Contacts of the strand formed by residues 273 - 277 (chain B) in PDB entry 3LMK
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 VAL 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B TRP* 3.7 58.8 - - + +
213B TYR 5.0 2.3 + - - +
214B VAL* 3.5 23.8 - - + +
215B SER* 2.9 25.1 + - - -
271B ALA* 4.3 1.6 - - - +
272B ARG* 1.3 88.7 - - + +
274B VAL* 1.3 69.0 + - - +
275B ALA* 4.7 0.7 - - + +
300B LEU* 3.3 23.3 - - + +
302B LEU* 4.5 9.9 - - + -
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B SER* 3.4 11.0 - - - +
217B VAL* 3.9 29.8 - - + -
264B LEU* 4.3 22.2 - - + -
271B ALA 4.9 0.7 - - - +
272B ARG 4.1 2.2 - - - +
273B VAL* 1.3 79.2 - - - +
275B ALA* 1.3 68.7 + - - +
276B CYS* 3.3 4.8 + - + +
286B LEU* 5.5 0.9 - - + -
299B PHE* 3.7 30.3 - - + -
300B LEU 2.9 8.7 + - - -
301B LEU* 3.7 25.0 - - + -
302B LEU 2.8 27.8 + - - -
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B MET* 4.5 6.5 - - + -
214B VAL* 5.0 3.8 - - + +
215B SER 2.7 15.5 + - - +
216B ALA* 3.4 1.8 - - - -
217B VAL 2.8 28.8 + - - +
228B MET* 3.5 6.9 - - + +
231B PHE* 3.6 40.8 - - + -
273B VAL* 4.1 3.1 + - + +
274B VAL* 1.3 71.5 - - - +
276B CYS* 1.3 58.3 + - - +
277B PHE 3.9 0.9 - - - -
302B LEU* 3.6 12.3 - - + -
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Residues in contact with CYS 276 (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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202B MET* 4.7 3.3 - - - -
217B VAL* 3.2 9.0 - - - -
274B VAL* 3.3 7.4 + - + +
275B ALA* 1.3 72.1 - - - +
277B PHE* 1.3 59.2 + - - +
278B CYS* 2.1 49.9 + - + +
283B VAL* 4.1 9.2 - - + -
286B LEU* 3.7 29.6 - - - -
301B LEU* 5.2 6.7 - - + -
302B LEU 2.7 16.2 + - - +
303B GLY* 3.3 6.2 - - - -
304B SER 3.0 23.2 + - - -
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Residues in contact with PHE 277 (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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195B ASP* 3.6 42.0 - - + -
198B GLN* 3.9 14.4 - - + -
199B ALA* 3.8 28.9 - - + -
202B MET* 3.8 24.9 - - + -
217B VAL 3.1 6.7 + - - -
218B HIS* 3.3 3.7 - - + -
219B THR 3.3 17.5 + - - -
223B TYR* 3.6 26.0 - + - -
224B GLY* 3.3 19.5 - - - +
227B GLY* 3.7 27.6 - - - -
228B MET* 4.0 15.8 - - + +
231B PHE* 4.7 2.9 - - + -
275B ALA 3.9 1.6 - - - -
276B CYS* 1.3 70.1 - - - +
278B CYS* 1.3 57.6 - - - +
304B SER* 3.3 14.6 - - - -
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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
------------------------------------------------------------
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