Contacts of the strand formed by residues 233 - 237 (chain B) in PDB entry 3MEU
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 LEU 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU* 3.7 40.4 - - + +
229A GLN* 4.0 27.1 - - - +
232A GLN* 4.9 0.4 + - - -
228B PHE* 5.6 0.3 - - - -
231B GLU 3.5 3.0 + - - -
232B GLN* 1.3 81.8 + - - +
234B VAL* 1.3 64.3 - - - +
246B ARG* 3.8 31.0 - - + +
247B ALA 3.4 22.9 - - - +
248B LEU* 4.0 13.9 - - + -
265B GLU* 4.4 6.5 - - - +
286B ALA* 5.1 1.0 - - - -
287B CYS* 3.8 24.3 + - + +
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Residues in contact with VAL 234 (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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228B PHE* 3.9 21.8 - - + -
232B GLN* 4.1 2.5 - - + +
233B LEU* 1.3 79.8 - - - +
235B LEU* 1.3 62.2 + - - +
236B ALA* 4.4 3.6 - - + -
246B ARG* 3.5 5.2 - - - -
247B ALA* 2.9 52.8 + - + +
249B ILE* 3.8 32.5 - - + +
262B VAL* 4.8 1.3 - - + -
284B VAL* 3.8 24.0 - - + -
285B VAL 3.4 12.8 - - - +
287B CYS* 3.7 11.8 - - - +
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Residues in contact with LEU 235 (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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163B ALA* 5.6 0.4 - - + -
175B TRP* 3.8 33.2 - - + +
211B ILE* 3.9 14.6 - - + -
234B VAL* 1.3 74.7 - - - +
236B ALA* 1.3 58.8 + - - +
244B PHE* 4.1 12.1 - - + +
245B TYR* 3.5 28.3 - - - +
246B ARG* 3.9 6.5 - - + +
283B TYR 3.8 0.5 - - - +
284B VAL* 3.4 2.4 - - - -
285B VAL* 2.8 46.0 + - + +
286B ALA 3.8 4.5 - - - +
287B CYS* 3.9 10.8 - - - +
288B LYS* 3.6 21.8 - - - +
289B GLU* 4.2 17.5 - - + +
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Residues in contact with ALA 236 (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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234B VAL* 4.0 5.4 - - + -
235B LEU* 1.3 76.5 - - - +
237B LEU* 1.3 64.5 + - - +
238B TYR 3.3 0.2 + - - -
244B PHE* 3.3 4.8 - - - -
245B TYR 2.9 28.1 + - - +
247B ALA* 4.3 11.4 - - + -
262B VAL* 4.4 3.4 - - + -
264B PHE* 3.3 26.2 - - + -
279B VAL* 4.2 7.6 - - + -
283B TYR 3.3 8.3 - - - +
284B VAL* 4.2 14.8 - - + -
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Residues in contact with LEU 237 (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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120B MSE 6.4 0.2 - - + -
123B LEU* 4.4 13.5 - - + -
177B LEU* 4.3 5.2 - - + -
236B ALA* 1.3 70.9 - - - +
238B TYR* 1.3 66.8 + - - +
239B PRO* 3.5 1.2 - - - +
241B THR 3.7 18.8 - - - +
242B THR* 3.5 22.4 - - - +
243B CYS 3.4 17.0 - - - +
244B PHE* 3.5 24.1 - - + -
264B PHE* 4.0 0.4 - - - -
279B VAL* 3.5 24.2 - - + +
283B TYR* 3.0 54.8 + - + -
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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