Contacts of the helix formed by residues 258 - 263 (chain E) in PDB entry 1G3I
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 258 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E GLU* 3.4 23.9 - - + +
83E ALA* 3.7 6.4 - - - +
84E THR* 4.9 1.5 + - - +
257E ASP* 1.3 92.6 + - - +
259E ILE* 1.3 61.1 + - - +
260E ASP* 2.9 23.3 - - - +
261E LYS* 3.0 42.2 + - + +
308E SER* 3.0 9.9 + - - -
309E GLY* 5.2 3.6 - - - -
310E ALA* 5.6 1.8 - - + +
454E ATP 4.0 7.7 + - - +
280F ARG* 3.5 17.9 + - - -
322F GLU* 2.6 29.9 - - - +
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Residues in contact with ILE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LEU* 4.3 12.6 - - + -
83E ALA* 3.7 9.0 - - - -
256E ILE* 3.6 28.5 - - + -
257E ASP 2.9 1.4 + - - -
258E GLU* 1.3 72.7 - - - +
260E ASP* 1.3 69.2 + - - +
261E LYS 2.9 7.5 + - - -
262E ILE* 3.0 32.6 + - + +
263E CYS 3.7 3.3 + - - -
282E LEU* 4.2 14.6 - - + -
307E ALA* 4.0 15.3 - - + -
308E SER 3.0 14.0 + - - +
311E PHE* 4.0 16.2 - - + -
319E LEU* 4.4 17.5 - - + +
323E LEU* 4.5 17.0 - - + -
327E LEU* 4.9 6.1 - - + -
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Residues in contact with ASP 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E GLU* 3.1 28.2 - - - +
259E ILE* 1.3 83.7 - - - +
261E LYS* 1.3 70.1 + - - +
262E ILE 3.4 0.2 - - - -
263E CYS* 3.2 19.7 - - - +
265E LYS* 5.8 3.8 + - - +
308E SER 4.2 0.2 + - - -
309E GLY* 3.3 4.1 - - - -
310E ALA* 3.2 19.3 + - - +
311E PHE* 3.1 58.5 + - + +
312E GLN* 4.8 2.3 + - - +
313E VAL* 5.6 7.8 - - + +
314E ALA* 4.7 5.6 - - + +
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Residues in contact with LYS 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E THR* 3.6 22.7 - - + -
258E GLU* 3.0 44.7 + - + +
259E ILE 2.9 0.8 - - - -
260E ASP* 1.3 87.4 - - - +
262E ILE* 1.3 58.2 + - - +
263E CYS 3.0 11.0 + - - +
265E LYS* 5.2 17.6 - - - +
275E ARG* 3.5 24.9 + - - -
312E GLN* 5.9 3.2 - - - +
280F ARG* 3.9 27.8 - - - +
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Residues in contact with ILE 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ALA* 3.6 43.7 - - + +
84E THR* 3.7 13.2 - - + +
87E THR* 4.9 2.5 - - - +
259E ILE* 3.0 28.3 + - + +
261E LYS* 1.3 75.8 - - - +
263E CYS* 1.3 62.3 + - - +
275E ARG* 3.7 25.0 - - + +
278E VAL* 3.6 31.4 - - + -
279E GLN* 3.0 34.0 + - + +
282E LEU* 4.4 7.9 - - + -
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Residues in contact with CYS 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E ILE 3.7 0.4 + - - -
260E ASP* 3.2 20.2 - - - +
261E LYS 3.0 8.2 - - - +
262E ILE* 1.3 82.5 - - - +
264E LYS* 1.3 67.6 + - - +
265E LYS* 5.1 1.6 - - - +
272E ASP* 4.5 0.9 - - - +
275E ARG* 4.1 16.8 + - - +
276E GLU 5.4 0.2 - - - -
279E GLN* 4.0 0.7 - - - +
311E PHE* 4.5 4.9 - - - -
314E ALA* 4.0 15.3 - - + -
315E ARG 4.1 4.0 - - - -
318E ASP* 3.7 34.3 - - - -
319E LEU* 3.3 31.4 - - - -
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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