Contacts of the helix formed by residues 205 - 211 (chain G) in PDB entry 6BAA
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 LYS 205 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203G GLU* 3.9 5.1 + - + +
204G VAL* 1.3 73.2 - - - +
206G PRO* 1.4 64.9 - - + +
207G PRO 3.5 0.4 - - - -
208G GLU* 3.0 3.5 + - - -
209G ASP* 2.5 41.8 + - + +
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Residues in contact with PRO 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G VAL* 4.1 2.9 - - + -
205G LYS* 1.4 91.8 - - + +
207G PRO* 1.3 57.7 - - + -
209G ASP* 4.5 3.8 - - + +
210G LEU* 2.6 37.5 + - - +
255G ILE* 3.6 35.9 - - + +
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Residues in contact with PRO 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G TRP* 5.0 9.6 - - + +
66G LEU* 6.4 0.2 - - - -
204G VAL* 3.7 22.7 - - + -
206G PRO* 1.3 93.9 - - + +
208G GLU* 1.3 60.3 + - - +
210G LEU* 3.3 7.0 - - + +
211G GLN* 2.9 28.9 + - - +
221G PHE* 3.6 49.7 - - + -
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Residues in contact with GLU 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ASN* 2.9 29.8 - - + +
50C ARG* 6.2 1.3 - - + -
331D SER* 5.0 6.8 + - - -
63G SER 5.9 3.4 - - - +
65G TRP 5.8 3.6 + - - +
203G GLU* 4.5 5.6 - - - +
204G VAL 3.3 23.1 - - - +
205G LYS* 3.0 4.4 + - - +
207G PRO* 1.3 81.0 - - + +
209G ASP* 1.3 59.6 + - - +
211G GLN* 3.3 13.2 - - - +
212G ASP* 3.7 1.4 + - - -
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Residues in contact with ASP 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D SER* 5.5 5.6 - - - -
205G LYS* 2.5 26.2 + - + +
206G PRO* 4.5 3.4 - - + +
208G GLU* 1.3 71.1 - - - +
210G LEU* 1.3 60.6 + - - +
212G ASP* 3.3 22.0 - - + +
255G ILE* 5.8 5.2 - - + -
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Residues in contact with LEU 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206G PRO 2.6 23.2 + - - +
207G PRO* 3.3 10.5 - - + +
209G ASP* 1.3 77.8 - - - +
211G GLN* 1.3 56.7 + - - +
212G ASP 3.1 6.1 + - - -
213G LEU* 3.8 2.9 + - - +
216G ARG* 3.0 37.0 + - - +
221G PHE* 4.7 10.5 - - + -
254G PRO* 4.9 11.7 - - + -
255G ILE* 4.7 12.3 - - + +
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Residues in contact with GLN 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LYS* 5.4 5.7 - - - +
48C ASN* 3.9 10.7 + - - +
63G SER* 5.3 8.1 - - - +
207G PRO 2.9 13.6 + - - +
208G GLU* 3.3 15.5 - - - +
209G ASP 3.3 0.4 - - - -
210G LEU* 1.3 74.5 - - - +
212G ASP* 1.3 61.7 + - - +
213G LEU 3.2 0.9 - - - -
214G GLY* 3.2 17.5 + - - +
216G ARG* 4.0 14.6 - - + +
221G PHE* 5.4 5.6 - - + -
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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