Contacts of the strand formed by residues 150 - 155 (chain D) in PDB entry 3LUE
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 GLY 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B MET* 1.3 91.5 - - - +
149D THR* 1.3 61.6 - - - +
151D ILE* 1.3 57.1 + - - -
165D ILE 2.9 16.1 + - - -
293D LEU* 3.0 22.1 - - - +
296D ASN* 3.4 11.2 - - - -
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Residues in contact with ILE 151 (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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44B MET* 2.9 1.1 - - - +
150D GLY* 1.3 75.0 - - - +
152D VAL* 1.3 72.6 + - - +
153D MET* 5.9 0.2 - - + -
162D THR* 4.3 6.7 - - - -
163D VAL 3.2 19.7 - - - +
164D PRO* 4.0 15.3 - - + -
278D THR* 4.0 20.9 - - + +
281D SER* 3.7 29.8 - - - -
282D ILE* 4.3 12.1 - - + -
293D LEU* 3.4 32.1 - - + +
296D ASN 2.9 5.8 + - - +
297D THR* 3.4 12.8 - - + +
298D VAL* 2.9 24.6 + - - +
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Residues in contact with VAL 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.0 15.5 - - + +
138D ALA* 3.5 23.6 - - + +
142D LEU* 2.1 52.5 - - + -
151D ILE* 1.3 78.9 - - - +
153D MET* 1.3 64.9 + - - +
154D ASP* 3.9 0.4 - - - -
161D HIS 3.7 0.7 - - - +
162D THR* 3.4 4.3 - - - -
163D VAL* 3.2 31.2 + - + +
165D ILE* 4.7 1.3 - - + -
297D THR* 6.3 0.2 - - - -
298D VAL* 3.2 10.5 - - + +
300D SER* 3.5 26.5 - - - +
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Residues in contact with MET 153 (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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152D VAL* 1.3 75.0 - - - +
154D ASP* 1.3 59.5 + - - +
155D SER* 3.9 4.7 + - - -
160D THR* 3.5 28.9 - - + -
161D HIS 3.5 2.7 - - - -
162D THR* 3.6 9.4 - - + -
261D LEU* 6.5 0.4 - - + -
274D ILE* 3.5 25.6 - - + -
278D THR* 3.5 24.9 - - + +
297D THR* 5.5 4.0 - - + -
298D VAL 2.8 14.1 + - - +
299D LEU* 3.5 15.6 - - + -
300D SER 2.9 23.3 + - - +
304D THR* 4.0 18.2 - - + +
309D ILE* 5.3 6.3 - - + -
313D MET* 3.8 20.4 - - + -
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Residues in contact with ASP 154 (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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109D PRO* 3.7 10.2 - - + +
137D GLN* 2.9 18.1 - - - +
138D ALA* 1.5 73.0 + - + +
141D SER* 3.4 1.2 + - - -
153D MET* 1.3 72.6 - - - +
155D SER* 1.3 59.8 + - - +
156D GLY 4.5 2.4 + - - -
159D VAL 3.6 1.4 - - - +
160D THR* 3.1 24.6 - - - -
161D HIS 2.9 12.4 + - - +
300D SER* 2.6 19.7 + - - +
301D GLY* 4.9 2.9 - - - -
339D VAL* 4.4 0.3 - - - +
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Residues in contact with SER 155 (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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153D MET* 3.9 6.9 + - - -
154D ASP* 1.3 73.2 + - - +
156D GLY* 1.3 60.0 + - - +
159D VAL 3.7 2.5 - - - -
160D THR* 2.9 24.2 + - - +
181D ALA* 4.2 3.5 - - - -
261D LEU* 4.4 6.0 - - - +
300D SER 3.0 10.3 + - - -
301D GLY* 3.3 12.3 - - - -
303D THR* 3.0 49.8 + - - +
304D THR* 4.1 13.7 - - - -
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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