Contacts of the strand formed by residues 251 - 255 (chain M) in PDB entry 5KZ5
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 251 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134M ALA* 3.5 32.5 - - + -
138M VAL* 3.7 19.5 - - + -
228M TYR* 4.0 27.8 - - + -
229M PHE 3.3 7.9 + - - +
230M HIS* 3.8 17.7 - - + -
231M THR 3.2 20.1 + - - -
249M ILE* 3.2 10.1 - - - +
250M ASP* 1.3 85.4 - - + +
252M MET* 1.4 59.5 + - - +
268M ILE* 4.5 5.4 - - + -
269M TYR 3.3 8.5 - - - +
277M ARG* 4.0 27.1 - - + +
278M VAL* 4.0 10.1 - - + -
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Residues in contact with MET 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204M THR* 4.9 0.4 - - - +
230M HIS* 4.4 2.7 - - - -
231M THR 3.3 7.2 - - - +
233M ALA* 3.8 23.3 - - + -
242M LEU* 3.9 29.8 - - + -
243M ASP 3.4 24.7 - - - +
244M VAL* 3.7 18.6 - - + -
249M ILE* 3.7 28.3 - - + -
251M LEU* 1.4 75.4 - - - +
253M SER* 1.4 72.2 + - - +
254M ILE* 5.4 0.2 - - - -
268M ILE* 3.6 4.4 - - - +
269M TYR* 2.9 55.0 + - + +
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Residues in contact with SER 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127M ALA* 3.7 10.9 - - - +
130M SER* 3.3 20.0 - - - -
131M ASN* 3.2 23.8 + - - -
230M HIS* 3.7 11.4 + - - -
231M THR 3.4 5.3 + - - -
232M ASP* 3.0 21.0 + - - -
233M ALA* 3.1 24.8 + - - -
234M ALA 3.4 1.7 + - - -
252M MET* 1.4 76.4 - - - +
254M ILE* 1.3 63.1 + - - +
267M ALA 3.8 4.9 - - - -
268M ILE* 4.8 0.9 - - - +
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Residues in contact with ILE 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M LEU* 6.2 3.1 - - + -
114M ILE* 5.8 1.6 - - + -
126M GLY 4.6 1.9 - - - -
130M SER* 4.5 2.1 + - - -
233M ALA 4.1 3.6 - - - +
234M ALA* 3.9 5.6 - - - +
237M VAL* 3.6 30.3 - - + -
242M LEU* 3.9 23.6 - - + -
252M MET* 5.3 0.9 - - + -
253M SER* 1.3 78.0 + - - +
255M SER* 1.4 65.1 + - - +
266M GLY* 3.2 5.6 - - - -
267M ALA* 3.2 39.2 + - + +
269M TYR* 3.6 41.7 - - + +
304M LEU* 6.1 7.9 - - + -
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Residues in contact with SER 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M SER 5.0 0.2 + - - -
126M GLY* 3.5 18.5 - - - -
127M ALA* 3.6 12.6 + - - +
234M ALA* 3.6 26.5 - - - +
235M GLN* 4.9 0.7 - - - -
237M VAL* 3.4 24.3 - - - +
254M ILE* 1.4 78.3 - - - +
256M GLY* 1.3 59.7 + - - +
257M HIS* 3.1 20.7 + - - +
259M ILE* 5.1 0.4 - - - +
264M GLY 5.9 0.5 + - - -
265M VAL 4.0 6.7 + - - -
266M GLY* 4.2 1.1 - - - -
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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