Contacts of the helix formed by residues 207 - 215 (chain A) in PDB entry 3Q8A
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ASN* 5.1 13.2 - - + +
205A PRO* 4.4 13.2 - - + +
206A TRP* 1.3 86.9 - - - +
208A SER* 1.3 67.5 + - - +
209A ASN* 3.1 32.3 - - - +
210A ILE* 3.4 19.7 + - + -
211A HIS* 3.1 35.7 + - + +
212A GLU 3.8 2.8 + - - -
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Residues in contact with SER 208 (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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206A TRP* 4.3 10.4 - - - +
207A ILE* 1.3 73.8 - - - +
209A ASN* 1.3 74.3 + - - +
210A ILE 3.1 1.4 + - - -
212A GLU* 2.6 37.6 + - - +
213A LYS 4.1 0.3 + - - -
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Residues in contact with ASN 209 (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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207A ILE* 3.1 16.3 - - - +
208A SER* 1.3 81.8 + - - +
210A ILE* 1.3 89.3 + - - +
213A LYS* 4.4 11.4 - - - +
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Residues in contact with ILE 210 (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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55A SER* 5.6 8.3 - - - +
207A ILE* 3.4 25.9 + - + +
208A SER 3.1 0.6 - - - -
209A ASN* 1.3 97.0 + - - +
211A HIS* 1.3 86.6 + - + +
212A GLU 3.3 1.1 + - - -
213A LYS* 3.8 2.6 + - - +
214A LYS* 3.4 20.1 + - + +
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Residues in contact with HIS 211 (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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193A THR* 3.6 22.9 - - + +
204A SER* 5.3 4.8 - - - -
205A PRO 3.4 21.5 - - - -
206A TRP* 3.2 26.8 - + + -
207A ILE* 3.1 33.3 + - + +
210A ILE* 1.3 94.9 - - + +
212A GLU* 1.3 56.3 + - - +
214A LYS* 3.4 6.5 - - + -
215A GLY 2.8 29.1 + - - -
216A LEU* 3.1 26.9 + - + -
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Residues in contact with GLU 212 (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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206A TRP* 3.7 17.1 - - + -
207A ILE 3.8 1.0 + - - -
208A SER* 2.6 33.3 + - - +
211A HIS* 1.3 78.3 - - - +
213A LYS* 1.3 60.2 + - - +
215A GLY* 3.3 11.3 + - - -
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Residues in contact with LYS 213 (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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208A SER 4.1 1.4 + - - -
209A ASN 4.4 9.4 - - - +
210A ILE 3.8 7.0 + - - +
211A HIS 3.3 0.4 - - - -
212A GLU* 1.3 74.6 - - - +
214A LYS* 1.3 58.1 + - - +
215A GLY* 3.0 10.1 + - - -
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Residues in contact with LYS 214 (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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210A ILE* 3.4 17.0 + - + +
211A HIS* 3.2 3.0 + - + +
213A LYS* 1.3 76.8 - - - +
215A GLY* 1.3 61.0 + - - +
216A LEU* 3.0 29.8 - - + +
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Residues in contact with GLY 215 (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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211A HIS 2.8 9.0 + - - -
212A GLU* 3.3 9.2 + - - -
213A LYS 3.0 6.4 - - - -
214A LYS* 1.3 78.4 - - - +
216A LEU* 1.3 63.2 + - - +
217A THR* 3.5 4.5 + - - -
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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