Contacts of the strand formed by residues 250 - 254 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C LEU* 3.5 3.1 - - - +
249C ASP* 1.3 80.3 - - - +
251C LEU* 1.3 60.5 + - - +
252C VAL* 4.6 1.6 - - + -
275C CYS* 3.1 8.5 - - - -
276C ARG* 3.7 24.2 - - + +
278C ILE* 3.8 23.1 - - + -
360C ALA* 3.5 35.7 - - + +
361C ALA* 3.9 9.2 - - - -
363C GLU* 3.1 21.3 - - + +
364C LEU* 3.5 24.5 - - + -
369C ARG 3.2 3.0 + - - -
370C CYS* 3.2 20.3 - - + -
371C VAL 2.7 31.7 + - - -
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C ILE* 4.4 13.7 - - + -
248C LEU* 4.6 8.1 - - + -
250C MET* 1.3 77.1 - - - +
252C VAL* 1.3 78.3 + - - +
253C ALA* 3.8 14.1 - - + -
261C ILE* 5.3 2.7 - - + -
264C ILE* 3.5 22.9 - - + -
268C LEU* 3.3 35.7 - - + -
275C CYS* 4.4 1.3 - - - -
276C ARG 3.0 11.3 + - - +
277C ILE* 3.8 9.1 - - + -
278C ILE* 3.0 26.1 + - - +
371C VAL* 3.1 15.5 - - + +
373C ILE* 4.6 9.9 - - + -
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C MET* 4.6 3.4 - - + -
251C LEU* 1.3 82.5 - - - +
253C ALA* 1.3 66.6 + - - +
278C ILE* 3.9 20.2 - - + -
280C VAL* 3.8 15.9 - - + -
353C THR* 3.5 37.9 - - + +
356C VAL* 4.0 12.8 - - + -
357C ALA* 4.0 22.4 - - + +
360C ALA* 4.8 4.3 - - + -
370C CYS* 4.1 17.3 - - - -
371C VAL 3.2 4.4 + - - -
372C VAL* 4.0 5.4 - - + -
373C ILE 3.7 14.0 + - - -
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Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LEU* 3.8 12.1 - - + -
252C VAL* 1.3 79.6 - - - +
254C SER* 1.3 58.3 + - - +
255C VAL* 4.5 0.4 - - - -
260C THR* 4.8 0.7 - - - +
261C ILE* 3.7 32.8 - - + -
278C ILE 3.2 6.3 + - - -
279C GLY* 3.0 5.9 - - - -
280C VAL* 2.4 38.2 + - - -
353C THR* 4.3 2.9 - - - -
373C ILE* 4.3 17.0 - - + -
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ALA* 1.3 77.0 - - - +
255C VAL* 1.3 62.1 + - - +
260C THR* 3.9 12.3 + - - -
261C ILE* 4.8 1.0 - - - +
280C VAL* 3.7 13.0 - - - -
306C ILE* 3.4 22.9 - - - -
349C SER* 4.6 8.1 - - - -
352C SER* 5.5 0.2 - - - -
353C THR* 3.4 18.9 + - - -
373C ILE* 4.6 2.8 + - - +
375C PRO* 3.6 25.9 - - - +
1310C PLP 3.6 13.7 + - - +
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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