Contacts of the helix formed by residues 280 - 285 (chain B) in PDB entry 5T4S
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 THR 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ASP* 3.6 25.6 - - - +
278B THR* 5.1 3.8 - - + -
279B LEU* 1.3 72.9 - - - +
281B SER* 1.3 57.0 + - - +
282B ALA* 3.6 16.3 + - - +
283B ASP* 2.7 50.4 + - - +
284B TYR* 3.2 9.7 - - - -
322B LYS* 4.4 9.6 + - - +
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Residues in contact with SER 281 (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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262B GLY 3.1 28.8 + - - -
263B PRO* 3.7 13.2 + - - +
265B LEU* 3.8 24.5 + - - -
266B PRO 4.7 1.4 + - - -
267B ASP* 4.5 2.6 + - - -
280B THR* 1.3 73.4 - - - +
282B ALA* 1.3 59.4 + - - +
284B TYR* 3.5 15.6 - - - -
285B VAL* 2.7 39.6 + - - +
287B GLN* 5.0 1.8 + - - -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B THR* 3.2 11.5 + - - +
281B SER* 1.3 81.7 + - - +
283B ASP* 1.3 63.2 + - - +
284B TYR 3.5 0.5 + - - -
285B VAL 3.6 12.4 - - - +
287B GLN* 5.1 9.9 - - - +
290B TYR* 5.7 4.9 - - - +
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 4.1 16.4 + - - +
279B LEU* 3.8 19.6 - - + +
280B THR* 2.7 39.0 + - - +
282B ALA* 1.3 74.1 - - - +
284B TYR* 1.3 55.7 + - - -
285B VAL 5.1 0.2 - - - -
299B ALA* 4.9 0.3 - - - +
318B THR* 3.5 20.7 - - - +
321B ARG* 4.8 8.0 + - - -
322B LYS* 2.8 46.4 + - + +
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Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 4.0 16.4 - - + +
265B LEU* 3.4 18.5 - - + +
266B PRO 2.6 28.7 + - - -
268B ILE* 3.6 29.7 - - + +
279B LEU* 3.9 18.6 - - + -
280B THR 3.2 19.3 - - - -
281B SER* 3.2 22.3 + - - -
283B ASP* 1.3 80.5 - - - +
285B VAL* 1.3 74.5 + - + +
298B LEU* 3.5 10.2 - - + -
299B ALA* 2.7 38.3 + - - -
300B ILE* 4.0 24.9 - - + -
318B THR* 4.3 10.3 - - + -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 4.1 11.7 - - + -
262B GLY* 4.5 3.8 - - - -
265B LEU* 3.9 18.4 - - + -
281B SER* 2.7 28.0 + - - +
282B ALA 3.6 14.2 - - - +
284B TYR* 1.3 85.3 - - + +
286B PHE* 1.3 63.0 + - - +
287B GLN* 3.0 37.0 + - + +
296B CYS* 4.1 18.4 - - + -
297B THR 4.0 9.0 - - - +
298B LEU* 3.8 16.8 - - + +
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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
------------------------------------------------------------
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