Contacts of the helix formed by residues 203 - 211 (chain G) in PDB entry 6H25
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 THR 203 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105G GLN* 3.8 18.8 - - + +
106G GLN 3.6 28.9 - - - +
107G LYS* 4.7 18.4 - - + +
202G VAL* 1.3 82.9 - - - +
204G LEU* 1.3 68.6 + - - +
205G GLY 3.8 9.4 - - - +
206G LEU* 3.2 25.0 + - - +
207G ILE* 3.6 4.3 + - - +
235G GLY* 5.0 0.4 - - - -
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Residues in contact with LEU 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G SER 5.3 1.6 - - - +
106G GLN* 3.7 27.6 - - + +
107G LYS* 3.6 25.8 - - - +
108G ARG 4.8 0.9 - - - +
109G TYR* 4.1 22.2 - - + +
202G VAL 4.9 0.9 - - - +
203G THR* 1.3 74.0 - - - +
205G GLY* 1.3 60.3 + - - +
207G ILE* 3.2 9.4 + - + +
208G ARG* 3.0 46.6 + - - +
233G MET* 3.9 22.0 - - + +
234G ASN 3.8 20.2 - - - +
235G GLY* 4.2 6.3 - - - +
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Residues in contact with GLY 205 (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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103G ASP* 6.6 0.2 - - - -
104G SER 4.8 4.4 + - - -
105G GLN* 4.3 29.5 - - - +
203G THR* 3.2 6.5 - - - +
204G LEU* 1.3 78.8 - - - +
206G LEU* 1.3 56.9 + - - +
208G ARG* 3.4 11.1 + - - +
209G LYS* 2.9 30.4 + - - +
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Residues in contact with LEU 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G GLN* 5.6 0.6 - - - +
202G VAL* 4.0 27.4 - - + -
203G THR* 3.2 20.0 + - - +
205G GLY* 1.3 77.4 - - - +
207G ILE* 1.3 56.8 + - + +
209G LYS* 3.3 16.0 + - + +
210G LEU* 2.9 53.6 + - + +
237G ILE* 5.1 2.0 - - + -
254G LEU 3.4 22.7 - - - +
255G GLU* 4.7 3.4 - - - +
257G CYS* 3.8 38.6 - - - +
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Residues in contact with ILE 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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202G VAL* 4.2 15.9 - - + -
203G THR 3.6 2.6 + - - +
204G LEU* 3.2 9.9 + - - +
206G LEU* 1.3 74.8 - - - +
208G ARG* 1.3 63.2 + - - +
210G LEU* 4.4 4.9 - - + +
211G LEU* 2.9 53.1 + - + +
231G PHE* 4.5 17.5 - - + -
232G GLY 3.3 31.6 - - - +
233G MET* 3.9 23.6 - - + +
235G GLY* 3.6 22.2 - - - +
236G ARG 4.0 5.6 - - - +
237G ILE* 5.0 1.6 - - + -
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Residues in contact with ARG 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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69G PRO* 5.8 3.9 - - - +
101G TRP* 3.8 34.0 - - + -
103G ASP* 4.1 22.9 - - - +
104G SER 5.1 6.7 + - - +
204G LEU* 3.0 41.8 + - - +
205G GLY* 3.9 8.1 - - - +
207G ILE* 1.3 77.8 - - - +
209G LYS* 1.3 61.3 + - - +
211G LEU* 4.7 1.5 - - - -
212G ALA* 4.3 12.5 + - - +
233G MET* 4.9 14.2 - - + +
64K PHE* 3.2 36.5 + - - +
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Residues in contact with LYS 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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234D LYS* 5.0 19.1 - - - +
105G GLN* 5.3 10.2 - - - +
205G GLY 2.9 17.7 + - - +
206G LEU* 3.6 17.8 - - + +
208G ARG* 1.3 78.7 - - - +
210G LEU* 1.3 67.2 + - + +
211G LEU 3.6 0.2 + - - -
212G ALA* 3.7 15.7 + - - +
214G ASP 4.6 4.3 - - - +
215G CYS* 4.8 3.1 - - - -
257G CYS 5.5 4.6 + - - -
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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 LEU* 2.9 47.3 + - + +
207G ILE* 3.2 4.2 + - + +
209G LYS* 1.3 83.8 - - + +
211G LEU* 1.3 62.0 + - + +
212G ALA 3.2 6.3 + - - +
215G CYS* 3.5 40.3 - - - +
217G ILE* 4.3 17.9 - - + -
218G ILE* 5.0 7.2 - - + +
231G PHE* 4.2 30.3 - - + -
237G ILE* 5.4 3.4 - - + -
254G LEU* 4.5 17.0 - - + +
257G CYS* 5.6 5.6 - - - -
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Residues in contact with LEU 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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207G ILE* 2.9 38.3 + - + +
208G ARG* 4.7 3.1 - - - +
209G LYS 3.4 0.2 - - - -
210G LEU* 1.3 77.2 - - + +
212G ALA* 1.3 60.8 + - - +
218G ILE* 5.8 3.1 - - + -
231G PHE* 3.7 45.3 - - + -
233G MET* 4.5 11.4 - - - -
69K ASP 4.1 1.2 - - - +
70K LEU* 3.2 32.6 - - + -
71K LEU* 3.3 27.6 - - + +
72K TYR* 5.2 9.0 - - + +
75K MET* 5.7 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