Contacts of the strand formed by residues 171 - 175 (chain B) in PDB entry 1LPB
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 ARG 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 5.7 4.4 - - - +
71B ARG* 4.9 4.9 - - - +
146B VAL 3.3 4.2 + - - -
147B HIS* 3.0 44.6 + - + -
148B VAL 3.0 24.8 + - - -
169B ILE* 3.5 4.3 + - - +
170B GLY* 1.3 77.8 - - - +
172B ILE* 1.3 64.2 + - - +
173B THR* 3.3 7.2 + - - -
196B ALA* 4.0 2.9 - - - -
198B PHE* 3.0 35.0 - - + +
200B ASP* 2.6 43.3 + - - -
270B TYR* 4.1 1.4 + - - -
308B GLY 3.4 8.9 + - - -
309B HIS* 2.5 37.2 + - - +
311B ALA* 4.3 1.4 - - - +
312B ASP* 3.8 26.0 + - + +
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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
----------------------------------------------------------
148B VAL* 3.1 18.2 - - + +
155B ALA 4.7 0.7 - - - +
158B ALA* 3.1 45.3 - - + +
159B GLY* 4.2 1.3 - - - -
162B GLY* 4.5 2.9 - - - -
169B ILE* 4.8 6.1 - - + -
171B ARG* 1.3 81.3 - - - +
173B THR* 1.3 73.0 - - - +
174B GLY* 4.0 2.0 - - - +
191B LEU* 3.6 25.1 - - + -
195B ASP* 4.0 21.3 - - + +
196B ALA* 3.8 20.6 - - + -
198B PHE 3.2 4.2 + - - -
199B VAL* 3.4 6.0 - - + +
200B ASP* 2.9 28.8 + - - +
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Residues in contact with THR 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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147B HIS* 2.8 27.8 + - - -
148B VAL 3.0 6.9 + - - -
149B ILE* 4.3 8.8 - - + +
150B GLY 3.0 24.9 + - - +
155B ALA* 5.2 0.2 - - - -
171B ARG* 3.3 5.7 + - - -
172B ILE* 1.3 74.7 - - - +
174B GLY* 1.3 63.0 + - - +
175B LEU* 3.6 26.8 + - + -
200B ASP* 3.0 28.4 + - - +
202B ILE* 5.1 4.7 - - + -
270B TYR* 3.9 16.8 - - + -
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Residues in contact with GLY 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLY 3.7 4.9 - - - -
155B ALA* 3.9 16.2 - - - -
172B ILE* 4.0 3.2 - - - +
173B THR* 1.3 73.1 - - - +
175B LEU* 1.3 63.0 + - - +
176B ASP 3.7 0.7 - - - -
177B PRO* 4.0 1.8 - - - -
191B LEU* 4.1 16.5 - - - +
200B ASP 3.2 8.5 + - - +
201B VAL* 3.1 25.8 - - - +
202B ILE 3.1 11.3 + - - -
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Residues in contact with LEU 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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85B TRP* 4.9 4.0 - - + -
149B ILE* 3.6 30.1 - - + -
150B GLY 2.9 13.0 + - - +
151B HIS* 3.2 19.5 - - + -
152B SER 3.0 19.8 + - - -
155B ALA* 4.4 0.2 - - - +
173B THR* 3.7 21.1 - - + -
174B GLY* 1.3 69.4 - - - +
176B ASP* 1.3 68.1 + - - +
202B ILE* 3.9 20.2 - - + -
266B SER* 3.7 28.7 - - - +
267B TYR* 3.8 27.4 - - + -
270B TYR* 4.0 11.0 - - + -
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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