Contacts of the strand formed by residues 240 - 244 (chain B) in PDB entry 1LBI
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B HIS* 2.7 47.1 + - - +
180B GLN 4.4 0.2 + - - -
181B GLN* 2.7 31.8 + - + -
238B VAL 4.9 2.2 - - - +
239B PRO* 1.3 76.5 - - - +
241B ALA* 1.3 53.5 + - - +
267B ASP 3.6 13.4 - - - +
268B ILE* 3.6 1.1 - - - -
269B SER 2.7 29.4 + - - -
332B PRO* 3.8 19.9 - - + +
333B ASN* 4.2 13.5 - - - +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 3.6 33.7 - - + -
179B HIS* 3.4 19.7 - - + +
181B GLN 3.4 1.2 + - - -
182B ILE* 3.0 13.1 - - + -
183B ALA 2.7 30.5 + - - -
239B PRO* 3.2 4.0 - - - +
240B THR* 1.3 84.8 + - - +
242B MET* 1.3 58.6 + - - +
269B SER* 3.5 7.6 - - - -
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Residues in contact with MET 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.3 4.3 - - - +
183B ALA* 3.3 10.8 - - + +
184B LEU 5.8 0.7 - - - -
185B LEU* 4.5 19.1 - - + +
216B ARG* 6.4 0.7 - - - -
229B THR* 3.2 43.5 - - + +
232B MET* 4.2 20.2 - - + -
239B PRO* 4.1 7.0 - - + -
241B ALA* 1.3 78.1 - - - +
243B LEU* 1.3 66.4 + - - +
244B VAL* 3.9 11.0 - - + -
253B ALA* 4.2 9.9 - - + -
257B ILE* 3.9 15.5 - - - -
268B ILE* 3.7 10.3 - - + -
269B SER 3.0 18.0 + - - +
270B VAL* 3.7 4.7 - - + -
271B VAL 3.3 22.0 + - - -
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Residues in contact with LEU 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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170B GLY* 3.9 17.5 - - - -
171B VAL* 3.8 24.9 - - + -
174B LEU* 3.6 27.4 - - + -
182B ILE* 3.6 15.0 - - + -
183B ALA 2.8 8.5 + - - -
184B LEU* 3.3 32.3 - - + -
185B LEU 2.9 23.7 + - - +
201B TRP* 3.8 34.1 + - + -
205B LEU* 3.8 4.7 - - + -
242B MET* 1.3 73.4 - - - +
244B VAL* 1.3 60.3 + - - +
271B VAL* 4.1 10.1 - - + -
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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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185B LEU* 3.4 29.4 - - + +
201B TRP* 3.9 10.0 - - - -
242B MET* 4.3 17.3 - - + -
243B LEU* 1.3 75.5 - - - +
245B ALA* 1.3 64.2 + - - +
246B ASN 3.2 26.3 + - - +
249B MET* 3.8 21.5 - - + -
250B ALA* 3.9 11.0 - - + +
253B ALA* 4.4 11.7 - - + -
270B VAL* 4.4 9.6 - - + -
271B VAL 3.1 19.7 + - - +
272B GLY* 3.8 2.3 - - - -
273B TYR* 3.7 12.3 - - - +
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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