Contacts of the strand formed by residues 170 - 178 (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 GLN 170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D TYR* 3.2 1.5 - - - -
167D PHE* 2.8 47.8 + - + +
168D ARG* 4.6 1.6 - - + +
169D ASN* 1.3 75.3 - - - +
171D LEU* 1.3 71.9 + - - +
172D LEU* 3.2 8.0 + - + +
203D LEU* 5.3 8.3 - - + +
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Residues in contact with LEU 171 (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 4.5 0.2 - - - +
69D GLN* 4.0 27.4 + - - +
164D ARG* 3.4 33.4 - - + +
165D HIS 3.5 15.5 - - - +
166D TYR* 3.5 36.5 - - + -
169D ASN 3.9 1.2 + - - -
170D GLN* 1.3 78.4 - - - +
172D LEU* 1.3 63.2 + - - +
173D LYS* 3.8 22.4 - - - +
174D SER* 4.2 5.8 - - - +
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Residues in contact with LEU 172 (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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165D HIS* 2.8 13.3 + - + +
166D TYR 3.9 8.1 - - - +
167D PHE* 3.7 29.6 - - + +
170D GLN* 3.9 12.3 - - + +
171D LEU* 1.3 79.9 - - - +
173D LYS* 1.3 62.5 + - - +
197D PRO* 3.8 18.3 - - + +
199D LEU* 4.4 5.2 - - + -
203D LEU* 3.8 29.2 - - + -
207D MET* 3.7 27.8 - - + -
214D THR* 4.2 6.3 - - + -
500J DAO 4.0 24.7 - - + -
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Residues in contact with LYS 173 (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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163D GLU 4.0 1.4 - - - +
164D ARG* 3.8 0.3 - - - -
165D HIS* 3.0 30.7 + - - +
171D LEU* 3.9 7.8 - - - +
172D LEU* 1.3 85.9 - - + +
174D SER* 1.3 72.5 + - - +
175D PHE* 3.7 30.7 - - + -
195D ASP* 2.7 41.0 + - - +
196D PHE 4.3 4.6 + - - -
197D PRO* 4.1 23.5 - - + +
500J DAO 4.9 1.1 - - + -
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Residues in contact with SER 174 (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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66D LEU* 4.6 4.1 - - - +
162D ILE* 3.6 12.1 - - - +
163D GLU 3.3 4.5 - - - -
164D ARG* 3.0 48.7 + - - +
171D LEU* 4.2 6.1 - - - +
173D LYS* 1.3 88.5 - - - +
175D PHE* 1.3 64.0 + - - +
176D ASP* 4.3 1.3 + - - +
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Residues in contact with PHE 175 (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 3.4 1.9 - - - +
162D ILE* 3.3 4.0 - - - +
163D GLU* 2.8 43.7 + - + +
165D HIS* 3.7 21.5 - + - -
173D LYS* 3.7 35.4 - - + -
174D SER* 1.3 75.5 - - - +
176D ASP* 1.3 60.6 + - - +
177D PHE* 3.6 29.0 - + + -
193D ILE 5.0 1.1 - - - -
194D TYR* 3.6 37.9 - + + -
195D ASP 3.4 31.0 - - - -
197D PRO* 4.9 0.2 - - + -
500J DAO 3.8 24.0 - - + -
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Residues in contact with ASP 176 (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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66D LEU* 4.3 11.0 - - + +
160D ARG* 2.7 54.0 + - - +
161D MET 3.3 2.5 - - - -
162D ILE* 3.8 12.3 - - + +
174D SER* 4.3 2.2 + - - +
175D PHE* 1.3 74.8 - - - +
177D PHE* 1.3 66.2 + - - +
178D HIS* 3.6 14.8 + - - -
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Residues in contact with PHE 177 (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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160D ARG* 3.3 4.5 - - - +
161D MET* 2.7 70.5 + - + +
175D PHE* 3.6 33.2 - + + -
176D ASP* 1.3 78.3 - - - +
178D HIS* 1.3 62.9 + - - +
179D PHE* 4.0 0.9 + - - -
192D HIS* 3.7 48.2 - + + +
193D ILE 3.5 28.5 - - - -
194D TYR* 3.8 22.0 - + - -
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Residues in contact with HIS 178 (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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158D ASN* 6.1 3.6 - - - +
159D PHE 3.9 5.5 + - - +
160D ARG* 3.7 35.3 + - - +
176D ASP* 3.6 23.2 + - - -
177D PHE* 1.3 79.2 - - - +
179D PHE* 1.3 67.4 + - - +
180D GLY 3.8 0.2 + - - -
190D CYS* 4.8 5.5 - - - -
192D HIS* 5.8 0.7 - - - -
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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