Contacts of the strand formed by residues 250 - 254 (chain E) in PDB entry 1M54
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 MET 250 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248E LEU* 2.6 25.7 - - - +
249E ASP* 1.3 84.9 - - - +
251E LEU* 1.3 65.7 + - - +
252E VAL* 4.2 6.3 - - + -
275E CYS* 2.8 5.6 - - - -
276E ARG* 3.1 16.6 - - + +
278E ILE* 3.7 35.2 - - + -
360E ALA* 3.5 23.3 - - - +
361E ALA* 3.8 18.8 - - - -
363E GLU* 3.2 28.0 - - - +
364E LEU* 4.0 16.2 - - + -
369E ARG 3.8 4.4 + - - +
370E CYS* 4.1 14.4 - - + -
371E VAL 3.0 13.6 + - - -
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Residues in contact with LEU 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E ILE* 3.6 33.9 - - + -
248E LEU* 4.2 1.8 - - + -
250E MET* 1.3 77.4 - - - +
252E VAL* 1.3 60.9 + - - +
253E ALA* 2.9 21.8 + - + +
261E ILE* 5.4 0.2 - - + -
264E ILE* 3.4 32.8 - - + -
268E LEU* 3.6 28.0 - - + -
276E ARG 3.3 4.8 + - - -
277E ILE* 4.1 10.8 - - + +
278E ILE 3.1 18.3 + - - +
371E VAL* 3.1 19.1 - - + +
373E ILE* 3.9 17.3 - - + -
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Residues in contact with VAL 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E MET* 4.2 15.0 - - - -
251E LEU* 1.3 67.4 - - - +
253E ALA* 1.3 59.4 + - - +
278E ILE* 3.6 15.3 - - + -
280E VAL* 3.4 29.8 - - + -
353E THR* 3.5 24.0 - - + +
356E VAL* 3.7 13.7 - - + -
357E ALA* 3.8 24.5 - - + -
360E ALA* 4.3 3.4 - - + -
370E CYS* 4.0 11.7 - - - -
371E VAL 3.1 7.4 + - - -
372E VAL* 3.7 13.4 - - + +
373E ILE* 3.9 13.1 + - - -
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Residues in contact with ALA 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E LEU* 2.9 20.7 + - + -
252E VAL* 1.3 73.2 - - - +
254E SER* 1.3 61.6 + - - +
260E THR* 5.1 2.9 - - - +
261E ILE* 3.3 43.1 - - + +
264E ILE* 5.8 0.2 - - + -
278E ILE 2.7 10.7 + - - +
279E GLY* 3.5 1.2 - - - -
280E VAL* 2.9 27.7 + - - +
353E THR* 4.1 1.8 - - - -
373E ILE* 4.4 10.5 - - + -
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Residues in contact with SER 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E ALA* 1.3 78.2 - - - +
255E VAL* 1.3 64.6 + - - +
256E GLY 4.3 0.4 - - - -
260E THR* 3.3 21.2 + - - -
261E ILE* 4.2 0.9 - - - +
280E VAL* 4.2 8.6 + - - +
306E ILE* 3.4 25.6 - - - +
349E SER 4.2 5.7 + - - -
352E SER* 5.2 1.7 - - - -
353E THR* 3.5 26.8 + - - +
373E ILE* 5.3 4.5 - - - +
375E PRO* 4.4 17.7 - - - -
1510E PLP 3.5 6.0 + - - +
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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