Contacts of the strand formed by residues 84 - 89 (chain R) 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 GLY 84 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R THR* 4.0 6.0 + - - -
78R ALA 4.6 0.2 - - - -
79R ASN* 3.7 8.0 - - - +
80R ASN* 2.9 40.9 + - - +
82R GLY 3.4 0.2 - - - -
83R LYS* 1.3 81.6 - - - +
85R LEU* 1.3 63.2 + - - +
106R ILE* 4.9 0.2 - - - -
291R LEU 3.5 9.6 - - - -
292R VAL* 4.8 7.0 - - - -
303R THR* 4.4 3.6 - - - +
308R LYS* 5.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R THR* 4.2 10.8 - - - +
49R ILE* 3.4 34.8 - - + -
50R LYS* 3.3 32.3 - - - +
77R TYR* 3.9 15.9 - - + -
78R ALA 3.6 12.6 - - - +
84R GLY* 1.3 75.4 - - - +
86R ILE* 1.3 80.7 + - - +
87R MET* 4.2 12.1 - - + -
106R ILE* 5.5 0.9 - - + +
289R THR 3.9 0.5 - - - +
290R ILE* 3.7 1.3 - - - +
291R LEU* 2.8 55.6 + - + +
292R VAL* 5.6 0.8 - - - +
308R LYS* 5.1 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R VAL 4.1 0.2 - - - +
77R TYR* 3.2 3.8 - - - -
78R ALA* 2.9 53.0 + - + +
85R LEU* 1.3 79.0 - - - +
87R MET* 1.3 67.0 + - - +
88R PHE* 3.5 31.9 - - + -
288R ILE* 4.9 2.9 - - + -
289R THR 3.1 14.4 - - - +
290R ILE* 4.4 11.2 - - + -
308R LYS* 3.7 17.3 - - + -
309R PHE* 3.6 40.8 - - + +
312R ASN* 4.5 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R GLU* 3.2 38.8 - - - +
57R TYR* 4.1 13.7 - - + -
76R VAL 3.5 3.8 - - - -
77R TYR* 4.3 7.4 - - + -
85R LEU* 4.2 22.9 - - + -
86R ILE* 1.3 76.0 - - - +
88R PHE* 1.3 64.3 + - - +
274R PHE* 3.3 30.5 - - + -
277R MET* 3.2 26.6 - - + +
288R ILE* 3.1 9.4 - - - +
289R THR* 2.8 53.0 + - + +
291R LEU* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R TYR* 3.1 24.9 + - - -
59R ASN* 5.9 1.1 - - - -
75R LYS* 3.5 7.2 - - - -
76R VAL* 2.8 34.8 + - + +
77R TYR* 5.3 1.3 - - - -
78R ALA* 5.3 1.3 - - + -
86R ILE* 3.5 35.4 - - + -
87R MET* 1.3 77.8 - - - +
89R LEU* 1.3 62.4 + - - +
90R ILE* 4.8 7.0 - - + -
95R LEU* 6.1 0.9 - - + -
99R PHE* 4.7 6.3 - + - -
277R MET* 4.0 1.1 - - - -
286R THR* 5.0 4.9 - - + -
287R CYS 3.8 1.3 - - - -
288R ILE* 3.1 31.0 - - + -
312R ASN* 3.5 26.7 - - - -
313R THR* 4.1 25.4 - - + -
316R ASP* 4.0 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R TYR* 4.7 4.9 - - - +
73R GLY* 4.8 6.7 - - - +
74R ASP 3.4 13.9 - - - +
75R LYS* 4.4 19.5 - - + -
88R PHE* 1.3 79.4 - - - +
90R ILE* 1.3 68.9 + - - +
277R MET* 4.2 11.0 - - + +
280R MET* 3.2 36.8 - - + +
281R LYS* 5.3 1.3 - - - -
282R ASN 6.1 0.7 - - - +
283R ALA* 4.0 18.6 - - + +
286R THR* 3.1 15.2 - - - +
287R CYS* 3.2 40.7 + - - +
----------------------------------------------------------
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