Contacts of the strand formed by residues 170 - 178 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A TYR* 3.2 2.7 - - - -
167A PHE* 2.8 42.6 + - + +
168A ARG 3.0 1.9 + - - +
169A ASN* 1.3 70.9 - - - +
171A LEU* 1.3 76.2 + - - +
172A LEU* 3.2 5.2 + - + +
203A LEU* 4.1 32.7 - - - +
94C ARG* 5.9 4.0 - - - +
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLN* 3.8 19.1 + - - +
164A ARG* 3.8 19.7 - - + +
165A HIS 3.5 14.6 - - - +
166A TYR* 3.5 34.6 - - + -
169A ASN 3.9 1.6 + - - -
170A GLN* 1.3 80.6 + - - +
172A LEU* 1.3 61.7 + - - +
173A LYS 3.9 20.6 - - - +
174A SER 4.2 0.9 - - - +
94C ARG* 3.9 15.2 + - - +
96C MET 3.8 12.1 - - - +
97C ASP 3.4 34.3 - - - +
98C SER* 3.8 11.4 - - - +
99C GLY* 3.9 2.2 - - - +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A HIS* 2.7 14.5 + - + +
166A TYR* 3.9 3.8 - - - +
167A PHE* 3.7 30.1 - - + +
170A GLN* 3.2 9.6 + - + +
171A LEU* 1.3 78.0 - - - +
173A LYS* 1.3 62.9 + - - +
197A PRO* 3.8 13.7 - - + +
199A LEU* 4.1 10.8 - - + -
203A LEU* 3.8 31.0 - - + -
207A MET* 3.5 28.7 - - + -
214A THR* 3.8 12.6 - - + -
94C ARG* 4.3 3.7 + - - +
99C GLY* 3.9 12.8 - - - +
500G DAO 4.0 22.9 - - + -
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLU 3.9 1.4 - - - +
164A ARG* 3.6 0.3 - - - -
165A HIS* 2.9 30.8 + - - +
171A LEU* 3.8 5.8 - - - -
172A LEU* 1.3 84.6 - - + +
174A SER* 1.3 69.1 + - - +
175A PHE* 3.7 31.4 - - + -
195A ASP* 2.8 39.7 + - - +
196A PHE 4.7 1.4 + - - -
197A PRO* 4.0 24.4 - - + +
98C SER 3.2 15.0 - - - +
99C GLY 4.5 5.4 - - - +
100C THR* 3.9 29.5 - - - +
101C VAL 5.6 0.6 - - - +
500G DAO 5.0 0.9 - - + -
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 4.8 3.2 - - - +
162A ILE* 3.6 12.3 - - - +
163A GLU 3.4 4.7 - - - -
164A ARG* 2.9 48.3 + - - +
171A LEU* 4.6 0.9 - - - -
173A LYS* 1.3 87.4 - - - +
175A PHE* 1.3 62.9 + - - +
176A ASP* 4.2 1.6 + - - +
98C SER* 2.8 30.6 + - - +
100C THR* 4.6 1.4 + - - -
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Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A MET 3.5 1.2 - - - +
162A ILE* 3.3 4.3 - - - +
163A GLU* 2.8 44.6 + - + +
165A HIS* 3.7 15.0 - + - -
173A LYS* 3.7 34.5 - - + -
174A SER* 1.3 74.4 + - - +
176A ASP* 1.3 60.1 + - - +
177A PHE* 3.6 27.3 - + + -
193A ILE 5.1 0.2 - - - -
194A TYR* 3.6 30.3 - + + -
195A ASP 3.3 34.1 - - - -
197A PRO* 4.6 1.8 - - + -
500G DAO 3.7 39.3 - - + -
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 4.6 8.9 - - + +
160A ARG* 2.7 51.9 + - - +
161A MET 3.3 2.7 - - - -
162A ILE* 3.8 10.4 - - + +
174A SER* 4.2 1.7 + - - +
175A PHE* 1.3 75.1 - - - +
177A PHE* 1.3 67.1 + - - +
178A HIS* 3.7 15.0 + - - -
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG* 3.4 4.5 - - - +
161A MET* 2.7 62.1 + - + +
175A PHE* 3.6 31.4 - + + -
176A ASP* 1.3 78.3 + - - +
178A HIS* 1.3 63.0 + - - +
179A PHE* 4.0 1.0 + - + -
192A HIS* 3.7 42.6 - + + +
193A ILE 3.3 36.6 - - - -
194A TYR* 3.8 28.3 - + - -
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN* 4.3 12.4 + - - -
159A PHE 3.7 6.0 + - - +
160A ARG* 3.5 35.4 + - - +
176A ASP* 3.7 20.7 + - - -
177A PHE* 1.3 77.8 - - - +
179A PHE* 1.3 60.8 + - - +
180A GLY 3.8 0.3 + - - -
190A CYS* 4.7 4.9 - - - -
192A HIS* 5.6 0.5 - - - -
130D ARG* 2.7 32.5 + - - +
211D PRO* 4.0 26.4 + - + +
212D TYR* 3.4 39.2 - + + +
213D GLU* 5.8 2.5 - - - -
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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