Contacts of the strand formed by residues 250 - 254 (chain B) in PDB entry 4L28
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B LEU* 3.7 6.7 - - - +
249B ASP* 1.3 80.6 - - - +
251B LEU* 1.3 63.5 + - - +
252B VAL* 4.2 4.7 - - + -
275B CYS* 3.8 4.9 - - - -
276B ARG* 3.4 17.3 - - + +
278B ILE* 3.9 34.5 - - + -
360B ALA* 3.5 28.9 - - - +
361B ALA* 3.9 14.6 - - - -
363B GLU* 3.9 12.3 - - - +
364B LEU* 3.7 31.2 - - + -
369B ARG 3.3 2.6 + - - -
370B CYS* 3.3 18.4 - - - -
371B VAL 2.9 24.6 + - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 4.4 6.1 - - + -
248B LEU* 5.0 3.4 - - + -
250B MET* 1.3 74.5 - - - +
252B VAL* 1.3 67.2 + - - +
253B ALA* 4.6 15.9 - - + -
261B ILE* 5.1 3.4 - - + -
264B ILE* 3.6 36.1 - - + -
265B ALA 5.3 0.2 - - - +
268B LEU* 4.3 7.4 - - + -
275B CYS* 4.2 11.2 - - - -
276B ARG 2.9 10.8 + - - +
277B ILE* 3.8 19.4 - - + -
278B ILE* 2.9 27.4 + - - +
371B VAL* 3.4 33.7 - - + +
373B ILE* 4.4 14.1 - - + -
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Residues in contact with VAL 252 (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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250B MET* 4.2 8.1 - - + -
251B LEU* 1.3 76.6 - - - +
253B ALA* 1.3 65.2 - - - +
278B ILE* 3.4 26.0 - - + +
280B VAL* 4.0 13.2 - - + -
353B THR* 3.6 28.1 - - + +
356B VAL* 4.3 4.5 - - + -
357B ALA* 4.2 12.8 - - + -
360B ALA* 5.3 0.4 - - + -
370B CYS* 3.6 24.7 - - - -
371B VAL 2.9 8.3 + - - +
372B VAL* 3.6 10.3 - - + -
373B ILE* 3.0 28.6 + - - +
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Residues in contact with ALA 253 (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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251B LEU* 4.1 8.3 + - + -
252B VAL* 1.3 76.6 - - - +
254B SER* 1.3 67.5 + - - +
255B VAL* 3.8 2.1 - - - +
260B THR* 5.0 4.5 - - + -
261B ILE* 4.1 28.7 - - + +
278B ILE 3.0 7.1 + - - -
279B GLY* 3.4 6.6 - - - -
280B VAL* 2.9 24.8 + - - -
353B THR* 4.2 2.5 - - - -
373B ILE* 4.1 18.6 - - + -
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Residues in contact with SER 254 (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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253B ALA* 1.3 79.5 - - - +
255B VAL* 1.3 61.8 + - - +
260B THR* 5.2 3.5 - - - +
261B ILE* 5.2 1.4 - - - +
280B VAL* 3.6 18.2 - - - -
306B ILE* 3.7 28.1 - - - +
349B SER* 4.0 5.8 - - - -
353B THR* 3.3 25.8 + - - +
373B ILE* 5.4 1.8 - - - +
375B PRO* 3.9 19.4 - - - +
601B PLP 3.7 13.0 + - - +
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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