Contacts of the strand formed by residues 233 - 237 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PHE* 5.5 0.3 - - - -
231A GLU 3.5 3.2 + - - -
232A GLN* 1.3 78.5 + - - +
234A VAL* 1.3 64.7 + - - +
246A ARG* 3.6 44.9 - - + +
247A ALA 3.4 24.7 - - - +
248A LEU* 3.9 15.2 - - + +
265A GLU* 4.1 9.9 - - - +
286A ALA* 5.0 1.0 - - - -
287A CYS* 3.8 34.2 + - + +
229B GLN* 6.0 10.7 - - + +
230B LYS 4.9 2.4 + - - -
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE* 3.8 27.8 - - + -
232A GLN 4.1 2.0 - - - +
233A LEU* 1.3 78.3 - - - +
235A LEU* 1.3 62.6 + - - +
236A ALA* 4.4 3.4 - - + -
246A ARG* 3.4 5.5 - - - -
247A ALA* 2.9 50.8 + - + +
249A ILE* 3.9 21.5 - - + -
262A VAL* 4.7 1.8 - - + -
284A VAL* 3.7 29.4 - - + -
285A VAL 3.3 14.8 - - - +
287A CYS* 3.6 11.8 - - - +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ALA* 5.6 0.7 - - + -
175A TRP* 3.7 42.0 - - + +
211A ILE* 3.8 26.5 - - + -
234A VAL* 1.3 72.6 - - - +
236A ALA* 1.3 59.4 + - - +
244A PHE* 4.2 11.0 - - + -
245A TYR* 3.5 25.8 - - - +
246A ARG* 3.7 17.7 - - + +
283A TYR 3.8 0.9 - - - +
284A VAL* 3.5 2.6 - - - -
285A VAL* 2.8 45.6 + - + +
286A ALA 3.9 4.7 - - - +
287A CYS* 3.7 18.9 - - + +
288A LYS 5.8 0.2 - - - +
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A VAL* 4.4 4.7 - - + -
235A LEU* 1.3 75.2 - - - +
237A LEU* 1.3 65.4 + - - +
238A TYR 3.3 0.3 + - - -
244A PHE* 3.3 5.1 - - - -
245A TYR 2.9 27.7 + - - +
247A ALA* 4.4 11.4 - - + -
262A VAL* 4.4 3.4 - - + -
264A PHE* 3.3 25.2 - - + -
279A VAL* 4.1 13.9 - - + -
283A TYR 3.3 8.3 - - - +
284A VAL* 4.3 8.1 - - + -
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.9 35.2 - - + -
177A LEU* 4.3 4.5 - - + -
236A ALA* 1.3 71.1 - - - +
238A TYR* 1.3 65.7 + - - +
239A PRO* 3.7 1.6 - - - +
241A THR 4.0 7.6 - - - +
242A THR* 3.4 32.1 - - - +
243A CYS 3.4 10.5 - - - +
244A PHE* 3.6 21.6 - - + -
264A PHE* 3.6 0.4 - - - -
278A ASN 5.1 0.2 - - - +
279A VAL* 3.6 23.9 - - + +
283A TYR* 3.1 48.1 + - + +
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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