Contacts of the helix formed by residues 207 - 212 (chain X) in PDB entry 1T6B
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 ILE 207 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33X MET* 5.7 0.7 - - - -
52X ASN 5.4 0.2 - - - +
53X ILE* 6.5 0.7 - - + -
54X PRO* 3.9 30.1 - - + -
57X ASN* 5.1 4.0 - - - +
205X PRO* 3.8 28.0 - - + +
206X TRP* 1.3 81.7 + - - +
208X SER* 1.3 67.0 + - - +
209X ASN* 3.7 25.1 - - - +
210X ILE* 3.7 18.6 - - + -
211X HIS* 3.0 35.4 + - + +
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Residues in contact with SER 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206X TRP* 4.1 19.3 + - - +
207X ILE* 1.3 72.7 - - - +
209X ASN* 1.3 61.5 + - - +
210X ILE 3.2 4.5 + - - -
212X GLU* 3.6 36.8 + - - +
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Residues in contact with ASN 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207X ILE* 3.7 16.3 - - - +
208X SER* 1.3 79.2 - - - +
210X ILE* 1.3 68.2 + - - +
212X GLU* 5.2 0.7 - - - -
213X LYS* 4.1 24.5 - - - +
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Residues in contact with ILE 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X GLU 4.5 2.2 - - - +
52X ASN* 4.5 9.2 - - - +
53X ILE 4.6 1.6 - - - +
54X PRO* 4.0 36.1 - - + -
207X ILE* 3.4 22.6 + - + +
208X SER 3.2 0.4 - - - -
209X ASN* 1.3 93.0 - - - +
211X HIS* 1.3 79.0 + - + +
212X GLU 3.6 0.9 - - - -
213X LYS* 3.9 13.7 - - - +
214X LYS* 3.5 37.5 + - - +
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Residues in contact with HIS 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X ASN* 3.0 49.8 + - + +
193X THR* 3.8 13.4 - - + +
205X PRO 3.5 17.0 - - - -
206X TRP* 3.4 32.1 - + + -
207X ILE* 3.0 48.3 + - + +
210X ILE* 1.3 83.5 - - + +
212X GLU* 1.3 67.2 + - - +
213X LYS 3.4 0.7 - - - -
214X LYS 3.4 7.1 + - - +
215X GLY 3.6 8.3 + - - -
216X LEU* 4.0 27.6 - - + +
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Residues in contact with GLU 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206X TRP* 3.4 32.6 + - + -
208X SER* 3.6 26.3 + - - +
209X ASN* 5.7 0.4 - - - -
211X HIS* 1.3 78.6 - - - +
213X LYS* 1.3 64.1 + - + +
214X LYS 3.0 1.6 + - - -
215X GLY* 3.4 9.2 + - - -
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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