Contacts of the strand formed by residues 159 - 167 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86F ILE* 3.8 35.0 - - + -
88F PHE* 4.1 3.8 - + - -
149F PHE* 3.9 17.3 - + - -
151F VAL* 6.0 0.2 - - + -
156F VAL* 3.7 20.0 - - + -
157F ASN 3.5 1.1 + - - -
158F ASN* 1.3 75.0 - - - +
160F ARG* 1.3 58.0 + - - +
178F HIS* 3.6 3.3 + - - +
179F PHE* 2.7 76.6 + + + +
180F GLY 5.7 0.8 + - - -
182F CYS* 3.9 21.3 - - - -
220F TYR* 4.0 34.1 - + + -
221F PHE 3.3 14.4 - - - -
222F VAL* 3.8 10.8 - - + +
227F VAL* 4.9 1.3 - - + -
228F MET* 5.4 0.7 - - - -
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Residues in contact with ARG 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F PRO* 3.4 32.8 - - - +
66F LEU* 4.0 19.0 - - - +
158F ASN 4.1 5.6 - - - +
159F PHE* 1.3 78.8 - - - +
161F MET* 1.3 63.7 + - - +
162F ILE* 3.9 8.4 - - + +
176F ASP* 2.8 42.2 + - - +
177F PHE 3.3 9.4 - - - +
178F HIS* 3.5 28.8 + - + +
179F PHE* 4.1 4.9 - - - -
219F PHE 3.8 0.3 - - - +
220F TYR* 3.4 3.5 - - - +
221F PHE* 2.8 45.5 + - + +
224F ASP* 3.5 15.6 + - - -
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Residues in contact with MET 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F ARG* 1.3 74.3 - - - +
162F ILE* 1.3 72.5 + - - +
163F GLU* 3.5 30.3 - - + +
175F PHE 3.6 1.0 - - - +
176F ASP* 3.5 2.8 - - - +
177F PHE* 2.8 71.5 + - + +
179F PHE* 4.0 9.9 - - + -
192F HIS* 3.8 13.7 - - + -
194F TYR* 3.7 12.3 - - - +
218F SER* 4.1 1.6 - - - -
219F PHE 3.2 12.8 - - - +
220F TYR* 3.5 43.1 - - + -
502L ALA* 5.4 3.4 - - + -
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Residues in contact with ILE 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F PRO* 3.8 22.2 - - + -
65F VAL* 4.0 16.6 - - + -
66F LEU* 3.8 27.4 - - + -
160F ARG* 3.9 12.5 - - - +
161F MET* 1.3 73.3 - - - +
163F GLU* 1.3 60.0 + - - +
164F ARG* 3.9 12.3 - - + -
174F SER* 3.6 19.7 - - - +
175F PHE 3.2 4.9 - - - +
176F ASP* 3.6 23.3 - - - +
219F PHE* 2.8 41.5 + - + -
221F PHE* 3.7 23.8 - - + -
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Residues in contact with GLU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F MET* 3.5 24.0 - - + +
162F ILE* 1.3 76.0 - - - +
164F ARG* 1.3 61.4 + - - +
165F HIS* 2.8 31.9 + - + +
174F SER* 3.4 1.2 - - - -
175F PHE* 2.8 42.8 + - + +
194F TYR* 2.7 31.8 + - - -
216F SER* 4.5 3.6 - - - -
217F ASP 3.3 7.0 - - - +
218F SER* 2.4 29.9 + - - +
500L DAO 3.5 9.9 - - - +
501L GLY 3.2 9.8 + - - -
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Residues in contact with ARG 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F VAL 3.2 22.4 + - - -
66F LEU* 3.0 36.3 + - - +
67F GLY* 4.0 2.2 - - - -
68F LEU* 3.0 23.3 + - - +
69F GLN* 4.6 2.4 - - - +
162F ILE* 3.9 8.1 - - + -
163F GLU* 1.3 74.8 - - - +
165F HIS* 1.3 61.8 + - - +
166F TYR* 3.0 37.6 + - + +
171F LEU* 3.6 24.7 - - + +
173F LYS 3.7 4.5 - - - -
174F SER* 2.9 36.8 + - - +
216F SER* 3.1 4.0 - - - -
217F ASP* 2.9 35.1 + - + +
219F PHE* 4.2 15.7 - - + -
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Residues in contact with HIS 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F GLU* 2.8 34.5 + - + +
164F ARG* 1.3 79.0 - - - +
166F TYR* 1.3 56.3 + - - +
171F LEU* 3.6 4.5 - - - +
172F LEU* 2.7 38.2 + - + -
173F LYS 2.9 13.5 + - - +
175F PHE* 3.7 23.8 - + - -
194F TYR* 4.3 0.4 - - - -
214F THR* 5.4 3.5 - - + +
215F GLN 3.4 4.3 - - - +
216F SER* 3.6 8.6 - - - -
234F TYR* 3.3 32.2 + + - -
500L DAO 3.8 46.9 - - + +
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Residues in contact with TYR 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F LEU* 3.4 10.7 + - - +
69F GLN* 3.5 7.6 - - - -
70F ARG* 3.5 38.2 + - - -
71F ILE* 3.8 35.9 - - + +
164F ARG* 3.0 54.3 + - + -
165F HIS* 1.3 75.0 - - - +
167F PHE* 1.3 60.8 + - - +
168F ARG 4.0 13.7 - - - +
170F GLN 3.1 9.0 - - - +
171F LEU* 3.6 32.5 - - + -
172F LEU* 3.8 4.7 - - - +
213F GLU 3.8 0.9 - - - +
214F THR* 3.2 4.7 - - - +
215F GLN* 2.9 34.0 + - + +
217F ASP* 4.5 3.7 + - - -
219F PHE* 5.4 0.2 - - - -
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Residues in contact with PHE 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F TYR* 1.3 73.0 - - - +
168F ARG* 1.3 86.8 + - + +
169F ASN 3.2 0.5 + - - -
170F GLN* 2.8 42.8 + - + +
172F LEU* 3.8 24.2 - - + +
203F LEU* 3.3 27.4 - - + -
206F GLU* 3.7 33.2 - - + -
207F MET* 3.8 15.7 - - + -
210F HIS* 3.8 26.2 - + + -
213F GLU* 3.6 14.6 - - + -
214F THR* 3.4 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