Contacts of the strand formed by residues 77 - 80 (chain E) in PDB entry 2GLJ
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 TYR 77 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E LYS* 3.4 56.5 - - + +
53E GLU* 5.4 5.6 - - + -
57E TYR* 3.6 28.0 - - + -
58E ARG* 3.0 61.1 + - - +
59E ASN* 3.1 13.3 - - - +
60E ILE* 3.2 23.7 + - + +
76E VAL* 1.3 76.9 - - - +
78E ALA* 1.3 66.1 + - - +
79E ASN* 4.7 2.0 - - + -
85E LEU* 3.9 10.1 - - + -
86E ILE 3.3 10.1 - - - +
87E MET* 4.3 10.5 - - + -
88E PHE* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ASN* 5.2 8.3 - - - +
60E ILE* 4.9 4.9 - - - +
77E TYR* 1.3 79.1 - - - +
79E ASN* 1.3 62.0 + - - +
85E LEU* 3.5 6.8 - - - +
86E ILE* 2.9 41.7 + - + +
88E PHE* 5.3 1.8 - - + -
308E LYS* 3.7 5.9 - - - +
312E ASN* 3.4 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E THR* 3.5 13.5 - - - +
50E LYS* 3.3 35.4 - - + +
60E ILE* 3.9 29.0 - - + +
77E TYR* 4.2 1.4 - - - -
78E ALA* 1.3 73.1 - - - +
80E ASN* 1.3 69.1 + - - +
81E ARG* 3.5 4.0 + - - -
82E GLY* 2.5 37.3 + - - -
84E GLY 3.6 6.8 - - - +
308E LYS* 3.5 7.1 + - - -
334I TYR* 4.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ASN* 1.3 72.8 + - - +
81E ARG* 1.3 75.3 + - - +
82E GLY 2.8 2.4 + - - -
83E LYS* 2.8 15.6 + - - +
84E GLY* 2.9 22.4 + - - +
302E ALA 3.5 11.9 + - - +
303E THR* 3.3 21.8 - - - +
306E GLN* 3.6 5.9 + - - +
308E LYS* 3.1 42.4 - - + +
334I TYR* 3.4 25.2 + - - -
427I GLY* 6.0 0.2 - - - -
----------------------------------------------------------
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