Contacts of the helix formed by residues 199 - 204 (chain A) in PDB entry 4JYY
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASP* 6.0 0.9 - - - -
52A THR* 5.3 2.5 - - - -
194A VAL 3.4 22.9 - - - -
195A TRP 3.4 12.6 - - - -
196A GLU* 3.0 25.9 + - + +
197A HIS 3.2 0.2 - - - -
198A ALA* 1.3 80.5 - - - +
200A TYR* 1.3 68.3 + + - +
201A LEU 3.4 2.9 + - - -
202A LYS* 3.5 2.9 + - - -
203A TYR* 2.8 35.9 + - + +
204A GLN 3.1 27.8 - - - -
205A ASN* 4.6 3.7 + - - -
207A ARG* 3.0 55.7 + - + +
210A TYR* 3.4 46.2 - + + -
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Residues in contact with TYR 200 (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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196A GLU* 2.9 45.0 + - + +
197A HIS* 4.5 4.2 + - - -
199A TYR* 1.3 79.6 - + - +
201A LEU* 1.3 68.3 + - + +
204A GLN* 2.8 75.2 + - + +
205A ASN* 3.5 16.2 + - + +
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Residues in contact with LEU 201 (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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49A ASP* 4.0 6.5 - - - +
51A GLU* 3.7 35.7 - - + +
52A THR* 3.6 23.9 + - - +
55A LEU* 3.7 22.7 - - + -
197A HIS 5.6 2.7 + - - +
199A TYR 3.4 1.0 - - - -
200A TYR* 1.3 80.8 - - + +
202A LYS* 1.3 58.3 + - - +
204A GLN* 2.9 15.4 + - - -
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Residues in contact with LYS 202 (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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46A PRO* 2.9 33.9 + - - +
47A TYR 3.7 5.8 - - - +
49A ASP* 3.3 35.3 + - + +
199A TYR* 3.5 2.9 + - - +
200A TYR 3.2 0.4 - - - -
201A LEU* 1.3 80.6 - - - +
203A TYR* 1.3 100.4 + - + +
204A GLN* 3.4 9.1 + - - -
206A ARG* 3.4 10.4 + - - -
213A ASN* 5.2 1.3 - - - +
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Residues in contact with TYR 203 (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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47A TYR* 2.5 27.4 + - - -
48A ILE* 5.3 2.0 - - + -
199A TYR* 2.8 22.0 + - + +
202A LYS* 1.3 107.8 - - + +
204A GLN* 1.3 76.5 + - - +
206A ARG* 2.9 43.8 + - + +
209A GLU* 3.7 20.0 - - + -
210A TYR* 3.7 49.1 - + + -
213A ASN* 3.1 35.3 + - + +
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Residues in contact with GLN 204 (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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199A TYR* 3.1 26.5 - - - -
200A TYR* 2.8 54.5 + - + +
201A LEU* 2.9 29.1 + - - +
202A LYS 3.4 7.1 + - - +
203A TYR* 1.3 76.9 - - - +
205A ASN* 1.3 64.5 + - - +
206A ARG* 2.8 38.8 + - - +
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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