Contacts of the helix formed by residues 199 - 206 (chain A) in PDB entry 4J2X
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 SER 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A GLN* 1.3 93.9 + - - +
200A LEU* 1.3 63.3 + - - +
201A LYS* 3.1 40.8 + - - -
202A ASN* 3.6 6.3 + - - -
206A CYS* 3.7 10.7 - - - -
305A PRO* 4.8 1.3 - - - -
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Residues in contact with LEU 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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199A SER* 1.3 70.2 - - - +
201A LYS* 1.4 64.3 + - - +
202A ASN 3.3 0.2 - - - -
203A ALA* 3.2 21.5 + - - +
206A CYS* 4.2 10.1 - - - -
267A TYR* 3.4 41.2 - - + -
269A HIS* 4.2 14.6 - - + +
305A PRO* 3.9 22.9 - - + -
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Residues in contact with LYS 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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199A SER* 3.1 28.0 + - - -
200A LEU* 1.4 78.6 - - - +
202A ASN* 1.4 57.1 + - + +
203A ALA* 3.5 3.1 + - - +
204A ASP* 4.5 2.3 - - - +
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Residues in contact with ASN 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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188A LYS* 4.2 11.2 + - - +
198A GLN* 3.7 20.9 + - - +
199A SER* 3.6 7.9 + - - +
200A LEU 3.3 0.2 - - - -
201A LYS* 1.4 75.2 - - + +
203A ALA* 1.4 54.2 + - - +
204A ASP* 3.0 44.4 + - - +
205A LEU* 3.2 34.5 + - - +
206A CYS* 4.1 1.2 + - - -
4G C 5.5 8.1 + - - -
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Residues in contact with ALA 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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200A LEU* 3.2 18.6 + - - +
201A LYS 3.4 2.7 + - - +
202A ASN* 1.4 68.7 - - - +
204A ASP* 1.3 57.4 + - - +
205A LEU 3.0 5.8 - - - -
206A CYS* 3.0 34.1 + - + +
267A TYR* 3.3 36.8 + - + +
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Residues in contact with ASP 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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80A LYS* 6.1 0.5 - - - +
81A VAL* 4.4 7.6 - - - +
164A HIS* 5.1 4.8 - - + -
188A LYS* 3.8 28.7 - - + +
201A LYS 4.5 1.7 - - - +
202A ASN* 3.0 25.6 - - - +
203A ALA* 1.3 80.7 + - - +
205A LEU* 1.3 62.3 + - - +
206A CYS 4.8 1.5 - - - +
308A GLN* 4.4 7.3 + - - +
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Residues in contact with LEU 205 (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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81A VAL* 4.8 1.6 - - + -
188A LYS* 3.8 24.5 - - + +
190A ILE* 3.7 31.4 - - + -
194A SER* 5.7 4.0 - - - -
198A GLN* 4.1 22.4 - - - +
202A ASN* 3.2 32.9 + - - +
203A ALA 3.0 0.4 - - - -
204A ASP* 1.3 83.8 - - - +
206A CYS* 1.3 60.7 + - - +
307A SER* 3.3 12.5 - - - +
308A GLN* 3.1 34.8 + - + -
4G C 5.4 3.6 - - - +
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Residues in contact with CYS 206 (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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198A GLN* 4.1 13.9 - - - -
199A SER 3.7 22.9 - - - -
200A LEU* 4.2 11.4 - - - -
202A ASN 4.3 0.7 - - - -
203A ALA* 3.0 25.0 + - - +
204A ASP 4.8 1.7 - - - +
205A LEU* 1.3 83.3 - - - +
207A ILE* 1.4 63.9 + - - +
208A ALA 4.0 2.4 + - - -
267A TYR* 3.7 23.0 - - + -
268A ILE 6.0 0.2 - - - +
305A PRO* 4.2 17.7 - - + -
306A VAL 3.9 5.4 - - - +
308A GLN* 4.1 5.5 + - - -
358A SER* 4.8 1.6 + - - -
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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