Contacts of the helix formed by residues 337 - 344 (chain T) 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 SER 337 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335T ALA 3.6 2.3 + - - -
336T LEU* 1.3 71.9 - - - +
338T ALA* 1.3 63.9 + - - +
339T ALA* 3.8 5.5 + - - +
340T ASP* 2.8 41.4 + - - +
341T PHE* 2.9 25.5 - - - -
382T PHE* 4.5 11.0 - - - -
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Residues in contact with ALA 338 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337T SER* 1.3 75.3 - - - +
339T ALA* 1.3 63.1 + - - +
340T ASP 3.1 1.1 + - - -
341T PHE* 3.2 14.4 + - - +
342T GLU* 3.5 7.6 + - - +
378T ALA* 3.9 9.0 - - - +
379T GLU* 4.8 18.3 + - + +
382T PHE* 3.9 35.2 - - + -
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Residues in contact with ALA 339 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337T SER* 3.4 6.1 + - - +
338T ALA* 1.3 79.0 - - - +
340T ASP* 1.3 63.8 + - - +
341T PHE 3.3 0.2 - - - -
342T GLU* 3.4 24.8 + - - +
343T ARG* 3.4 25.7 - - - +
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Residues in contact with ASP 340 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T ILE* 4.6 1.9 - - + +
19T GLY* 5.6 9.3 - - - -
334T THR* 5.3 1.6 + - - -
335T ALA 3.8 5.9 - - - +
336T LEU* 3.8 18.2 - - + +
337T SER* 2.8 45.9 + - - +
338T ALA 3.1 0.6 - - - -
339T ALA* 1.3 82.9 - - - +
341T PHE* 1.3 58.7 + - - +
343T ARG* 3.8 14.1 + - - +
344T ILE* 3.2 34.5 + - + +
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Residues in contact with PHE 341 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336T LEU* 3.1 47.6 - - + -
337T SER 2.9 23.3 - - - -
338T ALA* 3.2 2.1 + - - +
340T ASP* 1.3 77.4 - - - +
342T GLU* 1.3 60.6 + - - +
343T ARG 3.1 2.5 - - - -
344T ILE* 4.0 6.2 - - + +
345T LEU* 3.0 32.2 + - - +
378T ALA* 3.3 29.4 - - + +
381T ALA* 4.0 15.5 - - + -
382T PHE* 4.9 7.6 - + + -
385T ASN* 4.3 11.7 - - - -
390T ASN* 5.5 0.7 - - - -
392T GLY* 3.7 23.3 - - - -
393T ALA* 4.0 2.2 - - - -
395T ARG* 4.7 0.7 - - + -
396T LEU* 3.3 41.3 - - + +
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Residues in contact with GLU 342 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338T ALA 3.5 2.4 + - - +
339T ALA* 3.5 25.5 - - - +
341T PHE* 1.3 79.9 - - - +
343T ARG* 1.3 62.1 + - + +
345T LEU* 4.0 3.4 - - - +
346T THR* 4.1 7.6 + - - -
371T THR 5.1 3.1 - - - +
374T VAL* 3.6 28.6 - - + +
375T LYS* 3.6 45.1 + - + +
378T ALA* 3.2 16.8 - - + +
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Residues in contact with ARG 343 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T ILE* 3.2 37.8 - - + +
19T GLY* 5.6 2.1 - - - -
339T ALA* 3.4 21.5 + - - +
340T ASP* 4.1 13.0 + - - +
341T PHE 3.1 0.2 - - - -
342T GLU* 1.3 79.6 - - + +
344T ILE* 1.3 53.9 + - - +
345T LEU 2.6 15.9 + - - -
346T THR* 2.8 15.2 + - - -
347T GLU* 3.2 45.4 + - - +
348T PRO* 3.4 4.0 - - - +
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Residues in contact with ILE 344 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T ILE* 3.0 31.4 - - + +
336T LEU* 4.2 22.4 - - + -
340T ASP* 3.2 19.1 + - + +
341T PHE* 3.8 5.8 + - + +
343T ARG* 1.3 76.9 - - - +
345T LEU* 1.3 59.6 + - - +
346T THR 3.4 0.4 - - - -
348T PRO* 4.0 12.8 - - + +
351T SER* 4.2 8.1 - - - -
352T LEU* 4.9 4.5 + - + +
393T ALA* 5.0 1.8 - - + -
396T LEU* 4.1 18.4 - - + -
457T ATP 3.2 57.0 - - + +
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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