Contacts of the strand formed by residues 159 - 167 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C ILE* 3.7 38.4 - - + -
88C PHE* 4.2 12.8 - + - -
149C PHE* 3.7 22.0 - + - -
156C VAL* 3.9 10.5 + - + +
157C ASN 3.4 2.6 - - - -
158C ASN* 1.3 74.9 - - - +
160C ARG* 1.3 62.2 + - - +
178C HIS* 3.7 5.0 - - - -
179C PHE* 2.9 65.8 + + + -
180C GLY 4.4 6.7 + - - +
182C CYS* 3.8 29.6 - - - -
220C TYR* 3.9 24.5 - + + -
221C PHE 3.4 10.3 - - - -
222C VAL* 3.9 10.1 - - + -
228C MET* 5.4 0.4 - - - -
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Residues in contact with ARG 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PRO* 3.4 35.9 - - - +
63C GLU* 5.2 4.9 + - - -
66C LEU* 4.0 18.0 - - - +
158C ASN* 4.0 10.5 - - - +
159C PHE* 1.3 77.7 - - - +
161C MET* 1.3 65.3 + - - +
162C ILE* 4.2 5.3 - - + +
176C ASP* 2.7 41.9 + - - +
177C PHE 3.4 7.9 - - - +
178C HIS* 3.4 29.2 + - + +
179C PHE* 3.9 5.2 - - - -
219C PHE 3.7 0.2 - - - +
220C TYR* 3.4 4.5 - - - +
221C PHE* 2.8 43.4 + - + +
224C ASP* 4.0 9.2 + - - -
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Residues in contact with MET 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ARG* 1.3 74.5 - - - +
162C ILE* 1.3 73.7 + - - +
163C GLU* 3.6 31.2 - - + +
175C PHE 3.6 1.0 - - - +
176C ASP* 3.3 5.0 - - - +
177C PHE* 2.8 71.9 + - + +
179C PHE* 3.6 22.1 - - + -
194C TYR* 4.0 6.5 - - - +
218C SER* 4.1 0.7 - - - -
219C PHE 3.2 12.8 - - - +
220C TYR* 3.3 39.5 - - + -
502I ALA* 5.7 2.2 - - + -
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PRO* 3.7 26.2 - - + -
65C VAL* 3.7 22.4 - - + -
66C LEU* 3.6 36.8 - - + -
160C ARG* 4.2 7.4 - - - +
161C MET* 1.3 78.8 - - - +
163C GLU* 1.3 62.3 + - - +
164C ARG* 4.0 11.4 - - + -
174C SER* 3.6 21.3 - - - +
175C PHE 3.2 4.7 - - - +
176C ASP* 3.9 17.5 - - - +
219C PHE* 2.8 35.9 + - - +
221C PHE* 3.9 9.2 - - + -
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C MET* 3.6 24.7 - - + +
162C ILE* 1.3 76.1 - - - +
164C ARG* 1.3 64.1 + - - +
165C HIS* 2.9 29.4 + - + +
174C SER* 3.4 1.0 - - - -
175C PHE* 2.8 48.1 + - + +
194C TYR* 2.6 30.4 + - - -
216C SER* 4.5 4.7 - - - -
217C ASP 3.3 7.2 - - - +
218C SER* 2.5 29.9 + - - +
220C TYR* 4.4 0.2 + - - -
500I DAO 3.4 9.2 - - - +
501I GLY 3.0 11.9 + - - -
502I ALA 4.7 0.2 + - - -
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Residues in contact with ARG 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C VAL 3.4 22.4 + - - -
66C LEU* 3.5 33.1 + - - +
68C LEU* 2.7 22.1 + - - -
69C GLN* 3.9 6.7 - - - +
162C ILE* 4.0 9.6 - - + -
163C GLU* 1.3 75.8 - - - +
165C HIS* 1.3 63.4 + - - +
166C TYR* 2.9 37.7 + - + -
171C LEU* 3.6 23.9 - - + +
173C LYS 3.6 3.6 - - - -
174C SER* 2.8 45.0 + - - +
216C SER* 3.0 4.5 - - - -
217C ASP* 2.9 36.0 + - + +
219C PHE* 4.4 12.8 - - + -
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Residues in contact with HIS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLU* 2.9 31.2 + - + +
164C ARG* 1.3 78.9 - - - +
166C TYR* 1.3 54.6 + - - +
171C LEU* 3.5 4.3 - - - +
172C LEU* 2.7 46.8 + - + +
173C LYS 2.9 13.5 + - - +
175C PHE* 3.8 26.1 - + - -
194C TYR* 4.2 0.8 - - - -
214C THR* 5.6 3.4 - - + +
215C GLN 3.5 4.9 + - - +
216C SER* 3.7 7.5 - - - -
234C TYR* 3.2 32.4 + + - -
236C TYR* 5.9 0.6 + - - -
500I DAO 3.7 40.3 - - + +
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Residues in contact with TYR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.2 11.7 + - - +
69C GLN 3.5 28.3 - - - -
70C ARG* 3.6 16.9 + - - -
71C ILE* 3.7 33.4 - - + -
164C ARG* 2.9 53.5 + - + -
165C HIS* 1.3 74.8 - - - +
167C PHE* 1.3 59.6 + - - +
168C ARG 4.0 0.2 - - - -
169C ASN* 3.8 17.0 - - - +
170C GLN 3.1 8.3 - - - +
171C LEU* 3.6 33.2 - - + -
172C LEU* 3.9 6.0 - - - +
213C GLU 3.8 1.4 - - - +
214C THR* 3.3 3.8 - - - +
215C GLN* 2.9 35.1 + - + +
217C ASP* 4.5 4.1 + - - -
219C PHE* 5.8 0.3 - - - -
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Residues in contact with PHE 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C TYR* 1.3 71.6 - - - +
168C ARG* 1.3 101.4 + - + +
170C GLN* 2.9 28.6 + - + +
172C LEU* 3.7 12.1 - - + +
203C LEU* 3.6 26.7 - - + -
206C GLU* 3.7 38.4 - - + -
207C MET* 3.6 25.1 - - + -
210C HIS* 4.2 9.0 - - + -
213C GLU* 3.8 22.2 - - + -
214C THR* 3.2 21.8 - - - +
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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