Contacts of the strand formed by residues 225 - 231 (chain D) in PDB entry 1LO5
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 HIS 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D SER* 4.6 7.9 + - - -
125D VAL* 4.2 0.9 - - - -
126D PRO* 3.3 26.0 - - + +
128D ASN* 4.3 18.6 - - - +
187D HIS* 2.7 80.6 + - + +
188D THR* 5.5 3.6 - - - -
189D SER* 5.8 1.8 - - - -
223D ASN 3.9 7.8 + - - -
224D MET* 1.3 88.0 - - - +
226D ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 226 (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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125D VAL* 3.4 28.5 - - + -
126D PRO 2.6 11.1 + - - +
127D ILE* 3.5 28.9 - - + -
128D ASN* 2.9 29.5 + - - +
143D VAL* 4.8 4.5 - - + -
155D LEU* 4.9 5.8 - - + -
159D ALA* 5.1 2.0 - - + -
184D ILE* 4.0 26.0 - - + -
185D VAL 3.6 10.1 - - - +
186D PHE* 3.7 29.6 - - + -
187D HIS* 4.4 1.1 - - - -
224D MET* 4.5 6.5 - - - -
225D HIS* 1.3 82.2 - - - +
227D ALA* 1.3 72.6 + - - +
228D ILE* 4.3 8.1 - - + -
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Residues in contact with ALA 227 (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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1D SER* 4.6 2.9 - - - +
128D ASN 3.2 6.3 - - - +
130D TRP* 4.3 11.7 - - + -
184D ILE* 3.4 2.8 - - - +
185D VAL* 2.9 42.4 + - + +
187D HIS* 3.2 34.3 - - + +
226D ILE* 1.3 77.8 - - - +
228D ILE* 1.3 68.1 + - - +
229D TYR* 4.6 5.4 - - + -
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Residues in contact with ILE 228 (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 ILE* 3.7 26.0 - - + -
128D ASN 2.6 11.8 + - - +
129D LEU* 3.2 12.5 - - + -
130D TRP* 2.8 38.2 + - - -
159D ALA* 4.3 10.8 - - + -
162D TYR* 5.7 0.9 - - + -
163D LEU* 3.8 33.9 - - + -
183D LEU 3.6 9.2 - - - +
184D ILE* 4.0 20.9 - - + -
226D ILE* 4.3 2.2 - - + -
227D ALA* 1.3 80.7 - - - +
229D TYR* 1.3 65.0 + - - +
230D LEU* 3.4 29.2 - - + -
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Residues in contact with TYR 229 (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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1D SER* 3.5 10.3 - - - -
2D GLU* 2.6 44.9 + - + -
4D SER* 4.4 14.6 - - - -
7D ILE* 3.5 33.0 - - + -
130D TRP* 3.2 52.7 - + + -
182D GLY* 3.0 2.4 - - - -
183D LEU* 2.6 41.6 + - + +
185D VAL* 4.3 25.4 - - + -
227D ALA* 4.6 4.5 - - + -
228D ILE* 1.3 74.1 - - - +
230D LEU* 1.3 63.0 + - - +
231D TYR* 3.6 22.4 - - + +
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Residues in contact with LEU 230 (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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129D LEU* 5.1 4.5 - - + -
130D TRP* 3.0 13.9 + - - +
131D LEU* 4.8 7.9 - - + -
132D ASP 3.5 18.2 + - - -
163D LEU* 4.2 10.3 - - + -
167D TYR* 4.3 26.5 - - + -
169D LEU* 4.3 7.9 - - + -
179D VAL* 3.6 32.3 - - + -
181D ARG 3.5 3.4 - - - +
182D GLY* 3.6 1.8 - - - -
198D LEU* 3.3 30.1 - - + -
228D ILE* 3.4 17.7 - - + -
229D TYR* 1.3 86.6 - - - +
231D TYR* 1.3 78.0 + - - +
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Residues in contact with TYR 231 (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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4D SER* 3.4 31.7 + - - -
7D ILE* 3.3 26.0 - - + +
8D ASN* 3.2 34.2 + - - -
12D LEU* 4.0 19.3 - - + -
130D TRP* 6.3 0.4 - - + -
132D ASP* 4.5 10.3 - - - -
133D GLY 5.1 1.8 - - - -
179D VAL* 3.6 2.1 - - - +
180D GLN 2.8 22.2 + - - -
181D ARG* 2.9 61.9 + - + +
182D GLY 4.5 0.2 - - - -
183D LEU* 5.6 0.2 - - + -
229D TYR* 3.6 24.7 - - + +
230D LEU* 1.3 89.2 - - - +
232D THR* 1.3 61.9 + - - +
233D SER* 3.2 3.1 - - - +
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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