Contacts of the helix formed by residues 200 - 207 (chain A) in PDB entry 4XH9
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A LEU* 4.6 1.6 - - + -
196A ALA* 3.3 25.4 + - + +
199A ALA* 1.3 83.0 - - + +
201A HIS* 1.3 67.9 + - - +
202A ASP 3.5 0.2 - - - -
203A PRO* 3.5 1.1 - - - +
204A MET* 3.2 34.3 + - + +
219A PHE* 3.8 13.9 - - + -
289A PHE* 4.0 7.9 - + - -
290A LEU* 4.5 7.2 - - + -
293A CYS* 3.6 29.8 - - + +
298A PHE* 3.9 16.6 - + - -
299A SER* 3.3 28.8 - - - -
302A LEU 3.7 6.1 + - - -
304A LEU* 3.7 34.8 - - + -
307A PHE* 3.4 33.2 - + - -
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Residues in contact with HIS 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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196A ALA 3.4 2.8 + - - -
197A ARG* 3.3 42.0 + - - +
200A TYR* 1.3 81.3 - - - +
202A ASP* 1.3 86.4 + - - +
205A LEU* 3.0 44.6 + - + +
212A GLU* 5.5 0.4 + - - +
215A LEU* 3.6 41.2 - - + +
216A THR* 4.7 5.1 + - - -
219A PHE* 3.7 34.3 - + + -
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ARG* 2.9 34.2 + - - +
198A LYS* 3.7 27.0 + - + +
201A HIS* 1.3 97.5 + - - +
203A PRO* 1.4 67.8 - - + +
205A LEU* 3.3 7.3 + - - +
206A LYS* 3.0 48.5 + - - +
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Residues in contact with PRO 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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198A LYS 3.2 22.0 - - - +
199A ALA* 3.3 21.5 - - - +
200A TYR 3.5 9.9 - - - +
202A ASP* 1.4 90.5 - - + +
204A MET* 1.3 56.9 + - - +
206A LYS* 3.3 7.2 + - + +
207A LEU* 2.8 43.6 + - + +
289A PHE* 3.8 19.1 - - + -
292A ARG* 5.3 4.5 - - - +
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Residues in contact with MET 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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200A TYR* 3.2 36.7 + - + +
201A HIS 3.8 2.5 - - - +
203A PRO* 1.3 79.7 - - - +
205A LEU* 1.3 61.5 + - - +
208A SER* 3.2 1.9 + - - -
209A ILE* 2.9 54.4 + - + -
210A MET* 3.4 37.4 + - + +
215A LEU* 3.9 17.5 - - + -
219A PHE* 4.1 9.6 - - + -
286A VAL* 5.1 4.7 - - - -
289A PHE* 3.5 30.7 - - + -
290A LEU* 4.8 6.1 - - + -
304A LEU* 4.4 10.8 - - + -
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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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201A HIS* 3.0 35.2 + - + +
202A ASP* 3.6 8.1 - - - +
204A MET* 1.3 76.7 - - - +
206A LYS* 1.3 65.8 + - + +
208A SER* 3.3 12.3 + - - -
210A MET 4.3 2.7 - - - +
211A SER 4.5 0.7 - - - -
212A GLU* 3.7 50.3 - - + +
215A LEU* 3.5 14.2 - - + +
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Residues in contact with LYS 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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202A ASP* 3.0 41.7 + - - +
203A PRO* 3.8 6.1 - - + +
205A LEU* 1.3 81.2 - - + +
207A LEU* 1.3 64.6 + - + +
208A SER* 3.3 2.6 + - - -
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Residues in contact with LEU 207 (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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203A PRO* 2.8 31.7 + - + +
206A LYS* 1.3 81.0 - - + +
208A SER* 1.3 64.3 + - - +
209A ILE* 3.8 27.1 - - + -
285A ARG* 3.0 25.5 + - - +
289A PHE* 4.6 1.6 - - + -
292A ARG* 3.9 24.9 - - - +
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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