Contacts of the strand formed by residues 225 - 235 (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 ARG 225 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60F ILE 3.8 8.3 - - - +
83F ILE* 6.4 2.0 - - - -
84F TYR* 5.7 3.7 + - - -
221F PHE* 3.2 4.4 - - - +
222F VAL 3.0 33.6 + - - +
223F ASP* 4.1 5.2 + - + +
224F ASP* 1.3 80.5 - - - +
226F LEU* 1.3 71.8 + - - +
227F VAL* 3.3 10.4 + - - +
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Residues in contact with LEU 226 (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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60F ILE* 3.0 37.2 + - + +
76F LEU* 3.8 31.4 - - + +
77F CYS* 3.8 23.2 - - + +
81F GLU* 4.2 16.1 - - - +
219F PHE* 3.8 20.9 - - + -
220F TYR 3.4 24.2 - - - +
221F PHE* 3.4 12.9 - - + -
225F ARG* 1.3 78.0 - - - +
227F VAL* 1.3 62.5 + - - +
228F MET 3.4 15.7 - - - +
229F HIS* 4.5 3.8 - - + -
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Residues in contact with VAL 227 (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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77F CYS* 3.9 9.8 - - - -
78F SER 4.6 1.6 - - - +
79F PRO* 5.9 0.2 - - - +
81F GLU 3.6 19.8 - - - +
82F ASN* 3.2 24.7 + - - +
83F ILE* 5.1 0.9 - - + -
84F TYR* 3.9 25.4 - - + -
86F ILE* 4.5 10.5 - - + -
159F PHE* 4.9 0.2 - - + -
220F TYR* 2.8 24.9 + - + +
222F VAL* 3.8 24.5 - - + +
225F ARG* 3.3 17.0 + - - +
226F LEU* 1.3 78.5 - - - +
228F MET* 1.3 74.7 + - + +
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Residues in contact with MET 228 (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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77F CYS* 3.7 7.4 - - - -
82F ASN* 3.7 29.8 - - + +
86F ILE* 3.7 33.2 - - - +
88F PHE* 3.7 21.5 - - + +
127F ARG* 5.8 0.4 - - - +
159F PHE* 5.4 0.2 - - - -
220F TYR* 2.9 42.4 + - + -
226F LEU* 3.4 8.0 - - - +
227F VAL* 1.3 90.6 - - + +
229F HIS* 1.3 60.9 + - - +
230F ASN* 4.2 10.5 - - - +
505L SER* 3.6 23.3 - - - +
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Residues in contact with HIS 229 (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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72F THR* 3.3 23.8 - - - -
74F ASP 3.8 3.4 - - - -
75F TYR* 3.2 29.3 - + + -
76F LEU* 2.9 30.1 + - + +
77F CYS* 3.7 17.5 - - - +
127F ARG* 3.8 9.1 + - - +
217F ASP* 2.8 24.6 + - - -
218F SER 3.3 11.0 - - - +
219F PHE* 3.5 27.5 - + + -
226F LEU* 4.5 2.7 - - + -
228F MET* 1.3 77.8 - - - +
230F ASN* 1.3 79.1 + - - +
231F LYS* 3.9 5.7 - - - +
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Residues in contact with ASN 230 (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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88F PHE* 4.5 0.8 - - - -
126F GLY 3.9 0.7 - - - +
127F ARG* 3.5 20.8 - - - +
217F ASP 3.6 0.2 - - - -
218F SER* 2.7 39.9 + - - -
220F TYR* 3.9 16.0 + - + -
228F MET* 4.2 9.9 - - - +
229F HIS* 1.3 84.9 + - - +
231F LYS* 1.3 61.2 + - - +
501L GLY* 3.0 38.9 + - - +
502L ALA* 4.2 0.6 - - - +
504L ALA* 4.2 6.3 - - + -
505L SER* 3.0 29.0 + - - +
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Residues in contact with LYS 231 (chain F).
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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181C PHE* 3.6 36.6 - - + -
71F ILE* 3.8 9.9 - - - +
72F THR* 2.9 37.6 + - - -
74F ASP 3.9 20.4 - - - -
75F TYR* 3.7 20.0 - - + +
127F ARG 2.8 6.5 + - - +
128F PHE* 3.2 13.8 - - + -
129F VAL* 3.1 24.4 + - - +
216F SER 3.4 7.0 - - - +
217F ASP* 2.9 28.7 + - - +
229F HIS* 3.9 6.1 - - - +
230F ASN* 1.3 75.0 - - - +
232F ALA* 1.3 62.3 + - - +
501L GLY* 4.7 3.5 - - - -
504L ALA* 4.4 0.9 - - - +
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Residues in contact with ALA 232 (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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128F PHE* 3.9 4.3 - - - -
129F VAL* 3.0 26.7 - - + +
131F TYR* 3.9 5.2 - - + -
215F GLN* 3.3 6.6 - - - +
216F SER* 2.9 47.7 + - - +
231F LYS* 1.3 75.8 - - - +
233F ASP* 1.3 60.9 + - - +
234F TYR* 3.6 15.9 - - + +
501L GLY 4.7 5.8 - - - +
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Residues in contact with ASP 233 (chain F).
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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180C GLY* 3.4 3.0 - - - -
181C PHE* 2.7 15.3 + - - +
128F PHE* 3.3 15.1 - - + -
129F VAL 3.1 5.1 + - - +
130F ARG* 2.7 39.5 + - + +
131F TYR* 2.9 27.6 + - - +
212F TYR* 3.8 14.1 - - + -
214F THR 3.4 4.7 - - - -
215F GLN* 2.7 34.6 + - - +
232F ALA* 1.3 72.0 - - - +
234F TYR* 1.3 68.1 + - - +
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Residues in contact with TYR 234 (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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131F TYR* 3.6 25.8 - + + -
133F PHE* 3.9 21.8 - + + -
137F PHE* 5.4 1.1 - + - -
165F HIS* 3.3 21.8 - + - -
210F HIS 4.9 0.2 - - - +
211F PRO* 4.1 0.9 - - - +
212F TYR* 2.7 30.1 + - - -
214F THR* 2.8 30.1 + - + +
215F GLN 4.1 0.9 - - - -
216F SER* 2.6 39.0 + - - -
232F ALA* 3.6 18.0 - - + +
233F ASP* 1.3 79.1 - - - +
235F SER* 1.3 57.0 + - - +
236F TYR* 3.2 36.3 - + + +
500L DAO 3.6 26.2 - - + +
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Residues in contact with SER 235 (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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191C GLU 5.3 1.6 + - - -
131F TYR 2.9 7.7 + - - +
132F GLN* 3.6 17.6 + - - -
133F PHE* 2.6 37.0 + - - +
211F PRO* 3.4 21.4 - - - +
212F TYR* 3.6 26.9 - - - -
234F TYR* 1.3 75.0 - - - +
236F TYR* 1.3 61.3 + - - +
237F SER* 3.5 16.2 + - - -
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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
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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