Contacts of the helix formed by residues 337 - 345 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335D ALA 3.8 1.7 + - - -
336D LEU* 1.3 74.0 - - - +
338D ALA* 1.3 66.3 + - - +
339D ALA* 3.0 18.3 + - - +
340D ASP* 2.8 25.6 + - - +
341D PHE* 2.6 39.4 + - - -
382D PHE* 3.6 11.7 - - - -
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Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D SER* 1.3 75.0 + - - +
339D ALA* 1.3 55.9 + - - +
341D PHE* 2.8 27.2 + - - +
342D GLU* 2.9 17.3 + - - +
378D ALA* 4.0 2.9 - - - +
379D GLU* 4.2 26.9 - - + +
382D PHE* 3.0 34.9 - - + -
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Residues in contact with ALA 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D SER* 3.0 9.5 + - - +
338D ALA* 1.3 78.9 - - - +
340D ASP* 1.3 64.3 + - - +
342D GLU* 3.2 32.7 + - - +
343D ARG* 3.4 13.5 - - - +
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Residues in contact with ASP 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.5 11.3 - - + +
335D ALA 4.5 2.4 - - - +
336D LEU* 3.9 14.7 - - + +
337D SER* 2.8 42.3 + - - +
339D ALA* 1.3 76.6 - - - +
341D PHE* 1.3 53.6 + - - +
343D ARG* 2.7 34.7 + - - +
344D ILE* 2.6 32.3 + - + +
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Residues in contact with PHE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D LEU* 3.7 31.4 - - + -
337D SER 2.6 16.7 + - - -
338D ALA* 2.8 9.1 + - - +
340D ASP* 1.3 71.0 - - - +
342D GLU* 1.3 54.8 + - - +
343D ARG 2.8 0.3 + - - -
344D ILE* 3.0 11.2 + - + +
345D LEU* 2.7 37.1 + - - +
378D ALA* 3.6 18.2 - - + -
381D ALA* 3.8 11.9 - - + -
382D PHE* 3.3 51.4 - + + -
385D ASN* 4.0 8.1 - - - -
392D GLY* 3.8 19.3 - - - -
393D ALA* 3.9 18.8 - - - -
396D LEU* 3.8 19.3 - - + +
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Residues in contact with GLU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ALA 2.9 13.6 + - - +
339D ALA* 3.2 26.1 + - - +
340D ASP 3.1 0.2 - - - -
341D PHE* 1.3 76.9 - - - +
343D ARG* 1.3 58.6 + - + +
345D LEU* 3.5 11.9 - - - +
346D THR* 3.5 11.6 + - - -
374D VAL* 3.8 9.6 - - + +
375D LYS* 3.6 48.9 - - - +
378D ALA* 3.5 19.0 - - + +
379D GLU* 3.8 12.4 - - - +
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Residues in contact with ARG 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 3.8 35.2 - - + +
19D GLY* 5.0 4.6 - - - +
339D ALA* 3.4 16.8 - - - +
340D ASP* 2.7 22.8 + - - +
342D GLU* 1.3 72.1 - - + +
344D ILE* 1.3 54.1 + - - +
345D LEU 2.7 5.2 - - - -
346D THR 2.8 21.8 + - - -
347D GLU* 2.7 61.0 + - - +
348D PRO* 3.1 3.6 - - - +
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Residues in contact with ILE 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 3.8 21.3 - - + +
336D LEU* 4.6 12.6 - - + -
340D ASP* 2.6 38.1 - - + +
341D PHE* 3.1 20.4 - - + +
343D ARG* 1.3 74.4 - - - +
345D LEU* 1.3 61.3 + - - +
346D THR 3.4 0.5 + - - -
348D PRO* 3.5 21.2 - - + +
351D SER* 4.0 6.8 - - - -
352D LEU* 4.7 2.8 + - - +
393D ALA* 5.4 2.2 - - + -
396D LEU* 4.1 15.5 - - + -
453D ATP 3.1 47.8 - - + +
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D PHE 2.7 13.3 + - - +
342D GLU 3.5 2.0 - - - +
343D ARG 2.7 0.6 - - - -
344D ILE* 1.3 79.8 - - - +
346D THR* 1.3 57.9 + - - +
351D SER* 3.3 7.7 + - - -
352D LEU* 3.9 33.2 + - + -
353D THR* 3.0 25.8 + - + -
374D VAL* 3.5 33.2 - - + -
377D ILE* 3.7 26.9 - - + -
378D ALA* 3.8 21.3 - - + +
396D LEU* 4.3 15.0 - - + -
400D MET* 4.7 10.1 - - + -
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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