Contacts of the helix formed by residues 199 - 214 (chain D) 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 PRO 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D PHE* 3.2 45.3 - - + +
89D VAL* 4.6 6.3 - - + -
90D TYR* 4.2 28.5 - - + +
197D LEU 4.1 4.3 - - - +
198D ALA* 1.3 86.7 - - + +
200D LEU* 1.3 57.6 + - + +
201D PRO* 2.7 6.6 - - - -
202D ILE* 2.8 5.0 + - + +
203D GLY 2.7 32.1 + - - -
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LEU* 3.7 25.4 - - + -
204B PHE* 5.5 7.2 - - + -
86C PHE* 3.4 8.9 - - + -
200C LEU* 3.5 34.5 - - + -
86D PHE* 3.4 32.1 - - + -
199D PRO* 1.3 79.7 - - + +
201D PRO* 1.4 69.9 - - + +
203D GLY* 3.8 1.1 - - - +
204D PHE* 3.1 52.0 + - + +
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Residues in contact with PRO 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.3 24.9 - - + -
87C VAL* 3.9 5.3 - - + +
90C TYR* 3.9 44.4 - - + -
178D THR* 3.8 20.0 - - + +
182D ALA* 5.1 2.9 - - + -
198D ALA* 4.6 12.6 - - + +
199D PRO* 2.7 6.3 - - + +
200D LEU* 1.4 85.3 - - + +
202D ILE* 1.3 53.9 + - - +
204D PHE* 3.4 3.8 + - - +
205D ALA* 2.6 33.6 + - - +
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Residues in contact with ILE 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ILE* 3.1 29.8 - - + -
89D VAL* 4.6 19.1 - - + -
98D GLY 5.7 0.9 - - - +
175D LEU* 3.7 13.2 - - + -
178D THR* 4.6 10.3 - - + -
179D VAL* 3.7 31.6 - - + +
182D ALA* 4.6 9.0 - - + -
197D LEU* 5.4 4.3 - - + -
198D ALA 4.0 16.8 + - - +
199D PRO* 2.8 7.4 + - + +
201D PRO* 1.3 73.2 - - - +
203D GLY* 1.3 80.0 - - - +
204D PHE 2.5 2.2 + - - -
205D ALA* 2.7 11.9 + - - +
206D VAL* 2.8 24.3 + - + +
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Residues in contact with GLY 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TRP* 6.4 0.7 - - - -
82D GLY* 3.1 33.9 - - - -
86D PHE* 3.5 21.9 - - - +
199D PRO 2.7 17.7 + - - -
200D LEU* 4.0 2.9 - - - -
202D ILE* 1.3 81.3 - - - +
204D PHE* 1.3 61.0 + - - +
207D PHE* 3.2 17.1 + - - +
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Residues in contact with PHE 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B PHE* 5.5 2.9 - + - -
79C TRP* 3.7 38.1 - + - -
83C GLY* 4.0 18.6 - - - -
86C PHE* 3.9 21.8 - + + -
87C VAL* 3.9 11.2 - - + -
200C LEU* 5.4 5.6 - - + -
204C PHE* 5.4 5.6 - + - -
79D TRP* 3.9 24.9 - + - -
200D LEU* 3.1 43.5 + - + +
201D PRO 3.4 3.8 - - - +
202D ILE 2.5 4.6 + - - -
203D GLY* 1.3 69.9 - - - +
205D ALA* 1.3 57.5 + - - +
206D VAL 2.9 5.3 + - - -
207D PHE* 3.1 16.4 + + - -
208D MET* 2.8 36.8 + - + +
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Residues in contact with ALA 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C VAL* 3.9 11.2 - - + +
174D VAL* 4.3 5.7 - - + +
175D LEU* 4.5 13.8 - - - +
178D THR* 3.4 32.8 - - + +
201D PRO 2.6 20.7 + - - +
202D ILE* 2.7 12.7 + - + -
204D PHE* 1.3 71.8 - - - +
206D VAL* 1.4 56.4 + - - +
208D MET* 4.2 3.1 - - - -
209D VAL* 3.3 27.6 + - - +
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D PHE* 5.7 1.3 - - + -
81D PHE* 3.8 9.0 - - + +
82D GLY* 3.8 17.7 - - - +
85D ILE* 4.0 16.2 - - + -
175D LEU* 3.8 20.6 - - + -
202D ILE* 2.8 33.7 + - + +
203D GLY 3.8 2.9 - - - +
205D ALA* 1.4 75.1 - - - +
207D PHE* 1.3 67.1 + - - +
208D MET 3.2 0.4 - - - -
209D VAL* 3.3 2.9 + - - +
210D HIS* 2.9 50.6 + - + +
221D ILE* 4.6 9.2 - - + -
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Residues in contact with PHE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C TRP* 4.0 18.4 - + - -
75D LEU* 3.9 18.8 - - + -
78D ALA* 3.6 39.3 - - + -
79D TRP* 3.3 61.0 - + + -
82D GLY* 3.7 7.8 - - - -
203D GLY 3.2 12.0 + - - +
204D PHE* 3.4 17.0 - + - +
206D VAL* 1.3 78.6 - - - +
208D MET* 1.3 84.1 + - + +
210D HIS* 3.1 12.4 + - - +
211D LEU* 3.1 19.7 + - + +
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Residues in contact with MET 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE* 3.7 9.7 - - + +
79C TRP 3.3 28.0 - - - +
80C ALA* 3.6 12.1 - - - +
83C GLY* 3.5 26.7 - - - +
84C MET* 3.5 35.0 - - + -
87C VAL* 4.5 2.2 - - + -
204D PHE* 2.8 27.9 + - + +
205D ALA* 4.6 3.8 - - - +
207D PHE* 1.3 110.7 - - + +
209D VAL* 1.3 64.7 + - + +
211D LEU* 3.0 28.6 + - + +
212D ALA 3.4 8.5 + - - -
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE* 4.1 14.6 - - + -
171D GLY* 3.6 38.6 - - - +
174D VAL* 3.8 20.4 - - + -
175D LEU 4.9 0.4 - - - +
205D ALA 3.3 17.7 + - - +
206D VAL 3.3 7.7 + - - +
208D MET* 1.3 76.3 - - - +
210D HIS* 1.4 58.1 + - - +
212D ALA* 3.4 1.7 + - - +
213D THR* 2.9 43.9 + - + +
219D THR* 4.0 3.1 - - + -
221D ILE* 3.8 27.1 - - + -
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Residues in contact with HIS 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA* 3.8 17.5 - - + -
81D PHE* 3.1 54.2 - + + +
206D VAL* 2.9 44.8 + - + +
207D PHE 3.1 7.3 + - - +
209D VAL* 1.4 76.9 - - - +
211D LEU* 1.3 63.3 + - - +
214D ILE* 3.0 42.5 + - + +
218D GLY 4.4 1.0 + - - -
219D THR* 3.7 42.6 + - + +
220D GLY 5.0 1.7 + - - -
221D ILE* 4.6 10.0 - - + +
225D ARG* 5.3 0.4 - - - -
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C THR* 2.4 36.3 + - + +
61C GLY* 5.8 0.3 - - - -
72C VAL* 3.0 43.5 - - + +
76C GLY 3.6 19.1 - - - +
79C TRP* 4.0 6.5 - - + -
80C ALA* 3.9 10.3 - - + +
75D LEU* 3.9 13.7 - - + -
78D ALA* 3.8 17.3 - - + -
207D PHE* 3.1 15.3 + - + +
208D MET* 3.0 38.8 + - + +
210D HIS* 1.3 77.7 - - - +
212D ALA* 1.3 56.0 + - - +
214D ILE* 5.3 0.2 - - - +
215D PRO* 4.3 8.5 - - - +
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Residues in contact with ALA 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TYR* 4.6 4.0 + - + -
54C ILE* 3.5 35.4 - - + +
57C ALA* 3.3 30.0 - - + +
58C THR* 2.6 14.2 + - - +
141C MET* 4.8 0.2 - - - +
208D MET 3.4 1.4 + - - +
209D VAL 3.4 7.1 + - - +
210D HIS 3.2 0.2 - - - -
211D LEU* 1.3 76.5 - - - +
213D THR* 1.3 64.8 + - - +
214D ILE 3.7 0.7 - - - -
215D PRO* 3.8 8.8 - - - +
216D ILE* 4.6 10.4 - - - +
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Residues in contact with THR 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TYR* 4.6 10.4 + - - -
54C ILE* 5.7 0.2 - - - +
167D ALA* 4.5 27.1 + - + +
168D GLU* 4.1 7.4 - - - +
171D GLY* 5.1 0.2 - - - -
209D VAL* 2.9 28.5 + - + +
212D ALA* 1.3 79.9 - - - +
214D ILE* 1.3 67.6 + - - +
215D PRO* 3.3 2.9 - - - -
216D ILE* 3.4 7.2 + - + +
217D THR* 3.1 31.9 + - + +
218D GLY 3.4 0.7 + - - -
219D THR* 2.8 24.0 + - + +
221D ILE* 5.6 0.4 - - + -
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Residues in contact with ILE 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C VAL* 5.9 2.0 - - + -
74D LEU* 3.2 47.8 - - + +
77D ILE* 4.2 26.5 - - + -
78D ALA* 4.2 3.8 - - + +
210D HIS* 3.0 38.3 + - + +
211D LEU* 5.3 1.1 - - - +
213D THR* 1.3 75.9 - - - +
215D PRO* 1.3 71.4 - - + +
218D GLY* 3.0 30.5 + - - +
219D THR* 2.6 16.3 + - - +
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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
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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