Contacts of the strand formed by residues 162 - 173 (chain C) in PDB entry 3RBH
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 ASP 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C THR 4.4 0.7 - - - +
104C LEU* 3.3 24.9 - - - +
152C ARG* 2.8 35.8 + - - -
153C LEU 3.1 4.5 - - - -
154C ARG* 3.4 6.9 - - + -
158C GLY* 4.3 5.8 - - - -
161C GLN* 1.3 75.9 - - - +
163C THR* 1.3 60.6 + - - +
349C LEU 2.8 11.8 + - - +
350C GLU* 4.0 0.4 - - - +
351C SER* 2.5 33.2 + - - +
362C ARG* 2.4 35.4 + - - +
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Residues in contact with THR 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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104C LEU* 4.3 17.6 + - - +
151C GLN 3.4 0.7 - - - +
152C ARG* 3.4 6.3 - - - +
153C LEU* 2.8 37.2 + - + +
162C ASP* 1.3 78.6 + - - +
164C ASN* 1.3 61.1 + - - +
165C ILE* 3.9 17.9 + - + -
186C ARG* 2.7 32.2 + - - +
349C LEU* 3.5 31.8 - - + +
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Residues in contact with ASN 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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104C LEU* 3.5 13.6 - - + +
129C ARG* 3.4 53.2 + - - +
130C GLU* 3.8 12.8 + - - +
150C ARG* 3.2 29.0 + - + +
151C GLN 3.3 3.8 - - - +
152C ARG* 3.4 30.7 + - - +
163C THR* 1.3 71.3 + - - +
165C ILE* 1.3 61.3 + - - +
186C ARG* 2.9 20.8 + - - -
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Residues in contact with ILE 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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150C ARG* 3.6 8.8 - - - +
151C GLN 2.9 26.8 + - - +
153C LEU* 3.4 35.7 - - + -
163C THR* 4.0 8.5 - - + -
164C ASN* 1.3 74.4 - - - +
166C GLU* 1.3 75.0 + - - +
167C ALA* 3.3 4.0 + - - +
184C ALA* 4.0 16.2 - - + -
185C GLN* 4.0 14.6 - - - +
186C ARG* 3.4 36.3 - - + +
206C HIS* 4.5 4.7 - - + -
349C LEU* 3.8 24.5 - - + -
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Residues in contact with GLU 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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131C PHE* 5.1 2.9 - - + -
149C GLY* 3.7 7.2 - - - -
150C ARG* 3.8 16.1 + - + +
165C ILE* 1.3 76.9 - - - +
167C ALA* 1.3 59.3 + - - +
184C ALA* 3.3 5.7 - - - +
185C GLN 3.0 43.2 + - - +
186C ARG* 3.3 11.3 + - - +
187C PHE* 2.7 35.6 + - + -
188C SER 3.4 1.5 + - - +
190C TYR* 2.8 43.4 + - + +
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Residues in contact with ALA 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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148C PHE* 3.4 4.7 - - - -
149C GLY* 2.8 33.8 + - - +
151C GLN* 2.9 27.5 + - + +
153C LEU* 4.2 14.4 - - + -
165C ILE 3.9 5.6 - - - +
166C GLU* 1.3 77.0 - - - +
168C LEU* 1.3 62.0 - - - +
183C VAL 3.4 13.7 - - - +
184C ALA* 4.0 8.3 - - + -
208C PHE* 5.1 0.2 - - + -
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Residues in contact with LEU 168 (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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146C LEU* 3.4 40.2 - - + -
147C ARG 3.3 9.2 - - - +
148C PHE* 3.9 26.7 - - + -
167C ALA* 1.3 71.5 - - - +
169C ASN* 1.3 60.0 + - - +
181C ALA 4.9 0.2 - - - -
182C GLY* 3.0 4.5 - - - -
183C VAL* 2.9 48.0 + - + +
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Residues in contact with ASN 169 (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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145C HIS* 4.0 0.5 + - - +
146C LEU* 3.5 4.6 - - - +
147C ARG* 2.9 38.5 + - - +
151C GLN* 3.4 20.4 + - - +
152C ARG 5.8 0.4 + - - -
153C LEU* 3.8 24.3 - - + +
161C GLN* 5.2 5.6 + - - +
167C ALA* 4.0 0.6 - - + -
168C LEU* 1.3 76.0 - - - +
170C TRP* 1.3 61.9 + - - +
171C SER* 3.7 22.8 + - - -
180C HIS* 4.8 8.6 - - - +
181C ALA 3.4 16.4 + - - +
182C GLY* 4.7 0.2 - - - -
208C PHE* 3.5 19.5 - - + -
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Residues in contact with TRP 170 (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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138C LEU* 4.5 12.5 - - + +
139C THR* 5.2 6.0 - - + +
144C GLU* 3.0 29.4 + - + +
145C HIS 3.7 13.7 - - - -
146C LEU* 3.9 22.4 - - + -
169C ASN* 1.3 73.7 - - - +
171C SER* 1.3 62.7 + - - +
172C PHE* 3.6 41.5 - + + -
179C ALA* 4.6 14.6 - - + -
180C HIS* 3.2 8.7 - - - +
181C ALA* 2.7 55.3 + - + +
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Residues in contact with SER 171 (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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143C GLY 4.0 2.7 - - - -
144C GLU* 3.2 7.4 - - - +
145C HIS* 2.9 61.9 + - - +
169C ASN* 3.7 13.9 + - - -
170C TRP* 1.3 76.2 - - - +
172C PHE* 1.3 61.4 + - - +
173C GLU* 4.6 6.9 + - - -
180C HIS* 3.3 25.8 + - - -
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Residues in contact with PHE 172 (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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139C THR* 4.7 3.8 - - + -
141C TYR* 3.7 40.6 - + + -
143C GLY 3.7 2.5 - - - -
144C GLU* 3.8 20.9 - - + -
170C TRP* 3.6 27.4 - + + -
171C SER* 1.3 76.5 - - - +
173C GLU* 1.3 64.8 + - - +
174C THR* 3.5 28.7 - - + -
177C LEU* 3.8 30.5 - - + -
178C ASN* 3.1 4.0 - - - -
179C ALA* 2.8 45.5 + - + +
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Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLY* 3.1 37.9 + - - +
145C HIS* 5.6 1.9 + - - -
171C SER* 4.6 6.1 - - - -
172C PHE* 1.3 82.2 - - - +
174C THR* 1.3 69.2 + - - +
178C ASN* 3.4 22.2 + - - +
180C HIS* 3.3 26.8 + - - +
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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