Contacts of the helix formed by residues 210 - 218 (chain G) in PDB entry 1GUL
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 GLU 210 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C HIS* 4.4 18.4 - - + -
59C GLU* 3.5 22.3 - - - +
64C LYS* 4.3 17.2 - - - +
209G ASP* 1.3 75.7 - - - +
211G ILE* 1.3 64.7 + - + +
213G VAL* 3.7 6.6 - - - +
214G ARG* 2.9 43.7 + - - +
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Residues in contact with ILE 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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4C ARG 6.2 0.2 - - - +
6C LYS* 4.1 32.8 - - + +
59C GLU* 2.6 46.0 - - + +
209G ASP* 2.9 17.2 - - + +
210G GLU* 1.3 85.4 - - + +
212G TYR* 1.3 59.6 - - - +
214G ARG* 2.9 8.6 + - + +
215G THR* 2.7 45.2 + - - +
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Residues in contact with TYR 212 (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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9G TYR* 4.2 5.3 - + - -
10G PRO* 4.2 11.7 - - + +
11G ASN 3.9 9.4 - - - +
12G GLY* 3.6 32.3 - - - -
13G ARG 5.1 0.7 - - - -
14G GLY* 3.4 32.5 - - - -
110G PRO* 5.4 0.7 - - + -
111G PHE* 3.9 17.3 - + - -
208G PRO* 3.5 30.1 - - + -
209G ASP* 2.7 27.3 + - - +
211G ILE* 1.3 73.9 - - - +
213G VAL* 1.3 65.2 + - + +
215G THR* 3.0 7.7 + - + -
216G VAL* 2.7 59.9 + - + +
301G IBG 3.8 14.4 - - - +
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Residues in contact with VAL 213 (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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110G PRO* 3.8 35.2 - - + +
111G PHE* 3.8 15.9 - - + -
208G PRO* 4.7 2.5 - - + +
209G ASP 2.9 19.3 + - - +
210G GLU* 3.7 8.3 - - + +
212G TYR* 1.3 89.4 - - + +
214G ARG* 1.3 63.9 + - - +
216G VAL* 3.1 2.4 + - - +
217G TYR* 3.1 44.9 + - + -
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Residues in contact with ARG 214 (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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33C GLU* 5.3 10.5 + - - +
43C LYS* 5.6 13.5 - - - +
44C LEU* 6.2 2.0 - - - +
49C HIS* 5.2 9.9 + - - -
210G GLU* 2.9 30.5 + - - +
211G ILE* 2.9 12.5 + - + +
213G VAL* 1.3 76.0 - - - +
215G THR* 1.3 65.6 + - - +
217G TYR* 3.1 16.8 + - - +
218G ASN* 2.8 46.3 + - - +
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Residues in contact with THR 215 (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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6C LYS* 5.1 4.5 + - - -
10G PRO* 5.2 3.4 - - + -
11G ASN 6.2 0.2 - - - +
35G LEU 4.6 2.9 - - - +
36G GLU* 4.0 15.9 - - + +
211G ILE* 2.7 29.2 + - - +
212G TYR* 3.3 12.7 - - + -
214G ARG* 1.3 75.6 - - - +
216G VAL* 1.3 69.2 + - + +
218G ASN* 2.9 16.2 + - - +
219G ILE* 2.9 34.5 - - + +
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Residues in contact with VAL 216 (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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10G PRO* 4.5 12.1 - - + -
111G PHE* 3.0 41.1 - - + -
212G TYR* 2.7 59.4 + - + +
213G VAL 3.5 2.9 - - - +
215G THR* 1.3 72.4 - - - +
217G TYR* 1.3 68.8 + - + +
219G ILE* 2.9 13.6 + - - -
220G PHE* 3.0 35.2 + - + +
301G IBG 5.4 6.5 - - + -
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Residues in contact with TYR 217 (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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38G LYS* 4.3 1.6 + - - -
111G PHE* 3.7 42.1 + + + +
213G VAL* 3.1 42.6 + - + -
214G ARG* 3.3 15.0 - - - +
216G VAL* 1.3 81.3 - - + +
218G ASN* 1.3 72.1 + - - +
219G ILE 3.2 0.5 + - - -
220G PHE* 3.3 20.6 - - - +
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Residues in contact with ASN 218 (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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36G GLU 5.4 3.8 - - - +
37G THR* 6.0 0.9 - - - -
38G LYS* 3.1 27.0 + - - +
214G ARG* 2.8 47.8 + - - +
215G THR* 2.9 9.9 + - - +
217G TYR* 1.3 89.2 + - - +
219G ILE* 1.3 59.7 + - + +
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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