Contacts of the strand formed by residues 287 - 292 (chain J) 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 CYS 287 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J LEU* 3.2 33.5 + - - -
100J LYS* 3.1 33.4 - - + +
277J MET* 3.1 25.5 - - - +
280J MET* 3.6 31.2 - - + -
283J ALA* 4.7 1.1 - - - -
285J LYS 4.0 5.6 - - - +
286J THR* 1.3 72.7 - - - +
288J ILE* 1.3 67.7 + - - +
463J LEU* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ILE* 4.8 3.1 - - + -
87J MET 3.1 13.7 - - - +
88J PHE* 3.0 47.1 - - + -
89J LEU 4.4 0.7 - - - +
99J PHE* 3.6 27.1 - - + -
100J LYS 3.0 6.6 + - - +
101J ILE* 3.1 27.4 - - + +
102J LEU* 2.9 25.2 + - - +
277J MET* 3.4 2.5 - - - -
286J THR* 4.8 2.2 - - + -
287J CYS* 1.3 80.2 - - - +
289J THR* 1.3 62.1 + - - +
290J ILE* 5.2 0.4 - - + -
309J PHE* 3.8 29.2 - - + -
313J THR* 4.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 289 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85J LEU 3.9 0.3 - - - +
86J ILE* 3.1 6.5 - - - +
87J MET* 2.8 57.2 + - + -
102J LEU* 3.3 18.2 - - + +
273J SER* 4.1 13.3 + - - +
274J PHE* 5.1 0.9 - - - -
277J MET* 3.0 37.6 - - + +
288J ILE* 1.3 72.4 + - - +
290J ILE* 1.3 64.5 + - - +
291J LEU* 4.1 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85J LEU 3.8 4.3 - - - +
86J ILE* 4.3 15.0 - - + +
101J ILE* 3.4 29.2 - - + -
102J LEU 2.7 10.0 + - - +
103J GLY* 3.5 7.1 - - - -
104J ALA 3.1 17.2 + - - +
288J ILE* 4.8 1.1 - - + +
289J THR* 1.3 76.4 - - - +
291J LEU* 1.3 78.9 + - - +
292J VAL* 4.0 23.3 - - + +
308J LYS* 6.5 0.4 - - + -
309J PHE* 3.4 39.5 - - + -
338J MET* 5.0 0.9 - - - -
423J LEU* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ILE* 4.0 28.0 - - + -
84J GLY* 3.5 4.3 - - - -
85J LEU* 2.8 57.8 + - + +
87J MET* 5.5 0.7 - - + -
104J ALA* 3.1 17.0 - - + +
106J ILE* 3.9 21.7 - - + +
270J ALA* 3.9 30.5 - - + +
273J SER* 4.4 1.8 - - - +
274J PHE* 5.1 4.0 - - + -
289J THR* 4.1 19.3 - - + +
290J ILE* 1.3 92.2 - - - +
292J VAL* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 292 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J LYS 4.7 0.7 - - - -
84J GLY* 4.7 7.2 - - - -
85J LEU 5.6 0.4 - - - +
104J ALA 3.2 8.6 + - - +
105J HIS* 2.9 7.7 - - + -
106J ILE* 2.7 32.7 + - - +
290J ILE* 4.0 20.6 - - + -
291J LEU* 1.3 77.5 - - - +
293J ASP* 1.3 66.1 + - - +
295J GLU* 5.9 0.7 - - + -
303J THR 3.6 9.4 - - - +
304J GLY* 4.2 16.2 - - - +
306J GLN* 3.9 24.9 - - - +
308J LYS* 6.2 0.4 - - + -
419J ILE* 4.3 22.0 - - + -
----------------------------------------------------------
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