Contacts of the strand formed by residues 237 - 245 (chain B) in PDB entry 1LFD
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 GLU 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ARG* 3.4 19.9 + - - -
31A TYR* 3.0 30.8 + - - +
33A SER* 2.6 32.8 + - - +
235B THR* 3.4 0.8 - - - +
236B ILE* 1.3 84.6 - - - +
238B ASP* 1.3 67.8 + - - +
256B LEU* 3.7 31.6 - - + +
257B ASP 3.6 9.9 - - - +
258B THR* 4.8 3.8 - - + +
267B MET* 3.9 27.3 - - + +
271B TYR* 4.9 9.5 - - + +
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Residues in contact with ASP 238 (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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31A TYR* 3.7 9.2 - - - +
32A LYS* 3.3 21.7 - - + +
33A SER 3.2 18.9 + - - +
52A LYS* 4.5 10.3 + - - +
217B SER* 4.9 1.0 + - - -
235B THR* 3.7 20.0 + - - +
236B ILE 4.9 0.2 + - - -
237B GLU* 1.3 82.0 + - - +
239B SER* 1.3 62.3 + - - +
240B TYR* 4.0 21.5 + - + -
256B LEU* 3.7 5.6 - - - +
257B ASP* 2.8 46.4 + - + +
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Residues in contact with SER 239 (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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29A ASN* 3.1 8.5 + - - -
30A MET* 2.8 38.3 + - - +
31A TYR* 3.1 46.8 + - - -
238B ASP* 1.3 74.1 - - - +
240B TYR* 1.3 64.4 + - - +
254B ASP* 5.9 1.6 - - - +
255B ILE 3.5 8.1 + - - -
256B LEU* 4.4 7.0 - - - +
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Residues in contact with TYR 240 (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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28A GLY 3.4 16.2 - - - +
29A ASN* 3.5 31.0 - - + -
30A MET* 4.2 3.3 - - - +
32A LYS* 3.4 20.5 + - - -
220B THR* 3.5 25.1 - - + -
221B ILE* 3.5 27.1 - - + +
224B ILE* 3.8 30.3 - - + -
225B GLN* 3.8 17.0 - - - -
238B ASP* 4.0 21.0 + - + -
239B SER* 1.3 80.8 + - - +
241B ARG* 1.3 64.8 + - - +
254B ASP* 3.4 3.8 - - - +
255B ILE* 2.8 39.6 + - + +
257B ASP* 4.3 9.4 + - + -
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Residues in contact with ARG 241 (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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28A GLY* 2.9 25.7 + - - +
30A MET* 3.9 38.9 - - + +
203B GLU* 3.1 17.1 + - - -
224B ILE* 4.6 0.7 - - - -
240B TYR* 1.3 77.6 - - - +
242B LYS* 1.3 64.0 + - - +
252B LEU* 3.2 33.6 - - + +
253B LEU 3.1 6.7 - - - +
254B ASP* 3.0 33.9 + - - +
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Residues in contact with LYS 242 (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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28A GLY* 6.0 0.9 - - - -
223B LEU* 3.1 22.7 + - + +
224B ILE* 3.2 48.3 + - + +
226B ASN* 3.6 16.8 + - - +
241B ARG* 1.3 78.7 - - - +
243B GLN* 1.3 73.0 + - - +
244B VAL* 3.6 14.8 + - + +
252B LEU* 3.9 4.5 - - - -
253B LEU* 3.0 35.2 + - + +
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Residues in contact with GLN 243 (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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201B MET* 3.3 31.9 - - + +
242B LYS* 1.3 83.8 - - - +
244B VAL* 1.3 61.3 + - - +
250B THR* 3.3 30.1 - - + +
251B CYS 3.4 5.8 - - - +
252B LEU* 4.1 9.2 - - + +
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Residues in contact with VAL 244 (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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242B LYS* 4.2 15.9 - - + +
243B GLN* 1.3 76.7 - - - +
245B VAL* 1.3 75.7 + - + +
246B ILE* 4.1 11.0 - - + -
250B THR* 4.4 2.0 - - - -
251B CYS* 3.0 31.9 + - - +
253B LEU* 3.6 37.0 - - + -
357B TYR* 3.2 26.5 - - - +
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Residues in contact with VAL 245 (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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244B VAL* 1.3 82.5 - - + +
246B ILE* 1.3 64.0 + - - +
247B ASP 4.2 0.7 - - - -
248B GLY* 5.3 2.7 - - - +
249B GLU 3.7 11.2 - - - +
250B THR* 3.1 26.7 - - + +
357B TYR* 4.8 5.7 - - - -
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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