Contacts of the helix formed by residues 189 - 196 (chain A) in PDB entry 2Y48
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 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LEU* 3.4 31.2 - - + +
184A PRO* 4.0 21.5 - - + -
187A ARG* 6.3 0.7 - - - +
188A MET* 1.3 76.9 - - - +
190A SER* 1.3 64.5 + - - +
191A GLN* 3.6 7.1 + - - +
192A GLU* 2.9 37.1 + - - +
193A ALA* 3.1 21.7 + - - +
200A ILE* 4.8 0.3 - - - +
214A ARG* 4.4 1.8 - - - +
255A TYR* 4.2 3.3 + - - -
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Residues in contact with SER 190 (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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189A THR* 1.3 74.4 - - - +
191A GLN* 1.3 63.4 + - - +
193A ALA* 3.4 8.8 + - - +
194A ALA* 3.2 20.4 + - - +
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Residues in contact with GLN 191 (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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189A THR* 3.4 6.4 + - - +
190A SER* 1.3 78.9 - - - +
192A GLU* 1.3 59.9 + - - +
194A ALA* 3.5 11.0 - - - +
195A CYS* 3.3 23.7 - - - -
255A TYR* 2.9 24.6 + - + +
259A HIS* 3.1 44.3 + - - +
261A LEU* 5.4 4.8 - - - +
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Residues in contact with GLU 192 (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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183A LEU* 4.2 8.1 - - - +
188A MET* 3.4 9.8 - - + +
189A THR* 2.9 40.9 + - - +
190A SER 3.2 0.6 - - - -
191A GLN* 1.3 73.6 - - - +
193A ALA* 1.3 66.2 + - - +
194A ALA 3.0 2.0 + - - -
195A CYS 3.1 2.1 + - - -
196A PHE* 3.0 29.4 + - + +
210A PHE* 3.7 28.0 - - + -
214A ARG* 3.0 43.5 + - - +
255A TYR* 3.4 30.6 + - + +
256A LEU* 5.2 0.2 - - - +
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Residues in contact with ALA 193 (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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188A MET* 4.7 1.4 - - - +
189A THR 3.1 11.2 + - - +
190A SER* 3.7 11.0 - - - +
192A GLU* 1.3 75.2 - - - +
194A ALA* 1.3 62.4 + - - +
196A PHE 4.6 0.4 - - - +
197A PRO* 3.3 26.2 - - - +
200A ILE* 3.7 39.7 - - + +
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Residues in contact with ALA 194 (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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190A SER 3.2 12.8 + - - +
191A GLN* 3.5 15.3 - - - +
192A GLU 3.0 1.0 - - - -
193A ALA* 1.3 79.6 - - - +
195A CYS* 1.3 61.5 + - - +
197A PRO* 3.8 8.5 - - - +
835A THR* 5.1 2.3 - - - +
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Residues in contact with CYS 195 (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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191A GLN* 3.3 19.1 - - - -
192A GLU 3.1 1.6 + - - -
194A ALA* 1.3 76.3 - - - +
196A PHE* 1.3 78.5 + - + +
197A PRO* 3.3 7.6 - - - +
251A ARG* 3.5 11.3 + - - -
255A TYR* 3.8 20.2 - - - -
259A HIS* 4.6 6.7 - - - -
827A ASP* 5.9 0.4 - - - -
834A TYR* 3.9 17.3 - - + +
835A THR* 3.7 35.3 - - + -
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Residues in contact with PHE 196 (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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188A MET* 4.0 11.0 - - + -
192A GLU* 3.0 20.0 + - - +
193A ALA 3.7 3.1 - - - -
195A CYS* 1.3 91.1 - - + +
197A PRO* 1.3 68.7 - - - +
198A ASP* 3.0 9.2 - - - -
199A ILE* 2.9 28.1 + - + -
200A ILE* 3.3 10.9 + - - +
210A PHE* 3.6 35.7 - + - -
248A LEU* 4.8 0.9 - - + -
251A ARG* 3.7 38.1 - - + +
252A VAL* 3.9 15.3 - - + -
255A TYR* 3.8 39.3 - + + -
834A TYR 5.0 2.7 - - - -
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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