Contacts of the strand formed by residues 164 - 169 (chain D) in PDB entry 4OD9
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 ILE 164 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D PHE* 3.6 7.6 - - - -
162D GLN* 2.8 33.1 + - + +
163D ASN* 1.3 83.9 - - - +
165D PHE* 1.3 62.9 + - - +
184D GLY* 2.8 28.4 + - - -
185D GLY* 3.5 32.3 - - - +
186D THR* 3.8 16.8 - - + -
197D TYR* 6.1 0.4 - - - +
332D VAL* 4.2 10.3 - - + -
333D PHE 3.2 9.6 - - - +
334D ASP* 3.5 31.9 - - + +
336D ASP* 4.7 2.9 - - - +
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Residues in contact with PHE 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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34C THR* 3.7 14.8 - - + -
137D MET* 3.5 51.6 - - + -
151D PHE* 3.8 32.1 - + + -
164D ILE* 1.3 75.3 - - - +
166D SER* 1.3 63.8 + - - +
167D PHE* 3.7 14.1 - + - -
181D LEU* 4.0 7.6 - - + -
182D MET 3.1 13.2 - - - +
183D LEU* 4.2 11.2 - - + -
185D GLY 4.3 0.7 - - - -
206D TRP* 3.8 14.6 - + - -
332D VAL* 3.7 0.2 - - - -
333D PHE* 2.8 70.1 + + + +
335D ARG* 4.7 1.8 - - + -
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Residues in contact with SER 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D PHE* 1.3 76.6 + - - +
167D PHE* 1.3 65.4 + - - +
180D GLU 3.5 1.1 - - - +
181D LEU* 3.3 6.8 - - - +
182D MET* 2.8 33.1 + - - +
185D GLY 2.7 22.9 + - - -
186D THR* 3.6 4.4 - - - +
330D TYR* 3.2 29.1 + - - -
331D THR 3.2 11.4 - - - -
332D VAL* 3.5 17.6 - - - +
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Residues in contact with PHE 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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7C LEU* 4.1 22.7 - - + -
32C PHE* 3.7 43.5 - - + -
34C THR* 3.7 22.9 - - + -
137D MET* 4.2 3.1 - - - -
165D PHE* 3.7 8.5 - + - -
166D SER* 1.3 77.7 - - - +
168D TYR* 1.3 59.1 + - - +
169D LEU* 4.1 8.5 - - + -
180D GLU 3.4 2.9 - - - -
181D LEU* 3.7 25.8 - - + -
232D THR* 3.8 16.4 - - + -
326D ILE* 4.2 20.3 - - + +
330D TYR* 3.3 11.4 - - - -
331D THR 2.8 32.9 + - - +
333D PHE* 3.5 17.7 - + + -
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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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167D PHE* 1.3 73.0 - - - +
169D LEU* 1.3 78.0 + - - +
170D SER* 3.7 30.7 + - - -
175D ALA* 5.4 2.1 - - - +
177D PRO* 4.3 9.9 + - + -
179D GLY* 3.2 17.4 - - - -
180D GLU* 2.8 37.2 + - + +
190D TYR* 3.6 60.0 - + + -
326D ILE 5.6 0.2 - - - -
327D GLY 5.4 0.4 - - - -
330D TYR* 3.6 22.2 - + + +
345D ALA* 4.8 9.9 - - + -
346D ALA 4.3 19.1 + - - -
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Residues in contact with LEU 169 (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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7C LEU* 4.0 17.5 - - + -
15C TYR* 3.8 34.8 - - + -
167D PHE* 4.1 13.4 + - + -
168D TYR* 1.3 91.5 - - - +
170D SER* 1.3 64.3 + - - +
171D ARG 3.7 0.5 + - - -
178D GLY 4.1 2.7 - - - -
232D THR* 4.9 5.2 - - + -
323D ASP* 3.4 37.2 - - + +
326D ILE* 3.7 36.7 + - + -
327D GLY* 3.4 30.4 - - - +
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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