Contacts of the strand formed by residues 250 - 255 (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 LYS 250 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C GLU 6.2 0.2 - - - -
239D SER* 3.4 5.0 - - - -
240D PHE* 2.7 50.0 + - + +
241D TYR* 4.3 0.4 - - - +
242D SER* 5.5 4.7 - - - -
246D LEU* 4.2 20.4 - - + +
248D TYR 3.5 2.0 + - - +
249D PRO* 1.3 76.1 - - - +
251D THR* 1.3 67.6 + - - +
252D VAL* 4.0 8.4 - - + +
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Residues in contact with THR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C GLU* 2.6 44.5 + - - +
238C TYR* 5.7 0.2 - - - -
251C THR* 4.2 11.6 - - + +
237D GLU* 4.1 13.0 - - + -
238D TYR 3.5 9.8 + - - +
239D SER* 4.9 3.6 + - - -
250D LYS* 1.3 79.2 + - - +
252D VAL* 1.3 71.3 + - - +
253D ARG* 3.4 40.8 + - + +
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Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D TRP* 4.8 4.9 - - + -
236D ILE 3.3 1.8 - - - +
237D GLU* 3.2 24.9 - - - -
238D TYR* 2.9 47.2 + - + +
240D PHE* 3.7 33.2 - - + -
250D LYS* 5.3 8.3 - - + +
251D THR* 1.3 73.1 - - - +
253D ARG* 1.3 62.3 + - - +
254D VAL* 3.7 16.4 - - + -
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Residues in contact with ARG 253 (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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237C GLU* 3.4 26.3 + - - -
253C ARG* 2.9 33.5 - - - +
192D ASP* 4.1 18.4 - - - +
235D LEU* 4.2 23.7 - - + +
236D ILE 3.4 3.8 - - - -
237D GLU* 3.5 24.2 + - + -
251D THR* 3.4 28.8 + - + +
252D VAL* 1.3 80.4 - - - +
254D VAL* 1.3 64.8 + - - +
255D PRO* 4.2 1.9 - - - +
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D TRP* 3.6 41.7 - - + +
201D TRP* 4.1 20.4 - - + -
235D LEU* 3.6 3.8 - - - +
236D ILE* 2.9 45.1 + - + +
238D TYR* 4.4 4.0 - - + +
252D VAL* 3.7 16.4 - - + -
253D ARG* 1.3 79.2 - - - +
255D PRO* 1.3 82.3 - - + +
256D TYR* 3.0 2.8 + - + -
709D ASP* 5.6 2.0 - - + -
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Residues in contact with PRO 255 (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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192D ASP* 3.6 35.9 - - + +
195D TYR* 3.7 19.1 - - - +
200D ASP* 5.1 0.4 - - + +
201D TRP* 3.8 21.8 + - - +
230D ASP* 3.5 29.9 - - + +
233D VAL* 3.9 11.2 - - + +
234D PRO 3.5 8.3 - - - +
235D LEU* 3.4 16.8 - - + -
253D ARG 4.2 0.2 - - - +
254D VAL* 1.3 86.5 - - + +
256D TYR* 1.3 57.8 + - - +
257D PRO* 4.0 3.3 - - - +
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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