Contacts of the strand formed by residues 235 - 240 (chain D) in PDB entry 5Y7K
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 235 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C TYR* 3.6 16.5 - - - +
249C PRO 5.5 1.4 - - - +
192D ASP* 5.2 8.3 - - + +
230D ASP 6.2 0.2 - - - +
233D VAL 4.5 5.6 - - - +
234D PRO* 1.3 76.1 - - - +
236D ILE* 1.3 65.0 + - - +
237D GLU* 3.8 23.5 + - + +
253D ARG* 4.2 21.5 - - + +
254D VAL 3.3 8.5 - - - +
255D PRO* 3.4 39.5 - - + -
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C TYR* 4.4 4.7 - - + -
249C PRO* 3.7 31.0 - - + -
234D PRO 4.1 0.6 + - - -
235D LEU* 1.3 71.7 - - - +
237D GLU* 1.3 67.6 + - - +
238D TYR* 4.1 19.0 - - + -
252D VAL 3.3 5.0 - - - +
253D ARG* 3.4 1.4 - - - -
254D VAL* 2.9 43.8 + - + +
256D TYR* 3.5 20.0 - - + +
258D LYS* 4.3 4.9 - - - +
709D ASP* 5.4 0.9 - - + +
712D HIS* 3.3 52.9 - - + +
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Residues in contact with GLU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C SER* 3.3 14.3 + - - -
249C PRO* 4.6 19.2 + - - +
251C THR* 2.5 45.0 + - - +
253C ARG* 3.3 10.0 + - - -
235D LEU* 3.8 19.8 + - - +
236D ILE* 1.3 87.3 - - - +
238D TYR* 1.3 64.5 + - - +
251D THR* 4.1 4.3 - - + -
252D VAL 3.2 5.2 - - - +
253D ARG* 3.5 38.3 + - + +
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Residues in contact with TYR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C SER* 3.4 10.1 - - - +
241C TYR* 5.8 2.7 - - - +
124D TRP* 4.0 9.4 - - - -
236D ILE* 4.1 28.5 - - + -
237D GLU* 1.3 78.3 - - - +
239D SER* 1.3 73.2 + - - +
240D PHE* 5.1 1.6 - + + -
251D THR* 3.5 6.3 - - - +
252D VAL* 2.9 67.3 + - + +
254D VAL* 4.4 2.1 - - + +
706D THR 4.0 18.2 - - - +
707D ALA* 3.9 26.8 + - + -
708D ASP 4.6 5.2 - - - -
709D ASP* 3.5 31.0 - - + +
712D HIS* 5.2 2.5 - + + -
713D PHE* 6.1 3.8 - - + +
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Residues in contact with SER 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C GLU 3.7 8.0 + - - -
238C TYR* 3.7 26.7 - - - +
239C SER* 4.1 6.2 + - - -
238D TYR* 1.3 84.7 - - - +
240D PHE* 1.3 62.1 + - - +
241D TYR* 4.2 26.1 - - - -
249D PRO* 4.9 3.8 - - - -
250D LYS 3.4 7.5 + - - -
251D THR* 4.7 3.1 + - - +
706D THR* 4.2 14.8 + - - +
707D ALA* 5.0 0.2 - - - -
737D ASP* 4.6 0.2 - - - +
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Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D TYR* 3.8 2.0 + + + -
239D SER* 1.3 74.0 - - - +
241D TYR* 1.3 58.9 + - - +
242D SER* 3.5 32.5 - - - -
246D LEU* 4.7 0.2 - - - +
250D LYS* 2.7 46.0 + - + +
252D VAL* 3.7 27.8 - - + -
707D ALA* 3.7 21.5 - - + -
737D ASP* 3.7 37.0 - - + -
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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