Contacts of the strand formed by residues 250 - 258 (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 THR 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B MET* 3.5 25.5 - - + +
202B THR 4.4 0.7 + - - -
243B GLN* 3.3 42.6 - - + +
244B VAL* 3.7 10.5 - - - +
245B VAL* 3.1 22.0 - - + +
249B GLU* 1.3 74.6 - - - +
251B CYS* 1.3 63.9 + - - +
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Residues in contact with CYS 251 (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* 3.5 9.6 - - - -
202B THR* 3.1 22.7 - - - +
204B TYR* 3.6 29.2 - - + -
243B GLN* 3.4 3.1 - - - +
244B VAL* 3.0 42.4 + - - +
246B ILE* 4.0 24.5 - - - -
249B GLU* 4.3 8.3 - - + +
250B THR* 1.3 76.8 - - - +
252B LEU* 1.3 57.8 + - - +
253B LEU* 3.8 5.5 + - - -
360B VAL* 4.6 0.7 - - - -
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Residues in contact with LEU 252 (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* 3.8 28.3 - - + +
202B THR 3.0 7.5 + - - +
203B GLU* 3.3 35.4 - - + +
204B TYR* 2.7 34.3 + - - +
241B ARG* 3.2 48.9 - - + +
242B LYS 3.9 11.9 - - - +
243B GLN* 4.1 7.4 - - + +
251B CYS* 1.3 71.0 - - - +
253B LEU* 1.3 61.0 + - - +
254B ASP* 3.9 1.3 - - - +
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Residues in contact with LEU 253 (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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204B TYR* 3.7 24.0 - - + -
206B LEU* 4.0 10.3 - - + -
223B LEU* 4.5 17.7 - - + -
224B ILE* 5.2 0.8 - - + +
240B TYR 3.8 0.5 - - - +
241B ARG* 3.1 5.7 - - - -
242B LYS* 3.0 42.9 + - + +
244B VAL* 3.6 30.1 - - + -
246B ILE* 4.4 3.6 - - + -
251B CYS* 4.2 7.9 - - - -
252B LEU* 1.3 74.7 - - - +
254B ASP* 1.3 63.0 + - - +
255B ILE* 3.8 11.7 + - + +
356B PHE* 5.3 0.9 - - + -
357B TYR* 4.4 9.9 - - + -
360B VAL* 3.6 31.9 - - + -
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Residues in contact with ASP 254 (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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203B GLU* 3.1 29.2 - - - +
204B TYR 2.7 13.7 + - - +
205B LYS* 3.5 14.5 - - + +
206B LEU* 2.7 34.8 + - - +
239B SER* 5.9 1.3 - - - +
240B TYR 3.4 7.0 - - - +
241B ARG* 3.0 44.0 + - - +
252B LEU* 3.8 1.9 + - - +
253B LEU* 1.3 76.7 - - - +
255B ILE* 1.3 56.9 + - - +
256B LEU 4.1 0.2 - - - -
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Residues in contact with ILE 255 (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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206B LEU* 3.4 14.4 - - + +
208B VAL* 3.7 24.7 - - + -
220B THR* 3.7 21.1 - - + +
223B LEU* 3.5 31.9 - - + -
224B ILE* 3.6 21.5 - - + -
239B SER* 3.5 5.7 + - - -
240B TYR* 2.8 46.7 + - + +
253B LEU* 4.5 12.8 - - + +
254B ASP* 1.3 76.2 - - - +
256B LEU* 1.3 62.5 + - - +
257B ASP 3.7 1.0 + - - -
356B PHE* 3.7 13.9 - - + -
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Residues in contact with LEU 256 (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* 4.0 11.4 - - - +
206B LEU 2.8 16.1 + - - +
207B VAL* 3.5 14.4 - - + +
208B VAL* 3.0 26.0 + - - +
237B GLU* 3.7 35.7 - - + +
238B ASP 3.7 8.5 - - - +
239B SER* 4.4 7.2 - - - +
254B ASP 4.1 0.6 + - - -
255B ILE* 1.3 72.7 - - - +
257B ASP* 1.3 58.4 + - - +
258B THR* 3.5 11.7 + - + -
271B TYR* 3.4 37.5 - - + +
274B THR* 5.7 1.8 - - - +
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Residues in contact with ASP 257 (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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208B VAL* 4.5 5.2 - - - +
216B LYS* 3.6 14.2 - - - +
217B SER* 2.7 49.4 + - - -
220B THR* 4.1 14.3 + - + +
235B THR* 3.5 10.4 + - - +
237B GLU* 3.6 1.9 - - - +
238B ASP* 2.8 56.6 + - + +
240B TYR* 4.3 14.5 + - + -
255B ILE 3.7 1.2 + - - -
256B LEU* 1.3 70.5 - - - +
258B THR* 1.3 62.5 + - - +
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Residues in contact with THR 258 (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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207B VAL* 3.6 27.1 - - + -
208B VAL 2.8 21.0 + - - +
209B VAL* 3.8 7.3 - - - -
210B GLY 4.9 0.3 + - - -
216B LYS* 3.2 20.8 - - - -
235B THR* 3.9 10.9 - - - -
236B ILE 4.6 2.9 - - - -
237B GLU* 4.8 4.3 - - + +
256B LEU* 3.9 10.5 - - + +
257B ASP* 1.3 82.0 + - - +
259B ALA* 1.3 63.5 + - - +
260B GLY 3.8 0.2 + - - -
271B TYR* 3.6 42.4 + - + -
296B TYR* 5.7 0.5 - - - -
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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