Contacts of the helix formed by residues 258 - 263 (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 GLU 258 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 3.5 19.2 - - + +
83B ALA* 3.4 7.1 + - - +
84B THR* 4.9 0.7 + - - +
257B ASP* 1.3 94.1 + - - +
259B ILE* 1.3 59.5 + - - +
260B ASP* 3.0 18.8 - - - +
261B LYS* 3.0 43.9 + - + +
308B SER 3.2 8.2 + - - -
309B GLY* 5.2 3.4 - - - -
310B ALA* 5.4 3.1 - - + +
451B ATP 4.8 4.8 + - - +
280C ARG* 3.5 24.2 + - - -
322C GLU* 2.5 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 4.1 13.5 - - + -
83B ALA* 3.6 9.6 - - - -
256B ILE* 3.5 29.6 - - + -
257B ASP 2.9 3.6 + - - -
258B GLU* 1.3 69.9 - - - +
260B ASP* 1.3 68.6 + - - +
261B LYS 2.8 7.1 + - - -
262B ILE* 3.0 36.8 + - + +
263B CYS* 3.8 1.7 + - - +
282B LEU* 4.3 15.7 - - + -
307B ALA* 4.0 13.9 - - + -
308B SER 3.0 14.5 + - - +
311B PHE* 4.0 17.3 - - + -
319B LEU* 4.4 16.7 - - + +
323B LEU* 4.6 15.7 - - + -
327B LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU* 3.2 29.3 - - - +
259B ILE* 1.3 83.9 - - - +
261B LYS* 1.3 70.1 + - - +
263B CYS* 3.3 20.1 - - - +
265B LYS* 5.9 3.5 + - - +
308B SER 4.2 0.4 + - - -
309B GLY* 3.4 3.3 - - - -
310B ALA* 3.3 18.0 + - - +
311B PHE* 3.0 58.3 + - + +
312B GLN* 4.7 1.9 + - - +
313B VAL* 5.4 9.2 - - + +
314B ALA* 4.7 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 3.7 22.0 - - + +
258B GLU* 3.0 45.4 + - + +
259B ILE 2.8 0.8 - - - -
260B ASP* 1.3 85.9 + - - +
262B ILE* 1.3 56.9 + - - +
263B CYS 3.2 9.4 + - - +
265B LYS* 5.2 17.4 - - - +
275B ARG* 3.5 26.0 + - - -
312B GLN* 6.1 0.6 - - - +
280C ARG* 3.3 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA* 3.5 45.3 - - + +
84B THR* 3.7 12.1 - - + +
87B THR* 4.9 1.8 - - - +
259B ILE* 3.0 30.2 + - + +
261B LYS* 1.3 78.6 - - - +
263B CYS* 1.3 59.6 + - - +
275B ARG* 3.5 28.3 - - + +
278B VAL* 3.8 29.2 - - + -
279B GLN* 2.8 33.3 + - + -
282B LEU* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE 4.4 0.4 - - - +
260B ASP 3.3 18.8 - - - +
261B LYS 3.2 3.8 - - - +
262B ILE* 1.3 80.6 - - - +
264B LYS* 1.3 71.9 + - - +
265B LYS* 4.9 1.8 - - + +
272B ASP* 4.3 0.9 - - - +
275B ARG* 4.0 21.9 + - - +
276B GLU 5.4 0.7 - - - -
311B PHE* 4.6 3.8 - - - -
314B ALA* 4.1 15.3 - - + -
315B ARG 4.3 2.7 - - - -
318B ASP* 3.6 33.4 - - - -
319B LEU* 3.2 32.5 - - - -
----------------------------------------------------------
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