Contacts of the strand formed by residues 214 - 222 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D HIS* 5.4 4.5 - - + +
166D TYR 3.3 12.6 - - - +
167D PHE* 3.3 19.4 - - - -
172D LEU* 4.2 7.6 - - + -
207D MET* 3.4 25.3 + - + +
210D HIS 4.5 1.5 + - - -
212D TYR* 3.3 1.7 - - - +
213D GLU* 1.3 77.7 - - - +
215D GLN* 1.3 66.4 + - - +
233D ASP* 3.4 2.3 - - - +
234D TYR* 3.1 40.4 + - + -
236D TYR* 3.3 36.3 - - - +
500J DAO 5.9 1.1 - - + -
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Residues in contact with GLN 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ASN* 3.0 33.5 + - - +
158A ASN* 5.0 4.2 - - - +
181A PHE* 5.8 5.9 - - - -
71D ILE* 3.8 34.8 - - + +
165D HIS* 3.6 0.7 - - - +
166D TYR* 2.9 33.0 + - + +
168D ARG* 5.5 0.9 - - - -
169D ASN* 4.7 8.0 + - - +
212D TYR 3.5 18.6 + - - +
213D GLU* 4.0 10.5 - - - +
214D THR* 1.3 81.9 - - - +
216D SER* 1.3 62.1 + - - +
232D ALA 3.3 10.5 - - - +
233D ASP* 3.9 10.2 + - + +
234D TYR* 4.0 5.2 - - - -
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Residues in contact with SER 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ILE* 3.4 11.2 - - - +
163D GLU* 4.5 7.4 - - - +
164D ARG 3.1 13.9 - - - -
165D HIS* 3.6 26.4 - - - -
215D GLN* 1.3 74.6 - - - +
217D ASP* 1.3 59.5 + - - +
218D SER* 4.7 4.0 + - - -
231D LYS* 3.5 5.8 - - - +
232D ALA* 3.0 37.0 + - - +
234D TYR* 2.8 23.1 + - - -
501J GLY 5.0 0.3 + - - -
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Residues in contact with ASP 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 5.5 0.2 - - - +
70D ARG 4.4 1.2 - - - +
71D ILE* 3.4 16.8 - - + +
72D THR* 2.9 31.2 + - - +
162D ILE 3.8 1.6 - - - +
163D GLU* 3.2 4.0 - - - +
164D ARG* 2.8 35.4 + - + +
166D TYR* 4.5 2.5 + - + -
216D SER* 1.3 74.0 - - - +
218D SER* 1.3 60.5 + - - +
219D PHE* 3.5 25.7 - - + -
229D HIS* 2.8 24.1 + - - +
230D ASN 3.7 2.7 - - - -
231D LYS* 2.8 21.9 + - - +
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Residues in contact with SER 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D MET* 4.1 2.0 - - - -
162D ILE 3.8 3.4 - - - -
163D GLU* 2.5 33.4 + - - +
216D SER* 4.7 2.1 + - - -
217D ASP* 1.3 71.1 - - - +
219D PHE* 1.3 59.8 + - - +
220D TYR* 3.6 28.3 - - - -
229D HIS* 3.2 7.3 - - - -
230D ASN* 2.8 40.9 + - - -
501J GLY* 2.9 18.6 + - - -
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Residues in contact with PHE 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 3.7 30.3 - - + -
68D LEU* 3.7 23.3 - - + -
72D THR* 3.8 7.9 - - + -
76D LEU* 3.4 22.2 - - + -
161D MET* 3.3 3.0 - - - +
162D ILE* 2.9 50.4 + - + +
164D ARG* 4.2 11.4 - - - -
166D TYR* 5.6 0.2 - - - -
217D ASP* 3.5 27.6 - - + -
218D SER* 1.3 71.5 - - - +
220D TYR* 1.3 61.4 + - - +
221D PHE* 3.6 23.2 - - + -
226D LEU* 3.7 12.1 - - + -
228D MET 3.7 2.9 - - - -
229D HIS* 3.5 31.0 - + - -
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Residues in contact with TYR 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D PHE* 3.4 30.7 - + - -
159D PHE* 4.0 15.7 - + + -
160D ARG 3.3 4.5 - - - -
161D MET* 3.4 42.6 - - + -
179D PHE* 4.5 4.0 - + - -
218D SER* 3.6 27.9 - - - -
219D PHE* 1.3 72.5 - - - +
221D PHE* 1.3 55.3 - - - +
226D LEU* 3.6 3.8 - - - +
227D VAL* 2.8 32.2 + - + -
228D MET* 2.9 46.8 + - + +
230D ASN* 4.1 17.7 - - - -
502J ALA* 3.2 32.8 + - + +
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Residues in contact with PHE 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ILE* 3.7 9.6 - - + -
61D GLY 3.4 22.0 - - - -
62D PRO* 3.7 31.2 - - + -
65D VAL* 3.8 15.0 - - + -
158D ASN 3.5 1.5 - - - +
159D PHE* 3.3 8.1 - - - -
160D ARG* 2.8 45.4 + - + +
162D ILE* 3.7 22.2 - - + -
219D PHE* 3.6 26.7 - - + -
220D TYR* 1.3 74.3 - - - +
222D VAL* 1.3 63.1 + - - +
224D ASP* 4.0 7.6 - - - +
225D ARG 3.2 12.1 - - - +
226D LEU* 3.5 33.9 - - + -
227D VAL* 4.5 0.2 - - - -
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Residues in contact with VAL 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.6 42.4 + - + +
86D ILE* 3.9 3.8 - - + -
156D VAL* 3.9 15.7 - - + -
157D ASN 3.5 23.8 - - - +
158D ASN 3.7 3.4 - - - -
159D PHE* 3.8 17.9 - - + -
221D PHE* 1.3 77.3 - - - +
223D ASP* 1.3 77.2 + - + +
224D ASP 3.2 0.2 - - - -
225D ARG* 2.9 22.3 + - - +
227D VAL* 3.8 19.3 - - + +
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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