Contacts of the strand formed by residues 240 - 244 (chain C) in PDB entry 1LBH
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 240 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C HIS* 2.8 43.7 + - - +
180C GLN 4.3 1.2 + - - -
181C GLN* 3.2 27.0 + - + +
239C PRO* 1.3 77.6 - - - +
241C ALA* 1.3 58.3 + - - +
267C ASP 3.4 12.0 - - - +
268C ILE* 4.1 1.6 - - - -
269C SER* 2.8 22.4 + - - -
332C PRO* 4.7 15.8 - - + +
333C ASN* 5.2 6.1 - - + +
334C THR* 4.8 15.0 - - + -
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LEU* 3.3 31.4 - - + -
179C HIS* 3.6 24.5 - - + +
181C GLN 3.6 2.5 + - - +
182C ILE* 3.4 6.9 - - + +
183C ALA 3.0 24.3 + - - -
239C PRO* 3.4 4.9 - - - +
240C THR* 1.3 84.7 + - - +
242C MET* 1.3 62.9 + - - +
268C ILE* 4.5 0.9 - - - +
269C SER* 3.1 9.4 - - - +
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Residues in contact with MET 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU* 5.0 0.8 - - - +
183C ALA* 3.3 16.4 - - + +
185C LEU* 3.8 34.8 - - + +
229C THR* 3.8 33.4 - - - +
232C MET* 3.7 27.1 - - + +
233C LEU* 6.3 0.2 - - - -
239C PRO* 4.1 10.3 - - + -
241C ALA* 1.3 76.7 - - - +
243C LEU* 1.3 63.2 + - - +
244C VAL* 4.0 4.2 + - + -
253C ALA* 4.6 7.9 - - - -
257C ILE* 4.8 7.2 - - - -
268C ILE* 4.1 8.9 - - + +
269C SER 2.7 11.8 + - - +
270C VAL* 3.1 12.7 - - + +
271C VAL* 3.1 24.1 + - - +
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLY* 3.6 28.9 - - - +
171C VAL* 4.3 21.3 - - + +
174C LEU* 3.8 15.5 - - + -
182C ILE* 3.7 24.2 - - + -
183C ALA 3.0 6.1 + - - -
184C LEU* 3.6 18.6 - - + -
185C LEU* 2.8 26.7 + - - +
201C TRP* 4.1 24.9 - - + +
205C LEU* 4.9 3.4 - - + -
241C ALA 4.3 0.2 - - - -
242C MET* 1.3 72.7 - - - +
244C VAL* 1.3 62.8 + - - +
271C VAL* 3.8 22.4 - - + -
272C GLY 5.9 0.4 - - - +
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.3 39.0 - - + +
201C TRP* 3.6 8.8 - - - -
242C MET* 4.3 15.7 - - + +
243C LEU* 1.3 79.3 - - - +
245C ALA* 1.3 66.0 + - - +
246C ASN 3.3 6.9 + - - +
249C MET* 3.5 22.2 - - + -
250C ALA* 3.7 19.1 - - + +
253C ALA* 4.7 3.6 - - + -
270C VAL* 4.4 6.7 - - + -
271C VAL 3.3 18.3 + - - +
272C GLY 3.8 18.0 - - - +
273C TYR* 4.0 1.6 - - - +
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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