Contacts of the strand formed by residues 214 - 222 (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 THR 214 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C HIS* 5.6 3.6 - - - +
166C TYR 3.3 12.3 - - - +
167C PHE* 3.2 20.5 - - - +
172C LEU* 3.8 9.9 - - + -
207C MET* 3.5 25.2 + - + +
210C HIS 4.4 1.7 + - - -
212C TYR* 3.2 2.1 - - - +
213C GLU* 1.3 77.8 - - - +
215C GLN* 1.3 68.3 + - - +
233C ASP* 3.4 1.9 - - - +
234C TYR* 3.1 33.6 + - + -
236C TYR* 3.2 36.8 - - - +
500I DAO 6.3 0.2 - - + -
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Residues in contact with GLN 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE* 3.4 41.5 - - + +
165C HIS* 3.5 1.9 - - - +
166C TYR* 2.9 33.4 + - + +
168C ARG* 6.0 0.9 - - - -
169C ASN* 4.7 3.3 + - - +
212C TYR 3.2 10.4 + - - +
213C GLU* 4.0 7.4 - - - +
214C THR* 1.3 82.8 - - - +
216C SER* 1.3 62.6 + - - +
232C ALA 3.4 9.9 - - - +
233C ASP* 3.8 10.0 + - + +
234C TYR* 4.0 4.5 - - - -
157E ASN* 3.0 28.3 + - - +
158E ASN* 3.0 26.2 + - - +
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Residues in contact with SER 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE* 3.5 9.5 - - - +
163C GLU* 4.5 7.1 - - - +
164C ARG 3.0 12.3 - - - -
165C HIS* 3.7 21.7 + - - -
215C GLN* 1.3 76.5 - - - +
217C ASP* 1.3 60.9 + - - +
218C SER* 4.8 1.1 + - - -
231C LYS* 3.6 5.0 - - - +
232C ALA* 3.0 40.8 + - - +
234C TYR* 2.6 28.3 + - - -
501I GLY 4.8 3.1 + - - -
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Residues in contact with ASP 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 5.2 0.3 - - - +
70C ARG 4.4 1.7 - - - +
71C ILE* 3.4 17.1 - - + +
72C THR* 3.0 30.9 + - - +
162C ILE 3.8 1.4 - - - +
163C GLU* 3.3 3.2 - - - +
164C ARG* 2.9 33.3 + - + +
166C TYR* 4.5 2.6 + - - -
216C SER* 1.3 72.8 - - - +
218C SER* 1.3 61.7 + - - +
219C PHE* 3.5 24.6 - - + -
229C HIS* 2.9 17.2 + - - +
230C ASN 3.8 1.6 - - - -
231C LYS* 2.7 30.0 + - - +
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C MET* 4.1 2.0 - - - -
162C ILE 3.7 4.3 - - - -
163C GLU* 2.5 31.8 + - - +
216C SER* 4.2 2.5 + - - -
217C ASP* 1.3 70.7 - - - +
219C PHE* 1.3 62.9 + - - +
220C TYR* 3.4 30.4 - - - -
229C HIS* 3.3 6.1 - - - -
230C ASN* 2.8 36.3 + - - -
501I GLY* 3.0 17.2 + - - -
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Residues in contact with PHE 219 (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* 3.6 31.9 - - + -
68C LEU* 3.7 23.8 - - + -
72C THR* 4.0 2.5 - - + -
76C LEU* 3.5 16.4 - - + -
161C MET* 3.2 5.0 - - - +
162C ILE 2.8 46.0 + - - +
164C ARG* 4.4 11.9 - - - -
217C ASP* 3.5 33.7 - - + -
218C SER* 1.3 71.4 - - - +
220C TYR* 1.3 62.0 + - - +
221C PHE* 3.6 23.9 - - + -
226C LEU* 3.9 9.6 - - + -
228C MET 3.8 2.0 - - - -
229C HIS* 3.5 34.8 - + - -
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Residues in contact with TYR 220 (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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88C PHE* 3.5 31.0 - + - -
159C PHE* 3.9 15.5 - + + -
160C ARG 3.4 3.1 - - - -
161C MET* 3.3 38.8 - - + -
179C PHE* 4.1 13.5 - + - -
218C SER* 3.4 31.3 - - - -
219C PHE* 1.3 72.1 - - - +
221C PHE* 1.3 56.7 + - - +
226C LEU* 3.4 4.5 - - - +
227C VAL* 2.8 34.4 + - + +
228C MET* 2.9 38.3 + - + +
230C ASN* 4.2 15.5 - - - -
501I GLY 3.5 0.5 - - - -
502I ALA* 3.0 33.4 + - + +
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Residues in contact with PHE 221 (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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60C ILE* 3.7 11.4 - - + -
61C GLY 3.3 23.1 - - - -
62C PRO* 3.6 31.2 - - + -
65C VAL* 3.8 14.6 - - + -
158C ASN 3.3 2.0 - - - +
159C PHE* 3.4 6.1 - - - -
160C ARG* 2.8 48.1 + - + +
162C ILE* 3.9 23.3 - - + -
219C PHE* 3.6 35.9 - - + -
220C TYR* 1.3 73.3 - - - +
222C VAL* 1.3 62.3 + - - +
224C ASP* 4.2 7.6 - - - +
225C ARG 3.2 11.2 - - - +
226C LEU* 3.5 26.0 - - + -
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Residues in contact with VAL 222 (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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84C TYR* 3.8 35.6 + - + +
86C ILE* 3.8 19.5 - - + -
156C VAL* 3.7 17.9 - - + -
157C ASN 3.4 28.5 - - - +
158C ASN 3.6 3.8 - - - -
159C PHE* 3.9 4.3 - - + -
221C PHE* 1.3 78.4 - - - +
223C ASP* 1.3 74.6 + - - +
225C ARG* 3.0 20.9 + - - +
227C VAL* 3.7 23.0 - - + +
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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