Contacts of the strand formed by residues 250 - 254 (chain B) in PDB entry 3HO5
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 TYR 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ARG* 3.4 48.5 + - - +
245B LEU* 3.6 2.8 - - - -
246B GLU* 2.7 51.8 + - + +
248B GLU* 3.8 23.3 - - + -
249B GLY* 1.3 82.9 - - - +
251B VAL* 1.3 64.8 + - - +
252B LYS* 4.2 2.2 - - + -
264B PRO* 4.4 11.4 - - + -
266B LEU 3.3 6.7 - - - +
267B ASP* 3.4 39.3 - - + -
269B HIS* 3.2 32.4 + + + -
284B LEU* 3.8 2.1 - - - +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 3.8 31.0 - - + -
244B ILE 3.4 9.0 - - - +
245B LEU* 4.5 4.3 - - + -
250B TYR* 1.3 76.9 - - - +
252B LYS* 1.3 63.5 + - - +
264B PRO* 3.6 2.8 - - - +
265B TYR* 2.8 41.3 + - + +
266B LEU* 2.9 43.7 + - + +
284B LEU* 4.3 13.9 - - + -
287B LEU* 4.1 21.8 - - + -
301B VAL* 5.3 0.2 - - + -
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Residues in contact with LYS 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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225B GLY 4.4 10.9 + - - -
226B LEU* 4.5 10.4 - - + +
227B ARG* 3.9 23.4 - - - +
242B LEU 3.5 1.2 - - - +
243B PHE* 3.3 4.3 - - - -
244B ILE* 2.7 48.3 + - + +
246B GLU* 2.7 43.4 + - - +
250B TYR* 5.1 1.3 - - + -
251B VAL* 1.3 77.1 - - - +
253B ILE* 1.3 63.4 + - - +
260B ILE* 4.2 26.0 - - + +
261B PHE 5.3 3.6 - - - +
262B LYS 6.0 2.0 - - - +
264B PRO* 4.8 16.2 - - + -
265B TYR 4.5 1.8 - - - +
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Residues in contact with ILE 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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241B ARG* 3.6 26.9 - - + +
242B LEU 3.6 2.7 - - - -
243B PHE* 3.4 27.1 - - + -
252B LYS* 1.3 72.0 - - - +
254B LEU* 1.3 66.3 + - - +
255B THR* 4.2 1.6 - - - +
259B GLU 3.6 0.9 - - - +
260B ILE* 3.4 8.9 - - - +
261B PHE* 3.3 55.9 + - + +
263B GLU 5.5 1.9 + - - +
265B TYR* 3.7 24.2 - - + +
332B HIS* 3.6 42.4 - - + +
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Residues in contact with LEU 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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544A ARG* 4.9 3.1 - - - +
222B VAL* 3.8 26.9 - - + -
223B VAL* 3.8 17.7 - - + -
240B GLN 4.2 0.9 - - - +
241B ARG* 3.7 3.5 - - - -
242B LEU* 2.7 55.2 + - + +
244B ILE* 4.7 5.8 - - + -
252B LYS 3.9 0.4 + - - -
253B ILE* 1.3 73.0 - - - +
255B THR* 1.3 67.5 + - - +
256B PRO 3.8 0.2 - - - -
258B GLY* 3.5 27.1 - - - +
259B GLU 3.4 16.6 - - - +
260B ILE* 3.9 10.5 - - + +
563B TYR* 5.7 1.6 - - - +
579B LEU* 3.9 18.6 - - + -
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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