Contacts of the strand formed by residues 29 - 33 (chain J) in PDB entry 1XFB
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 29 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J ILE 4.8 1.8 - - - -
24J VAL* 6.5 0.2 - - - -
28J LYS* 1.3 74.3 - - - +
30J ILE* 1.3 63.8 + - - -
73J CYS 2.7 10.7 + - - -
74J ILE* 3.5 4.4 - - - -
75J GLY* 2.7 24.9 + - - -
76J GLY 3.4 3.3 + - - -
299J THR* 3.5 11.0 - - - -
300J PHE* 3.2 25.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J ILE* 3.6 33.7 - - + +
29J GLY* 1.3 75.7 - - - +
31J LEU* 1.3 65.0 + - - +
74J ILE* 4.9 0.4 - - - -
76J GLY* 3.3 14.8 - - - +
78J ILE* 3.6 34.5 - - + -
145J PHE* 4.4 2.7 - - + -
186J ILE* 3.8 26.0 - - + -
228J LEU* 4.5 1.1 - - + -
269J THR* 3.9 21.5 - - + -
299J THR* 5.7 0.2 - - - +
300J PHE* 2.8 24.7 + - - +
301J SER* 3.4 10.9 - - - +
302J TYR 3.3 24.3 + - - +
306J LEU* 3.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J GLY 4.3 0.2 + - - -
30J ILE* 1.3 71.4 - - - +
32J ALA* 1.3 63.0 + - - +
33J ALA* 3.4 6.1 + - + +
63J LEU* 4.2 20.2 - - + -
64J PHE* 4.3 11.0 - - + -
74J ILE* 4.5 12.8 - - + +
76J GLY 2.9 12.0 + - - +
77J VAL* 3.3 25.1 - - + +
78J ILE 2.8 27.0 + - - -
302J TYR 4.2 0.2 - - - +
306J LEU* 3.7 26.2 - - + -
307J GLN* 3.8 22.9 - - + +
328J PHE* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ILE 3.6 1.0 + - - -
31J LEU* 1.3 70.9 - - - +
33J ALA* 1.3 56.4 + - - +
34J ASP* 3.4 20.4 + - - +
35J GLU* 3.7 5.0 - - - +
78J ILE* 4.1 12.8 - - + -
147J LYS* 5.1 0.4 - - - +
230J LYS* 4.1 20.6 - - - +
301J SER* 4.4 2.9 - - - +
302J TYR 2.9 26.6 + - - +
303J GLY* 3.5 11.2 - - - +
307J GLN* 3.3 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 3.4 15.8 + - + -
32J ALA* 1.3 72.2 - - - +
34J ASP* 1.3 55.7 + - - +
35J GLU* 3.0 15.8 + - - +
60J ARG* 3.1 25.7 + - - +
63J LEU* 4.4 13.9 - - + -
64J PHE* 4.4 22.2 - - + -
77J VAL* 4.8 0.4 - - + -
78J ILE 3.0 17.3 + - - +
79J PHE* 4.3 0.7 - - - -
80J PHE 3.7 8.1 + - - -
83J THR* 4.9 2.1 + - - +
307J GLN* 4.2 1.6 - - - +
----------------------------------------------------------
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