13.5 - + - -
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Residues in contact with ARG 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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72A HIS* 4.0 8.9 - - - +
73A CYS* 4.2 6.9 - - - -
74A ASN* 3.8 22.4 - - - +
129A TYR* 3.0 42.8 + - + +
130A GLN* 3.1 7.4 + - - +
132A PHE* 1.3 74.3 - - - +
134A SER* 1.3 66.3 + - - +
136A ALA* 2.9 7.1 + - - +
137A TYR* 2.8 23.9 + - - +
301A CYS* 4.1 11.0 - - - -
324A PRO 3.6 14.3 + - - -
325A LEU* 3.8 12.9 + - - +
327A ASN* 2.8 49.2 + - - -
328A PHE* 3.3 19.2 - - + +
332A GLU* 2.9 34.2 + - - +
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A HIS* 4.6 1.8 - - - -
74A ASN* 2.8 39.8 + - - +
75A ILE* 4.1 12.8 - - - -
130A GLN 3.0 9.9 + - - -
131A LEU* 3.5 9.1 + - - +
133A ARG* 1.3 75.8 - - - +
135A LEU* 1.3 69.8 + - - +
137A TYR* 3.2 8.2 + - - +
138A ILE* 3.0 28.6 + - - +
162A LEU* 5.2 1.2 - - - +
164A LEU* 4.3 14.1 + - - +
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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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131A LEU* 2.7 49.5 + - + +
132A PHE* 3.5 17.0 - - + +
134A SER* 1.3 78.8 - - - +
136A ALA* 1.3 65.7 + - - +
138A ILE* 3.2 7.6 - - + +
139A HIS* 2.9 43.0 + - + +
148A ILE* 3.5 28.3 - - + -
164A LEU* 4.5 6.3 - - + -
205A ASP* 4.0 21.8 - - + +
206A VAL* 4.6 3.1 - - + +
209A ALA* 4.1 15.9 - - + -
297A PRO* 3.7 11.9 - - + -
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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 PHE 2.7 16.0 + - - +
133A ARG* 2.9 11.4 + - - +
135A LEU* 1.3 72.6 - - - +
137A TYR* 1.3 62.6 + - - +
139A HIS* 3.8 1.6 - - - +
140A SER* 3.2 22.5 + - - -
297A PRO* 3.3 22.4 - - + +
298A LEU* 4.1 20.2 - - + +
301A CYS* 5.6 0.2 - - - -
328A PHE* 6.2 0.4 - - + -
332A GLU* 4.4 21.4 - - + +
335A ILE* 5.9 1.1 - - + -
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Residues in contact with TYR 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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69A LYS 3.9 5.4 + - - -
70A LEU* 3.0 34.9 - - + +
71A ASP* 3.1 31.6 + - - +
72A HIS* 3.8 24.0 - - + +
75A ILE* 3.2 26.9 - - + -
133A ARG 2.8 12.2 + - - +
134A SER* 3.4 9.4 - - - +
136A ALA* 1.3 73.8 - - - +
138A ILE* 1.3 63.1 + - - +
140A SER* 2.6 31.6 + - - -
141A GLN* 3.7 2.8 + - - +
329A SER* 5.2 4.5 - - - -
331A GLY* 5.6 2.2 - - - -
332A GLU* 3.8 22.9 - - + +
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Residues in contact with ILE 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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70A LEU* 3.6 29.6 - - + -
75A ILE* 3.8 11.9 - - + -
134A SER 3.0 12.7 + - - +
135A LEU* 3.2 18.6 - - + +
137A TYR* 1.3 76.8 - - + +
139A HIS* 1.3 81.3 + - + +
141A GLN* 3.0 13.2 + - - +
143A VAL* 2.7 44.9 + - + +
145A HIS* 4.0 27.4 - - + +
164A LEU* 4.5 10.3 - - + -
167A PHE* 4.5 9.9 - - + -
205A ASP* 4.1 2.5 - - - +
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Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 2.9 34.9 + - + +
136A ALA* 3.8 4.5 - - - +
138A ILE* 1.3 88.2 - - + +
140A SER* 1.3 58.1 + - - +
142A GLY* 2.6 24.7 + - - -
143A VAL 3.4 18.6 - - - -
202A SER* 3.7 41.1 + - - +
205A ASP* 3.1 29.5 + - + +
206A VAL* 4.6 7.2 - - + +
297A PRO* 3.5 21.8 - - + +
335A ILE* 6.3 2.7 - - + -
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA 3.2 12.8 + - - -
137A TYR* 2.6 25.7 + - - -
139A HIS* 1.3 76.6 - - - +
141A GLN* 1.3 61.3 + - - +
142A GLY 3.5 0.2 + - - -
331A GLY* 3.4 28.6 + - - -
332A GLU 5.3 1.1 - - - -
334A SER* 5.0 7.0 - - - -
335A ILE* 5.8 4.3 - - - -
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 4.6 30.4 - - + +
70A LEU* 5.1 10.0 - - + +
137A TYR 4.6 2.5 - - - +
138A ILE* 3.0 15.2 + - - +
139A HIS 3.0 0.4 - - - -
140A SER* 1.3 80.1 + - - +
142A GLY* 1.3 57.1 + - - +
143A VAL* 3.6 23.7 - - + +
172A GLN* 4.8 12.9 + - - +
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A HIS* 2.6 21.8 + - - -
140A SER 3.2 0.9 - - - -
141A GLN* 1.3 73.5 - - - +
143A VAL* 1.3 63.5 + - - +
144A CYS* 3.8 0.7 + - - +
172A GLN* 4.3 3.1 - - - -
173A LEU* 3.0 36.3 + - - +
202A SER* 6.1 2.2 - - - -
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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