Contacts of the helix formed by residues 235 - 241 (chain A) in PDB entry 1Y7V
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A GLU* 4.6 0.7 - - - +
234A ASN* 1.3 90.6 + - - +
236A PRO* 1.3 70.9 - - - +
237A SER* 3.1 3.1 - - - +
238A ALA* 2.9 26.1 + - + +
239A GLY 4.3 0.5 + - - -
244A TYR* 3.8 17.5 + - - -
246A PHE* 5.8 0.2 - - - -
248A CYS* 5.3 0.9 - - - +
249A LEU 5.1 0.3 + - - +
282A ASP 2.8 14.1 + - - +
283A ASP* 3.1 19.2 - - - +
311A HIS* 2.8 28.5 + - - +
313A TYR* 2.2 31.7 + - - -
340A GLU* 3.9 2.3 - - - +
507A INS 3.9 14.7 + - - -
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Residues in contact with PRO 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLU* 3.4 31.2 - - + +
234A ASN 3.1 0.6 - - - -
235A GLU* 1.3 85.0 - - - +
237A SER* 1.3 61.8 + - - +
238A ALA 3.1 1.1 + - - -
239A GLY 3.4 0.3 + - - -
240A LEU* 4.1 0.2 - - - +
249A LEU 3.9 2.7 - - - +
250A GLY* 3.2 10.2 - - - -
251A PHE* 3.2 44.6 + - + -
256A GLN* 3.8 8.7 - - - +
281A LEU 2.9 29.2 - - - +
283A ASP* 3.4 6.1 - - + +
291A TRP* 3.4 22.7 - - + -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A PRO* 1.3 75.3 - - - +
238A ALA* 1.3 64.2 + - - +
239A GLY 3.4 0.2 - - - -
240A LEU* 3.3 31.1 + - - +
241A LEU* 3.9 10.5 - - - +
251A PHE 4.4 1.3 - - - -
283A ASP* 2.8 31.9 + - - -
284A GLN* 4.7 6.9 + - - -
287A LEU* 3.8 25.0 - - - +
291A TRP* 4.7 5.8 - - - -
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU* 2.9 25.0 + - + +
237A SER* 1.3 81.3 + - - +
239A GLY* 1.3 57.8 + - - +
241A LEU* 2.9 37.7 + - - +
244A TYR* 3.7 45.8 - - + +
248A CYS* 4.1 5.4 - - + -
283A ASP* 4.2 0.2 + - - -
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Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLY 4.1 2.2 - - - -
194A LYS* 3.4 7.0 - - - +
195A GLY 3.3 25.6 + - - +
236A PRO 3.4 4.8 + - - -
237A SER 3.4 0.8 - - - -
238A ALA* 1.3 77.6 - - - +
240A LEU* 1.3 57.0 + - - +
241A LEU 3.2 2.2 - - - -
248A CYS* 4.0 19.3 - - - +
249A LEU 3.9 1.7 - - - -
250A GLY* 3.1 29.5 - - - +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LYS* 3.7 25.6 + - - +
196A SER* 5.5 3.4 - - - -
236A PRO 4.1 2.5 - - - +
237A SER* 3.6 21.5 - - - +
238A ALA 2.9 1.2 + - - -
239A GLY* 1.3 78.4 - - - +
241A LEU* 1.3 65.0 + - + +
242A SER 3.9 0.5 + - - -
250A GLY* 3.6 5.8 - - - -
251A PHE 3.3 45.3 - - - +
252A THR* 3.9 24.9 - - + +
253A PRO* 5.5 2.2 - - + -
291A TRP* 5.5 0.9 - - + -
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLY 3.8 0.2 - - - -
194A LYS* 3.3 14.6 + - - +
237A SER* 3.9 8.5 - - - +
238A ALA* 2.9 23.6 + - - +
239A GLY 3.2 0.2 - - - -
240A LEU* 1.3 83.3 - - + +
242A SER* 1.3 67.5 + - - +
244A TYR* 3.3 37.7 + - + +
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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