Contacts of the helix formed by residues 275 - 280 (chain B) in PDB entry 1YSD
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 GLU 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLN* 4.7 10.4 - - - +
154A GLU* 4.8 13.4 - - - +
158A GLU 5.7 0.7 - - - +
274B LEU* 1.3 75.6 - - - +
276B GLY* 1.3 67.9 + - - +
277B LYS* 4.3 22.7 - - + +
278B VAL* 3.0 33.8 + - + +
279B TYR* 3.9 3.5 - - - -
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Residues in contact with GLY 276 (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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154A GLU* 5.2 4.4 - - - +
157A GLY* 3.3 37.9 - - - -
158A GLU 3.8 11.4 + - - -
274B LEU 3.4 3.4 + - - -
275B GLU* 1.3 74.5 + - - +
277B LYS* 1.3 61.7 + - - +
278B VAL 3.2 1.0 + - - -
279B TYR* 3.4 14.8 + - - -
280B LYS* 2.8 19.6 + - - -
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Residues in contact with LYS 277 (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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158A GLU 4.8 3.0 + - - -
275B GLU* 4.3 24.0 - - + -
276B GLY* 1.3 75.4 - - - +
278B VAL* 1.3 68.7 + - + +
280B LYS* 3.2 27.0 + - + +
281B ASP* 4.2 3.8 + - - +
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASN* 4.6 13.9 + - - +
246B LEU* 3.9 28.9 - - + -
274B LEU* 4.3 19.7 - - + -
275B GLU* 3.0 33.3 + - + +
277B LYS* 1.3 81.6 - - + +
279B TYR* 1.3 62.8 + - - +
280B LYS 3.3 0.7 + - - -
281B ASP* 3.5 8.0 + - - +
282B THR* 3.1 16.3 - - - +
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Residues in contact with TYR 279 (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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53A ARG* 5.5 0.7 + - - -
59A ALA* 3.7 17.3 - - - +
157A GLY* 5.3 0.2 - - - -
237B LEU* 4.1 16.6 - - + -
268B LEU* 4.3 15.8 + - + -
271B CYS* 5.5 2.0 - - + -
272B GLY 4.0 3.6 + - - -
274B LEU* 3.9 49.2 + - + +
275B GLU 3.9 3.8 - - - -
276B GLY* 3.4 16.7 + - - +
277B LYS 3.3 0.2 - - - -
278B VAL* 1.3 76.4 - - - +
280B LYS* 1.3 57.8 + - - +
281B ASP 3.0 5.0 + - - -
282B THR* 2.7 27.3 + - - -
301B TYR* 3.3 71.4 - + + +
302B GLY 4.4 1.6 - - - -
303B ILE* 3.7 12.5 - - + -
304B PRO* 3.4 8.1 - - - +
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Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY* 2.8 30.5 + - - -
158A GLU* 5.6 4.0 - - - -
276B GLY 2.8 20.3 + - - +
277B LYS* 3.4 21.3 - - + +
278B VAL 3.2 0.8 - - - -
279B TYR* 1.3 73.8 - - - +
281B ASP* 1.3 57.4 + - + +
282B THR 3.6 0.9 - - - -
300B MET 5.3 0.6 + - - -
301B TYR 2.8 22.6 + - - -
302B GLY* 3.6 24.2 - - - +
304B PRO* 3.4 17.8 - - - +
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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
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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