Contacts of the helix formed by residues 198 - 218 (chain A) in PDB entry 2B5F
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 ALA 198 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 4.6 7.7 - - + +
182A ALA* 4.3 28.3 - - - +
184A ASP* 4.9 9.9 + - - +
194A VAL* 6.5 1.6 - - + -
197A LEU* 1.3 73.7 - - - +
199A PRO* 1.3 70.4 - - + +
201A PRO* 4.5 4.3 - - - +
202A ILE* 4.2 20.3 + - - +
90B TYR* 4.9 6.3 + - - -
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Residues in contact with PRO 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 3.1 42.6 - - + +
89A VAL* 4.5 9.9 - - + -
90A TYR* 3.8 36.8 - - + +
196A ILE* 5.6 3.4 - - + -
197A LEU 2.4 22.7 - - - +
198A ALA* 1.3 88.6 - - + +
200A LEU* 1.3 52.4 + - - +
201A PRO 3.1 3.2 - - - -
202A ILE* 3.2 2.9 + - + +
203A GLY* 2.6 34.8 + - - -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 3.4 31.7 - - + -
196A ILE* 5.6 7.9 - - + -
197A LEU* 2.8 16.2 + - + +
199A PRO* 1.3 73.4 - - - +
201A PRO* 1.4 66.8 - - + +
203A GLY* 3.8 0.8 - - - +
204A PHE* 3.1 52.3 + - + +
86B PHE* 3.5 9.6 - - + -
200B LEU* 3.4 35.4 - - + -
200C LEU* 3.7 24.9 - - + -
204C PHE* 5.4 7.9 - - + -
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Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 3.8 20.3 - - + +
182A ALA* 5.1 3.8 - - + -
197A LEU* 3.6 13.9 - - + +
198A ALA 4.5 7.2 - - - +
200A LEU* 1.4 87.9 - - + +
202A ILE* 1.3 54.7 + - - +
204A PHE* 3.4 3.8 + - - +
205A ALA* 2.6 33.6 + - - +
86B PHE* 3.3 24.0 - - + -
87B VAL* 3.9 5.6 - - + +
90B TYR* 3.9 45.1 - - + +
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Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 3.1 30.5 - - + -
89A VAL* 4.6 20.9 - - + -
98A GLY 5.7 1.3 - - - +
175A LEU* 3.7 13.5 - - + -
178A THR* 4.6 10.5 - - + -
179A VAL* 3.7 31.2 - - + +
182A ALA* 4.6 9.6 - - + -
198A ALA 4.2 14.8 + - - +
199A PRO* 3.2 5.5 + - + +
201A PRO* 1.3 75.6 - - - +
203A GLY* 1.3 79.4 - - - +
204A PHE 2.5 2.6 + - - -
205A ALA* 2.7 12.1 + - - +
206A VAL* 2.8 24.6 + - + +
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Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 6.4 0.7 - - - -
82A GLY* 3.1 34.3 - - - -
86A PHE* 3.5 16.4 - - - +
199A PRO 2.6 23.5 + - - -
200A LEU* 3.9 2.5 - - - -
202A ILE* 1.3 81.3 - - - +
204A PHE* 1.3 61.1 + - - +
207A PHE* 3.2 17.6 + - - +
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Residues in contact with PHE 204 (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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79A TRP* 3.9 24.7 - + - -
200A LEU* 3.1 42.4 + - + +
201A PRO 3.4 4.5 - - - +
202A ILE 2.5 4.8 + - - -
203A GLY* 1.3 71.4 - - - +
205A ALA* 1.3 57.3 + - - +
206A VAL 2.9 5.1 + - - -
207A PHE* 3.1 17.1 + + - -
208A MET* 2.8 36.9 + - + +
79B TRP* 3.7 37.5 - + - -
83B GLY* 4.0 19.5 - - - -
86B PHE* 3.9 23.8 - + + -
87B VAL* 3.9 11.0 - - + -
200B LEU* 5.4 5.2 - - + -
204B PHE* 5.4 6.3 - + - -
204C PHE* 5.6 3.6 - + - -
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Residues in contact with ALA 205 (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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174A VAL* 4.3 5.8 - - + +
175A LEU* 4.5 13.5 - - - +
178A THR* 3.4 32.8 - - + +
201A PRO 2.6 22.0 + - - +
202A ILE* 2.7 13.3 + - + -
204A PHE* 1.3 70.1 - - - +
206A VAL* 1.4 57.0 + - - +
208A MET* 4.2 4.2 - - - +
209A VAL* 3.3 27.2 + - - +
87B VAL* 4.0 10.9 - - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 5.7 1.8 - - + -
81A PHE* 3.8 8.7 - - + +
82A GLY* 3.8 18.2 - - - +
85A ILE* 4.0 16.8 - - + -
175A LEU* 3.8 20.2 - - + -
202A ILE* 2.8 34.2 + - + +
203A GLY 3.8 2.2 - - - +
205A ALA* 1.4 75.3 - - - +
207A PHE* 1.3 67.1 + - - +
208A MET 3.2 0.2 - - - -
209A VAL* 3.3 3.1 + - - +
210A HIS* 2.9 50.7 + - + +
221A ILE* 4.6 9.4 - - + -
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Residues in contact with PHE 207 (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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75A LEU* 3.9 14.4 - - + -
78A ALA* 3.6 39.9 - - + -
79A TRP* 3.3 59.9 - + + -
82A GLY* 3.7 8.0 - - - -
203A GLY 3.2 11.9 + - - +
204A PHE* 3.4 16.6 - + - +
206A VAL* 1.3 79.6 - - - +
208A MET* 1.3 84.8 + - + +
210A HIS* 3.1 12.6 + - - +
211A LEU* 3.1 18.9 + - + +
79B TRP* 4.0 23.1 - + - -
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Residues in contact with MET 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A VAL* 5.7 0.2 - - + -
204A PHE* 2.8 28.0 + - + +
205A ALA* 4.6 4.3 - - - +
207A PHE* 1.3 111.2 - - + +
209A VAL* 1.3 64.5 + - + +
211A LEU* 3.0 29.7 + - + +
212A ALA 3.4 8.5 + - - -
54B ILE* 3.8 11.2 - - + +
79B TRP* 3.4 27.8 - - + +
80B ALA* 3.7 12.6 - - - +
83B GLY* 3.5 15.0 - - - +
84B MET* 3.5 43.5 - - - -
87B VAL* 4.5 2.5 - - + -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLY* 3.6 39.9 - - - +
174A VAL* 3.8 19.7 - - + -
175A LEU 4.9 0.2 - - - +
205A ALA 3.3 18.8 + - - +
206A VAL 3.3 7.6 + - - +
208A MET* 1.3 74.0 - - - +
210A HIS* 1.4 57.3 + - - +
212A ALA* 3.4 1.2 + - - +
213A THR* 2.9 43.5 + - - +
219A THR* 3.7 16.8 - - + -
221A ILE* 3.8 13.0 - - + -
54B ILE* 4.2 14.1 - - + -
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Residues in contact with HIS 210 (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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78A ALA* 3.8 17.0 - - + -
81A PHE* 3.1 55.8 - + + +
206A VAL* 2.9 44.8 + - + +
207A PHE 3.1 7.6 + - - +
209A VAL* 1.4 77.2 - - - +
211A LEU* 1.3 63.1 + - - +
214A ILE* 3.0 40.8 + - + +
218A GLY 4.1 4.9 + - - -
219A THR* 3.8 40.4 + - + +
220A GLY 5.3 1.0 + - - -
221A ILE* 4.6 7.1 - - + +
225A ARG* 5.3 0.2 - - - -
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Residues in contact with LEU 211 (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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75A LEU* 3.9 14.8 - - + -
78A ALA* 3.8 17.5 - - + -
207A PHE* 3.1 16.4 + - + +
208A MET* 3.0 39.5 + - + +
210A HIS* 1.3 78.6 - - - +
212A ALA* 1.3 56.3 + - - +
214A ILE* 5.3 0.4 - - - +
215A PRO* 4.4 8.0 - - - +
58B THR* 2.5 29.6 + - + +
72B VAL* 3.1 42.5 - - + +
76B GLY 3.7 19.7 - - - +
79B TRP* 4.0 3.1 - - + -
80B ALA* 3.9 11.2 - - + +
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Residues in contact with ALA 212 (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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208A MET 3.4 6.0 + - - +
209A VAL 3.4 6.8 + - - +
210A HIS 3.2 0.2 - - - -
211A LEU* 1.3 77.6 - - - +
213A THR* 1.3 64.8 + - - +
214A ILE 3.7 0.4 - - - -
215A PRO* 4.0 8.5 - - - +
216A ILE* 4.9 7.3 - - - +
53B TYR* 4.6 5.4 + - + -
54B ILE* 3.6 30.5 - - + +
57B ALA* 3.4 28.7 - - + +
58B THR* 2.7 14.4 + - - +
141B MET* 5.5 2.4 - - - +
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Residues in contact with THR 213 (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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167A ALA* 4.5 25.9 + - + +
168A GLU* 4.1 10.1 - - - +
171A GLY* 5.1 0.7 - - - -
209A VAL* 2.9 25.0 + - + +
212A ALA* 1.3 80.1 - - - +
214A ILE* 1.3 67.8 + - - +
215A PRO* 3.2 2.9 - - - -
216A ILE* 3.0 16.0 + - + -
217A THR* 3.1 13.9 + - - +
218A GLY 3.5 0.9 + - - -
219A THR* 2.6 38.5 + - + +
221A ILE* 5.6 0.4 - - + -
53B TYR* 4.7 8.2 + - - -
54B ILE* 5.9 0.2 - - - +
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Residues in contact with ILE 214 (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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74A LEU* 3.4 41.3 - - + +
77A ILE* 4.2 26.0 - - + -
78A ALA* 4.2 11.9 - - + +
156A ALA* 5.4 0.9 - - - +
210A HIS* 3.0 44.5 + - + +
211A LEU* 5.3 0.7 - - - +
213A THR* 1.3 76.7 - - - +
215A PRO* 1.3 70.2 - - + +
218A GLY* 3.1 36.1 + - - +
219A THR* 3.0 3.0 + - - -
72B VAL* 5.9 3.6 - - + -
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Residues in contact with PRO 215 (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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74A LEU* 5.5 5.2 - - + -
156A ALA* 3.1 23.9 - - - +
159A TYR* 3.6 20.1 + - - +
211A LEU 4.4 7.6 - - - +
212A ALA 4.0 12.8 - - - +
213A THR 3.5 3.4 - - - -
214A ILE* 1.3 98.8 - - + +
216A ILE* 1.3 56.7 + - + +
61B GLY* 3.6 33.9 - - - +
64B LYS* 6.1 0.4 - - + +
65B GLU* 5.4 5.2 - - - +
72B VAL* 6.2 2.0 - - + -
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Residues in contact with ILE 216 (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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155A VAL* 5.2 0.5 - - - +
156A ALA* 3.2 21.8 + - - +
159A TYR* 3.6 35.7 - - + +
163A THR* 3.6 28.9 - - + -
164A ALA* 4.1 7.4 - - - -
167A ALA* 3.8 24.5 - - + -
212A ALA 4.9 7.0 - - - +
213A THR* 3.0 15.4 + - + +
215A PRO* 1.3 78.7 - - + +
217A THR* 1.3 85.3 + - + +
53B TYR* 6.0 0.7 - - - +
140B PHE* 5.7 0.9 - - + -
141B MET* 4.0 20.6 - - + -
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Residues in contact with THR 217 (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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153A ASN* 3.6 16.6 + - - +
154A SER 3.1 28.8 - - - +
155A VAL* 3.9 5.4 - - - -
156A ALA* 4.7 2.0 - - - +
164A ALA* 3.3 34.1 - - + +
168A GLU* 2.8 27.5 + - - +
213A THR* 3.1 4.0 + - - +
216A ILE* 1.3 92.8 - - + +
218A GLY* 1.3 54.6 + - - +
219A THR* 2.6 17.2 + - - -
245A PHE* 3.7 16.0 - - + -
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Residues in contact with GLY 218 (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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81A PHE* 5.7 1.4 - - - -
152A ALA 5.6 4.0 - - - -
153A ASN* 4.3 5.3 + - - -
156A ALA* 5.7 0.6 - - - +
210A HIS* 4.1 5.4 + - - -
213A THR 3.5 0.2 + - - -
214A ILE* 3.1 35.6 + - - +
216A ILE 3.8 0.2 - - - -
217A THR* 1.3 74.0 - - - +
219A THR* 1.3 74.0 + - - +
225A ARG* 4.8 6.6 + - - -
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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