Contacts of the strand formed by residues 160 - 168 (chain D) in PDB entry 3ORH
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 LEU 160 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLY* 3.4 9.0 - - - -
129D PHE 3.4 14.6 - - - +
131D GLY* 4.2 3.8 - - - -
132D ILE* 3.8 24.9 - - + -
156D ALA 3.2 21.1 + - - +
158D ARG 3.4 0.4 - - - -
159D LEU* 1.3 77.0 - - - +
161D LYS* 1.3 65.2 + - - +
162D PRO* 4.7 0.2 - - - +
164D GLY 3.8 15.7 - - - +
165D VAL 3.7 24.2 - - - +
166D LEU* 4.1 15.9 - - + -
202D PHE* 3.9 27.6 - - + -
235D LYS* 2.9 35.9 + - + -
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Residues in contact with LYS 161 (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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63D ARG* 3.7 25.4 - - - +
127D GLY* 3.3 23.6 - - - +
128D HIS 3.8 5.4 - - - -
129D PHE 2.9 18.1 + - - +
130D ASP* 3.3 39.8 + - - +
159D LEU 3.7 0.2 + - - -
160D LEU* 1.3 76.1 - - - +
162D PRO* 1.4 74.6 - - + +
163D GLY 3.2 0.3 + - - -
164D GLY* 2.8 23.5 + - - +
235D LYS* 3.7 5.8 - - - +
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Residues in contact with PRO 162 (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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127D GLY* 5.5 2.5 - - - +
160D LEU 4.7 0.7 - - - +
161D LYS* 1.4 89.5 - - + +
163D GLY* 1.3 59.2 + - - +
164D GLY 3.4 0.3 + - - -
235D LYS* 4.4 10.0 - - + +
236D GLY 3.7 20.6 - - - +
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Residues in contact with GLY 163 (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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60D LYS* 3.9 20.1 - - - +
162D PRO* 1.3 71.5 - - - +
164D GLY* 1.3 66.0 + - - +
165D VAL* 3.9 1.2 + - - +
234D THR* 3.7 13.4 - - - +
235D LYS 2.9 21.4 + - - -
236D GLY 4.0 2.2 + - - -
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Residues in contact with GLY 164 (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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60D LYS* 5.0 0.7 - - - -
129D PHE 4.5 1.8 - - - -
130D ASP* 3.2 18.2 - - - -
160D LEU* 3.8 15.2 - - - +
161D LYS* 2.8 19.3 + - - +
162D PRO 3.2 1.6 + - - -
163D GLY* 1.3 79.0 - - - +
165D VAL* 1.3 58.5 + - - -
233D VAL 3.8 0.9 - - - +
234D THR* 3.3 2.6 - - - -
235D LYS* 2.9 25.0 + - - +
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Residues in contact with VAL 165 (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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56D ALA* 3.7 25.4 - - + +
57D ALA* 4.7 2.2 - - - +
59D SER* 4.2 7.2 - - - +
60D LYS* 3.9 22.2 - - + -
130D ASP 2.9 12.9 + - - +
131D GLY* 3.2 4.6 - - - -
132D ILE 2.9 25.8 + - - +
160D LEU* 3.7 4.6 - - - +
163D GLY 4.0 2.9 - - - +
164D GLY* 1.3 74.8 - - - +
166D LEU* 1.3 72.6 + - - +
232D LEU* 4.4 16.6 - - + -
233D VAL 3.5 10.5 - - - +
234D THR* 3.6 20.2 - - + +
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Residues in contact with LEU 166 (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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132D ILE* 3.6 25.8 - - + +
134D TYR* 4.9 0.9 - - + -
151D PHE* 4.7 3.4 - - + -
152D ILE* 3.7 33.0 - - + -
156D ALA* 3.7 28.0 - - + -
160D LEU* 4.1 12.8 - - + +
165D VAL* 1.3 74.1 - - - +
167D THR* 1.3 80.4 + - - +
168D TYR* 4.6 7.4 - - + -
197D LEU* 4.7 2.2 - - + -
202D PHE* 4.1 11.4 - - + -
231D PRO 3.7 0.3 - - - +
232D LEU* 3.7 3.6 - - - -
233D VAL* 2.7 58.6 + - + +
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Residues in contact with THR 167 (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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53D LEU* 3.3 44.9 - - + +
56D ALA* 4.0 9.4 - - - -
57D ALA* 3.8 12.6 - - + +
132D ILE 2.9 18.3 + - - +
133D LEU* 3.9 11.9 - - + -
134D TYR 3.0 20.5 + - - -
165D VAL* 5.3 0.2 - - - -
166D LEU* 1.3 76.7 - - - +
168D TYR* 1.3 67.4 + - - +
230D THR* 3.8 4.3 - - - +
231D PRO* 2.7 24.7 + - - +
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Residues in contact with TYR 168 (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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53D LEU* 3.8 7.5 - - - +
133D LEU* 5.5 0.4 - - - -
134D TYR* 3.1 29.6 - - + +
148D GLN* 3.7 26.9 - - + -
149D PHE* 4.4 1.4 - - - -
152D ILE* 3.8 22.4 - - + -
166D LEU* 4.6 9.9 - - + -
167D THR* 1.3 82.5 + - - +
169D CYS* 1.3 70.7 + - - +
174D TRP* 3.6 17.0 - + - -
189D PHE* 3.6 7.1 - + - -
193D GLN* 2.9 45.6 + - - +
197D LEU* 3.9 19.0 - - + +
231D PRO* 3.2 44.4 - - + +
233D VAL* 4.8 2.0 - - + -
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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