Contacts of the strand formed by residues 159 - 167 (chain E) in PDB entry 3RBQ
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 PHE 159 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E ILE* 4.0 31.9 - - + -
88E PHE* 4.3 2.2 - + - -
149E PHE* 3.8 20.0 - + - -
156E VAL* 3.7 20.2 + - + -
157E ASN 4.3 0.7 - - - -
158E ASN* 1.3 77.0 - - - +
160E ARG* 1.3 61.7 + - - +
178E HIS* 3.8 3.8 + - - +
179E PHE* 3.0 68.1 + + + +
180E GLY 5.7 1.0 + - - -
182E CYS* 3.8 20.4 - - - -
220E TYR* 3.9 41.3 - + + -
221E PHE 3.3 14.4 - - - -
222E VAL* 3.7 11.4 - - + +
227E VAL* 5.0 0.4 - - + -
228E MET* 5.4 0.4 - - - -
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Residues in contact with ARG 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C HIS* 5.8 4.4 - - - -
213C GLU* 5.2 1.8 + - - -
62E PRO* 3.3 32.8 - - - +
66E LEU* 4.1 13.7 - - - +
158E ASN 4.1 5.8 - - - +
159E PHE* 1.3 77.1 - - - +
161E MET* 1.3 63.0 + - - +
162E ILE* 4.0 12.8 - - + +
176E ASP* 2.7 38.0 + - - +
177E PHE 3.2 16.4 - - - +
178E HIS* 3.6 28.0 + - - +
179E PHE* 4.2 4.5 - - - -
219E PHE 3.7 0.5 - - - +
220E TYR* 3.3 4.0 - - - +
221E PHE* 2.7 47.8 + - + +
224E ASP* 3.4 16.4 + - - -
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Residues in contact with MET 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E ARG* 1.3 73.6 - - - +
162E ILE* 1.3 72.1 + - - +
163E GLU* 3.6 23.6 - - + +
175E PHE 3.6 1.6 - - - +
176E ASP* 3.6 1.7 - - - +
177E PHE* 2.8 75.8 + - + +
179E PHE* 4.0 10.9 - - + -
192E HIS* 3.9 13.9 - - - +
194E TYR* 3.5 21.8 - - - +
218E SER* 4.1 4.7 - - - -
219E PHE 3.3 7.6 - - - +
220E TYR* 3.5 43.7 - - + -
502K ALA* 5.5 3.6 - - - -
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Residues in contact with ILE 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E PRO* 3.7 27.4 - - + -
65E VAL* 3.9 17.7 - - + -
66E LEU* 3.6 31.0 - - + -
160E ARG* 4.0 10.5 - - - +
161E MET* 1.3 72.6 - - - +
163E GLU* 1.3 62.1 + - - +
164E ARG* 4.1 10.8 - - + -
174E SER* 3.7 20.0 - - - +
175E PHE 3.3 4.3 - - - +
176E ASP* 3.7 22.9 - - + +
219E PHE* 2.8 44.5 + - - +
221E PHE* 3.8 15.2 - - + -
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Residues in contact with GLU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E MET* 3.6 24.7 - - + +
162E ILE* 1.3 74.9 - - - +
164E ARG* 1.3 61.7 + - - +
165E HIS* 2.8 31.9 + - + +
174E SER* 3.3 1.2 - - - -
175E PHE* 2.7 49.2 + - + +
194E TYR* 2.9 27.1 + - - -
216E SER* 4.5 3.6 - - - -
217E ASP 3.3 5.6 - - - +
218E SER* 2.6 28.2 + - - +
500K DAO 3.4 11.1 - - - +
501K GLY 3.2 11.6 + - - -
502K ALA 4.8 0.2 + - - -
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Residues in contact with ARG 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ASP* 3.0 20.7 + - - +
98D SER* 5.4 0.4 - - - -
65E VAL 3.3 23.4 + - - -
66E LEU* 3.1 29.1 + - - +
67E GLY 3.8 2.0 - - - -
68E LEU* 2.6 26.7 + - - +
69E GLN* 4.6 0.2 - - - +
162E ILE* 4.1 9.3 - - + +
163E GLU* 1.3 75.0 - - - +
165E HIS* 1.3 61.2 + - - +
166E TYR* 2.9 37.9 + - + +
171E LEU* 3.8 11.5 - - + +
173E LYS 3.7 3.8 - - - -
174E SER* 2.9 37.8 + - - +
216E SER* 3.1 4.5 - - - -
217E ASP* 2.9 35.7 + - + +
219E PHE* 4.2 18.2 - - + -
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Residues in contact with HIS 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLU* 2.8 33.5 + - + -
164E ARG* 1.3 79.4 - - - +
166E TYR* 1.3 55.7 + - - +
171E LEU* 3.6 4.9 - - - +
172E LEU* 2.7 39.0 + - + -
173E LYS 2.9 13.3 + - - +
175E PHE* 3.8 21.6 - + - -
214E THR* 5.4 3.3 - - + +
215E GLN 3.5 4.7 - - - +
216E SER* 3.6 7.0 - - - -
234E TYR* 3.2 34.8 + + - -
236E TYR* 5.8 0.6 + - - -
500K DAO 3.7 49.2 - - + +
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Residues in contact with TYR 166 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E LEU* 3.3 10.6 + - - +
69E GLN* 3.4 15.7 - - - -
70E ARG* 3.4 33.2 + - - -
71E ILE* 3.7 35.2 - - + +
164E ARG* 2.9 57.3 + - + -
165E HIS* 1.3 76.0 - - - +
167E PHE* 1.3 59.4 + - - +
168E ARG 4.1 0.4 - - - +
169E ASN 4.6 10.3 - - - +
170E GLN 3.2 8.5 - - - +
171E LEU* 3.6 28.7 - - + -
172E LEU* 3.8 5.6 - - - +
213E GLU 3.7 0.9 - - - +
214E THR* 3.2 4.2 - - - +
215E GLN* 2.8 34.5 + - + +
217E ASP* 4.4 5.2 + - - -
219E PHE* 5.5 0.2 - - - -
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Residues in contact with PHE 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E TYR* 1.3 74.5 - - - +
168E ARG* 1.3 106.7 + - + +
170E GLN* 2.8 31.8 + - + +
172E LEU* 3.7 24.7 - - + +
203E LEU* 3.4 18.2 - - + -
206E GLU* 3.7 35.7 - - + -
207E MET* 3.8 18.6 - - + -
210E HIS* 3.9 19.3 - - + -
213E GLU* 3.6 16.6 - - + -
214E THR* 3.2 19.7 - - - +
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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