Contacts of the strand formed by residues 167 - 175 (chain B) in PDB entry 2R3U
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 3.6 12.3 - - - -
175A ALA* 4.8 1.1 - - + -
191A GLN* 3.8 34.4 + - - +
157B ALA 3.4 4.3 - - - +
158B ILE* 3.5 3.6 - - - +
159B GLY 3.0 25.4 + - - -
161B PRO* 3.4 29.8 - - + +
164B LEU* 4.6 7.0 - - + -
165B GLY 3.0 17.9 - - - +
166B GLN* 1.3 73.4 - - - +
168B ILE* 1.3 66.0 + - - +
169B THR* 4.2 12.1 - - - +
200B ASN* 5.0 1.4 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 3.7 18.2 - - + -
172A ILE* 3.6 20.7 - - + +
174A SER* 2.5 49.3 + - - +
51B VAL* 4.2 22.4 - - + -
55B ALA* 4.5 0.2 - - + -
156B LEU* 4.0 32.8 - - + -
157B ALA 3.4 4.5 - - - +
158B ILE* 3.6 31.4 - - + -
166B GLN* 4.3 11.4 - - + +
167B THR* 1.3 82.8 - - - +
169B THR* 1.3 59.4 + - - +
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Residues in contact with THR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 4.2 2.2 - - - -
174A SER* 4.3 2.5 - - - +
191A GLN* 6.2 0.7 - - - +
193A ASP* 3.8 16.2 - - + -
231A GLY 4.7 3.8 - - - +
232A ILE* 6.1 1.6 - - + -
156B LEU* 3.2 4.0 - - - -
157B ALA* 2.8 45.4 + - - +
161B PRO* 6.0 0.7 - - + -
167B THR* 4.2 13.2 - - - +
168B ILE* 1.3 78.7 - - - +
170B GLN* 1.3 60.4 + - - +
194B ALA* 3.8 1.8 - - - +
195B SER* 2.8 51.3 + - - +
197B ASN* 5.5 4.0 - - - +
200B ASN* 5.7 2.9 - - - +
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Residues in contact with GLN 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TYR* 5.6 2.6 + - - -
154A VAL* 5.5 1.4 - - - +
170A GLN* 3.8 19.6 + - - +
171A GLY* 4.6 5.7 - - - -
172A ILE* 3.5 26.0 - - + +
193A ASP* 3.1 20.7 + - - +
47B TYR* 4.1 20.5 + - - -
154B VAL* 4.1 6.2 - - - +
155B VAL 3.4 3.4 - - - -
156B LEU* 3.2 25.4 - - + -
169B THR* 1.3 73.8 - - - +
171B GLY* 1.3 90.3 + - - +
193B ASP 4.8 0.7 - - - +
194B ALA* 3.8 7.6 - - - -
195B SER 5.0 0.3 + - - -
170C GLN* 3.4 24.1 + - - +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B VAL* 3.8 0.3 - - - -
155B VAL* 2.9 28.3 + - - -
170B GLN* 1.3 86.6 + - - +
172B ILE* 1.3 66.3 + - - +
193B ASP* 3.1 16.8 - - - -
194B ALA* 3.4 13.0 - - - +
170C GLN* 4.8 3.8 - - - -
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLY* 3.9 22.2 - - - +
153B ASP 3.4 9.9 - - - +
154B VAL* 4.2 7.4 - - - -
155B VAL* 3.9 4.0 - - - -
171B GLY* 1.3 77.5 - - - +
173B ILE* 1.3 64.3 + - - +
174B SER 3.2 6.8 + - - -
192B THR* 2.9 22.8 + - - -
193B ASP* 2.7 19.4 + - - +
47C TYR* 4.2 8.5 - - + -
156C LEU* 3.8 23.8 - - + -
168C ILE* 3.3 37.5 - - + +
170C GLN* 3.3 34.1 - - + +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 4.2 13.7 - - + -
150B HIS 3.6 26.9 - - - +
151B ILE* 3.4 12.2 - - + +
152B GLY* 3.0 22.1 + - - +
153B ASP* 3.1 14.7 + - + +
155B VAL* 4.4 12.1 - - + -
172B ILE* 1.3 78.0 - - - +
174B SER* 1.3 58.7 + - - +
175B ALA 3.5 25.4 - - - +
176B THR* 4.7 4.0 - - - +
190B LEU* 4.1 24.2 - - + -
191B GLN 3.8 2.5 - - - -
192B THR* 4.7 0.9 - - - +
213B MET* 4.1 29.4 - - + -
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 3.8 10.5 - - - +
172B ILE 3.2 1.7 + - - -
173B ILE* 1.3 72.3 - - - +
175B ALA* 1.3 59.0 + - - +
191B GLN* 2.6 40.5 + - - -
192B THR 3.5 1.2 - - - -
193B ASP* 3.4 27.5 + - - +
231B GLY 4.8 0.3 + - - -
166C GLN 4.2 1.7 - - - +
167C THR* 3.8 5.6 - - - -
168C ILE* 3.0 44.3 + - - +
169C THR* 4.4 2.1 - - - +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 4.3 10.1 - - + -
173B ILE* 3.4 15.9 - - - +
174B SER* 1.3 75.8 - - - +
176B THR* 1.3 60.3 + - - +
177B GLY 4.3 5.6 - - - +
178B ARG* 3.0 40.2 - - - +
189B PHE 5.2 1.1 - - - +
190B LEU* 3.6 3.6 - - - +
191B GLN* 3.0 35.8 + - + -
166C GLN 4.5 0.2 - - - +
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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