Contacts of the helix formed by residues 337 - 344 (chain S) 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 S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335S ALA 3.6 3.4 + - - -
336S LEU* 1.3 73.4 - - - +
338S ALA* 1.3 64.6 + - - +
339S ALA* 3.8 5.8 + - - +
340S ASP* 2.8 40.9 + - - +
341S PHE* 2.9 25.5 - - - -
382S PHE* 4.5 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337S SER* 1.3 74.9 - - - +
339S ALA* 1.3 63.2 + - - +
340S ASP 3.1 0.2 - - - -
341S PHE* 3.2 15.6 + - - +
342S GLU* 3.5 7.4 + - - +
378S ALA* 3.9 9.6 - - - +
379S GLU* 4.8 17.7 + - + +
382S PHE* 3.9 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337S SER* 3.3 6.6 + - - +
338S ALA* 1.3 78.5 - - - +
340S ASP* 1.3 64.2 + - - +
341S PHE 3.2 0.4 - - - -
342S GLU* 3.4 24.3 + - - +
343S ARG* 3.4 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 340 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ILE* 4.4 3.3 - - + +
19S GLY* 5.4 10.6 - - - -
334S THR* 5.3 1.6 + - - -
335S ALA 3.9 5.0 - - - +
336S LEU* 3.8 18.2 - - + +
337S SER* 2.8 46.3 + - - +
338S ALA 3.1 0.8 - - - -
339S ALA* 1.3 83.6 - - - +
341S PHE* 1.3 58.3 + - - +
342S GLU 3.3 0.2 - - - -
343S ARG* 3.9 14.1 + - - +
344S ILE* 3.2 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 341 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336S LEU* 3.1 49.1 - - + -
337S SER 2.9 21.1 - - - -
338S ALA* 3.2 2.5 + - - +
340S ASP* 1.3 76.8 - - - +
342S GLU* 1.3 60.5 + - - +
343S ARG 3.1 1.8 - - - -
344S ILE* 4.0 6.0 - - + +
345S LEU* 3.0 31.7 + - - +
378S ALA* 3.2 29.3 - - + +
381S ALA* 4.0 15.7 - - + -
382S PHE* 4.9 8.3 - + + -
385S ASN* 4.3 11.2 - - - -
390S ASN* 5.4 0.9 - - - -
392S GLY* 3.8 24.2 - - - -
393S ALA* 4.0 1.8 - - - -
395S ARG* 4.7 0.9 - - + -
396S LEU* 3.3 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 342 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338S ALA 3.5 2.6 + - - +
339S ALA* 3.5 24.6 - - - +
341S PHE* 1.3 79.8 - - - +
343S ARG* 1.3 62.0 + - + +
345S LEU* 4.0 2.6 - - - +
346S THR* 4.1 7.8 + - - +
371S THR* 5.1 3.1 - - - +
374S VAL* 3.6 28.8 - - + +
375S LYS* 3.6 45.5 + - + +
378S ALA* 3.2 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ILE* 3.0 43.8 - - + +
19S GLY* 5.5 2.2 - - - -
339S ALA* 3.4 20.8 + - - +
340S ASP* 4.1 10.5 + - - +
341S PHE 3.1 0.4 - - - -
342S GLU* 1.3 80.0 - - + +
344S ILE* 1.3 54.4 + - - +
345S LEU 2.7 15.5 + - - -
346S THR* 2.8 15.1 + - - -
347S GLU* 3.1 44.0 + - - +
348S PRO* 3.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ILE* 3.0 31.4 - - + +
336S LEU* 4.2 25.4 - - + -
340S ASP* 3.2 18.0 + - + +
341S PHE* 4.1 5.8 - - + +
343S ARG* 1.3 77.6 - - - +
345S LEU* 1.3 60.2 + - - +
346S THR 3.4 0.6 + - - -
348S PRO* 4.0 13.8 - - - +
351S SER* 4.3 7.8 - - - -
352S LEU* 4.9 4.2 + - + +
393S ALA* 5.0 1.6 - - + -
396S LEU* 4.1 20.1 - - + +
456S ATP 2.9 59.9 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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