Contacts of the strand formed by residues 78 - 82 (chain F) 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 PHE 78 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F THR* 5.0 2.0 - - + -
67F ALA* 3.9 17.5 - - + -
68F ARG* 3.6 52.5 - - + -
71F ALA* 3.4 29.2 - - + -
76F ALA 3.1 3.8 + - - +
77F PRO* 1.3 74.4 - - - +
79F ILE* 1.3 79.7 + - - +
80F LYS* 4.3 6.5 - - + -
103F LEU* 3.9 2.2 - - - +
106F SER* 4.1 16.0 + - - -
253F ILE* 3.4 21.3 - - + -
255F PHE* 3.6 35.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F PHE* 1.3 86.8 - - - +
80F LYS* 1.3 78.3 + - - +
81F VAL* 4.1 13.0 - - + -
99F ILE* 4.3 7.0 - - + +
102F ASP* 4.6 24.0 - - + +
103F LEU* 3.3 34.8 - - + -
106F SER* 5.9 0.2 - - - -
253F ILE 3.2 2.0 + - - -
254F VAL* 3.5 22.4 - - + +
255F PHE* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 3.2 26.8 + - - +
64F THR* 3.5 21.0 + - + +
68F ARG* 3.9 21.1 - - - +
78F PHE* 4.3 10.8 - - + -
79F ILE* 1.3 84.4 - - - +
81F VAL* 1.3 76.1 + - - +
82F GLU* 5.0 6.1 - - - -
255F PHE* 3.2 31.2 - - + +
257F ASP* 3.5 34.1 + - + -
455F ATP 4.5 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ILE* 4.1 16.6 - - + +
80F LYS* 1.3 84.9 - - - +
82F GLU* 1.3 68.3 + - - +
83F ALA* 3.4 0.4 + - - -
85F LYS* 5.0 13.2 - - + +
86F PHE* 4.4 9.9 - - + -
99F ILE* 3.9 39.3 - - + -
102F ASP* 5.8 2.5 - - - +
254F VAL* 5.0 2.7 - - + -
255F PHE 2.9 13.9 + - - +
256F ILE* 4.2 14.6 - - + -
257F ASP* 2.8 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ARG* 2.8 47.7 - - + +
283A LEU* 4.4 13.0 - - - +
284A PRO* 5.6 6.8 - - + +
322A GLU* 5.5 2.3 - - - +
80F LYS* 5.0 5.2 - - - -
81F VAL* 1.3 73.9 - - - +
83F ALA* 1.3 66.5 + - - +
84F THR* 3.2 24.5 - - - +
85F LYS* 3.1 29.0 + - + +
86F PHE* 3.6 6.8 - - - -
257F ASP* 4.0 23.5 - - - +
258F GLU* 3.5 13.8 - - + +
----------------------------------------------------------
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