Contacts of the helix formed by residues 337 - 347 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B ALA 3.6 1.9 + - - -
336B LEU* 1.3 76.0 - - - +
338B ALA* 1.3 68.1 + - - +
339B ALA* 2.9 17.3 + - - +
340B ASP* 2.7 26.7 + - - +
341B PHE* 2.6 37.6 + - - -
382B PHE* 3.6 10.7 - - - -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B SER* 1.3 73.8 + - - +
339B ALA* 1.3 65.5 + - - +
341B PHE* 2.7 18.4 + - - +
342B GLU* 3.0 15.8 + - - +
378B ALA* 4.0 1.7 - - - +
379B GLU* 4.3 26.2 - - + +
382B PHE* 2.8 41.6 - - + -
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B SER* 2.9 8.6 + - - +
338B ALA* 1.3 81.5 - - - +
340B ASP* 1.3 64.8 + - - +
342B GLU* 3.1 34.6 + - - +
343B ARG* 3.5 12.7 + - - +
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Residues in contact with ASP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.3 11.4 - - + +
19B GLY* 5.1 6.4 - - - -
335B ALA 4.6 2.5 - - - +
336B LEU* 4.3 14.5 - - + +
337B SER* 2.7 51.7 + - - +
339B ALA* 1.3 73.9 - - - +
341B PHE* 1.3 62.4 + - - +
343B ARG* 2.8 23.9 + - - +
344B ILE* 2.8 28.5 + - + +
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Residues in contact with PHE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B LEU* 3.7 32.3 - - + -
337B SER 2.6 17.9 + - - -
338B ALA* 2.7 8.1 + - - +
340B ASP* 1.3 70.9 - - - +
342B GLU* 1.3 65.4 + - - +
343B ARG 2.7 0.5 + - - -
344B ILE* 2.9 11.7 + - + +
345B LEU* 2.7 27.6 + - - +
378B ALA* 3.7 13.5 - - + -
381B ALA* 3.8 14.6 - - + -
382B PHE* 3.3 48.2 - + + -
385B ASN* 4.2 7.2 - - - -
392B GLY* 3.5 21.3 - - - -
393B ALA* 3.8 19.5 - - + -
396B LEU* 3.8 20.7 - - + +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B ALA 3.0 12.3 + - - +
339B ALA* 3.1 25.0 + - - +
341B PHE* 1.3 75.3 - - - +
343B ARG* 1.3 61.6 + - + +
345B LEU* 3.0 17.5 - - - +
346B THR* 3.7 8.1 + - - -
374B VAL* 3.5 15.0 - - + +
375B LYS* 3.6 41.4 + - - +
378B ALA* 3.7 18.4 - - + +
379B GLU* 3.6 19.8 - - - +
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Residues in contact with ARG 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.6 33.3 - - + +
19B GLY* 4.7 6.5 - - - +
339B ALA* 3.5 16.6 - - - +
340B ASP* 2.8 11.7 + - - +
341B PHE 2.7 0.4 + - - -
342B GLU* 1.3 79.1 - - + +
344B ILE* 1.3 64.0 + - - +
345B LEU 2.6 6.6 + - - -
346B THR* 2.9 11.9 + - - -
347B GLU* 2.6 63.3 + - - +
348B PRO* 3.0 3.7 - - - +
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.4 22.9 - - + -
336B LEU* 4.5 5.2 - - + -
340B ASP* 2.8 37.3 + - + +
341B PHE* 2.9 25.5 + - + +
343B ARG* 1.3 72.1 - - - +
345B LEU* 1.3 61.8 + - - +
348B PRO* 3.3 21.5 - - + +
351B SER* 3.8 7.1 - - - -
352B LEU* 4.7 2.3 + - - +
393B ALA* 5.3 2.0 - - + -
396B LEU* 4.3 10.3 - - + -
451B ATP 2.9 55.4 - - + +
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B PHE 2.7 11.1 + - - +
342B GLU 3.0 17.9 - - - +
343B ARG 2.6 0.8 - - - -
344B ILE* 1.3 80.4 - - - +
346B THR* 1.3 54.8 + - - +
351B SER* 2.9 16.5 + - - -
352B LEU* 3.7 33.1 + - + -
353B THR* 3.3 23.8 + - + -
374B VAL* 3.7 23.3 - - + -
377B ILE* 3.5 30.3 - - + -
378B ALA* 4.0 12.8 - - + +
396B LEU* 4.3 14.1 - - + -
400B MET* 4.7 6.1 - - + -
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B GLU 3.9 8.3 + - - +
343B ARG* 2.9 5.8 + - - -
345B LEU* 1.3 87.6 - - + +
347B GLU* 1.3 71.0 + - - +
348B PRO* 3.6 2.2 - - - -
351B SER* 3.4 13.8 + - - -
353B THR* 3.9 12.3 - - + +
354B GLU* 3.8 11.6 - - - +
369B PHE* 6.3 0.2 - - + -
374B VAL* 3.9 28.7 - - + -
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN 4.7 1.4 - - - +
18B ILE* 3.7 9.7 - - + +
343B ARG* 2.6 69.9 + - + +
346B THR* 1.3 77.4 - - - +
348B PRO* 1.3 77.6 - - + +
349B HIS* 3.5 5.5 + - - -
354B GLU* 4.3 3.6 - - - +
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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