Contacts of the strand formed by residues 162 - 173 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A THR 4.4 3.3 - - - +
104A LEU* 2.7 31.6 - - - +
152A ARG* 2.8 35.1 + - - -
153A LEU 3.1 4.3 - - - -
154A ARG* 3.3 8.2 - - + -
158A GLY* 4.3 5.4 - - - -
161A GLN* 1.3 76.3 - - - +
163A THR* 1.3 56.6 + - - +
349A LEU 2.8 12.4 + - - +
350A GLU* 4.0 0.4 - - - +
351A SER* 2.7 32.7 + - - +
362A ARG* 2.5 34.7 + - - +
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Residues in contact with THR 163 (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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104A LEU* 4.3 13.7 + - - +
151A GLN 3.4 0.5 - - - +
152A ARG* 3.4 7.0 - - - +
153A LEU* 2.8 37.5 + - + +
162A ASP* 1.3 79.0 + - - +
164A ASN* 1.3 61.6 + - - +
165A ILE* 3.8 18.3 + - + -
186A ARG* 2.7 33.1 + - - +
349A LEU* 3.4 31.9 - - + +
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Residues in contact with ASN 164 (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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104A LEU* 4.8 7.3 - - + +
129A ARG* 3.5 53.1 + - - +
130A GLU* 3.8 12.9 + - - +
150A ARG* 3.3 27.9 + - - +
151A GLN 3.2 3.8 - - - +
152A ARG* 3.4 32.8 + - - +
163A THR* 1.3 73.5 + - - +
165A ILE* 1.3 61.3 + - - +
186A ARG* 2.9 22.2 + - - -
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Residues in contact with ILE 165 (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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149A GLY 3.5 0.2 - - - +
150A ARG* 3.6 9.5 - - - +
151A GLN 2.9 26.7 + - - +
153A LEU* 3.4 36.3 - - + -
163A THR* 4.1 7.0 - - + -
164A ASN* 1.3 75.4 - - - +
166A GLU* 1.3 79.0 + - - +
167A ALA* 3.3 4.0 + - - +
184A ALA* 4.0 10.5 - - + -
185A GLN* 3.9 20.6 - - - +
186A ARG* 3.5 33.4 - - + +
206A HIS* 4.5 5.4 - - + +
349A LEU* 3.9 23.6 - - + -
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Residues in contact with GLU 166 (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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131A PHE* 5.1 3.1 - - + -
149A GLY* 3.6 6.7 - - - -
150A ARG* 3.8 15.3 + - + +
165A ILE* 1.3 77.7 - - - +
167A ALA* 1.3 58.7 + - - +
184A ALA* 3.3 4.5 - - - +
185A GLN 3.0 42.2 + - - +
186A ARG* 3.4 9.9 + - - +
187A PHE* 2.7 37.9 + - + +
188A SER 3.4 1.9 + - - +
190A TYR* 2.8 42.9 + - + +
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Residues in contact with ALA 167 (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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148A PHE* 3.4 5.3 - - - -
149A GLY* 2.8 33.2 + - - -
151A GLN* 3.0 25.2 + - + +
153A LEU* 4.2 14.6 - - + -
165A ILE 3.8 6.5 - - - +
166A GLU* 1.3 77.4 - - - +
168A LEU* 1.3 62.2 + - - +
169A ASN* 4.8 0.2 - - + -
183A VAL 3.4 13.5 - - - +
184A ALA* 3.9 9.4 - - + +
208A PHE* 5.1 0.2 - - + -
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Residues in contact with LEU 168 (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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146A LEU* 3.4 39.5 - - + -
147A ARG 3.3 9.2 - - - +
148A PHE* 3.9 26.9 - - + -
167A ALA* 1.3 73.0 - - - +
169A ASN* 1.3 58.6 + - - +
182A GLY* 3.0 4.5 - - - -
183A VAL* 2.9 49.3 + - + +
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Residues in contact with ASN 169 (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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145A HIS* 4.0 1.6 + - - +
146A LEU* 3.6 3.8 - - - -
147A ARG* 2.8 36.9 + - - +
151A GLN* 3.4 19.7 + - - +
152A ARG 5.7 1.0 + - - -
153A LEU* 3.8 27.2 - - + +
161A GLN* 5.1 5.9 + - - +
167A ALA* 4.8 0.4 - - + -
168A LEU* 1.3 75.8 - - - +
170A TRP* 1.3 61.8 + - - +
171A SER* 3.8 20.2 + - - -
180A HIS* 4.8 9.9 - - - +
181A ALA 3.4 16.2 + - - +
208A PHE* 3.6 18.8 - - + -
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Residues in contact with TRP 170 (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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138A LEU* 4.5 12.0 - - + +
139A THR* 5.3 6.1 - - + -
144A GLU* 3.0 31.1 + - + +
145A HIS 3.7 11.4 - - - -
146A LEU* 3.8 23.5 - - + +
169A ASN* 1.3 73.0 - - - +
171A SER* 1.3 61.4 + - - +
172A PHE* 3.6 42.0 - + + -
179A ALA* 4.6 13.2 - - + -
180A HIS* 3.1 9.6 - - - +
181A ALA* 2.7 55.8 + - + +
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Residues in contact with SER 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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143A GLY 4.0 2.7 - - - -
144A GLU* 3.2 7.6 - - - +
145A HIS* 2.9 62.2 + - - +
169A ASN* 3.8 13.5 + - - -
170A TRP* 1.3 76.5 - - - +
172A PHE* 1.3 62.4 + - - +
173A GLU* 4.5 6.2 + - - -
180A HIS* 3.4 26.3 - - - -
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Residues in contact with PHE 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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139A THR* 4.8 3.6 - - + -
141A TYR* 3.7 40.4 - + + -
143A GLY 3.7 2.2 - - - -
144A GLU* 3.8 21.3 - - + -
170A TRP* 3.6 27.1 - + + -
171A SER* 1.3 74.4 - - - +
173A GLU* 1.3 63.8 + - - +
174A THR* 3.5 28.9 - - + -
177A LEU* 3.8 29.8 - - + -
178A ASN* 3.1 4.5 - - - -
179A ALA* 2.8 46.5 + - + +
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY* 3.1 36.8 + - - +
145A HIS* 5.6 2.0 + - - -
171A SER* 4.5 6.0 - - - -
172A PHE* 1.3 81.0 - - - +
174A THR* 1.3 68.5 + - - +
178A ASN* 3.5 22.0 + - - +
180A HIS* 3.3 28.0 + - - +
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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