Contacts of the strand formed by residues 253 - 257 (chain U) 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 ILE 253 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31U LEU* 5.7 2.0 - - + -
34U ARG* 4.1 15.5 - - - +
67U ALA 4.5 1.3 - - - +
70U LEU* 3.1 44.9 - - + +
71U ALA* 4.7 2.7 - - - -
74U ALA* 5.8 0.2 - - + -
76U ALA* 4.6 12.3 - - + -
77U PRO 3.0 15.4 + - - +
78U PHE* 3.5 28.6 - - + -
79U ILE 3.4 21.8 + - - -
103U LEU* 3.8 4.4 - - - +
252U GLY* 1.3 78.2 - - - +
254U VAL* 1.3 65.1 + - - +
304U LEU* 3.2 22.9 - - + +
306U ILE* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79U ILE* 3.8 9.0 - - + +
81U VAL* 4.7 6.7 - - + -
99U ILE* 3.4 32.5 - - + -
100U ILE* 5.1 2.7 - - + -
103U LEU* 4.3 12.1 - - + -
253U ILE* 1.3 76.9 - - - +
255U PHE* 1.3 58.6 + - - +
256U ILE* 4.2 5.3 - - + +
303U ILE* 3.7 20.4 - - + -
304U LEU 2.7 9.7 + - - +
305U PHE* 3.3 40.3 - - + +
306U ILE* 2.7 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55U MET* 3.3 3.8 - - + -
63U LYS 2.8 32.5 - - - -
64U THR* 2.9 30.1 - - + -
67U ALA* 3.4 16.2 - - + -
78U PHE* 4.0 16.8 - + + -
79U ILE 2.9 15.5 + - - +
80U LYS* 3.3 28.1 - - + -
81U VAL* 2.7 35.7 + - - +
253U ILE 4.1 0.2 + - - -
254U VAL* 1.3 73.6 - - - +
256U ILE* 1.3 58.1 + - - +
257U ASP* 3.8 3.5 + - + -
306U ILE* 3.0 43.7 - - + -
308U SER* 3.8 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81U VAL* 3.5 22.0 - - + +
83U ALA* 4.8 11.9 - - + +
99U ILE* 5.7 1.6 - - + -
254U VAL* 4.8 9.2 - - + +
255U PHE* 1.3 74.6 - - - +
257U ASP* 1.3 69.4 + - - +
259U ILE* 4.4 24.8 + - + -
262U ILE* 6.1 0.2 - - + -
282U LEU* 3.4 32.5 - - + -
286U VAL* 5.6 5.6 - - + -
305U PHE* 5.0 17.3 - - + -
306U ILE 2.9 11.1 + - - +
307U ALA* 3.4 14.4 - - + +
308U SER 2.9 25.8 + - - +
323U LEU* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 257 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283T LEU* 5.4 3.8 - - - +
287T GLU* 5.4 1.6 - - - +
322T GLU* 5.3 1.0 - - - +
63U LYS* 3.5 0.2 + - - -
64U THR* 4.0 4.5 + - - -
80U LYS* 4.1 24.4 + - + -
81U VAL 2.9 17.9 + - - +
82U GLU* 3.5 22.7 - - - +
83U ALA 4.1 4.9 + - - -
255U PHE* 3.8 4.7 + - + -
256U ILE* 1.3 76.0 - - - +
258U GLU* 1.3 81.4 + - - +
308U SER* 2.5 26.3 + - - +
458U ATP 2.5 42.0 + - - -
----------------------------------------------------------
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