Contacts of the strand formed by residues 92 - 97 (chain B) in PDB entry 1SXG
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 ASN 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 3.4 25.8 + - - +
61B THR 3.0 20.8 + - - -
62B THR* 3.2 22.5 + - - +
63B VAL 2.9 24.3 + - - -
91B TYR* 1.3 75.9 - - - +
93B ILE* 1.3 67.2 + - - +
107I HIS* 3.4 30.0 + - - -
108I LEU* 5.4 2.3 - - + +
111I ASN* 4.2 4.9 + - - +
115I LYS* 3.8 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.3 25.6 - - + +
65B VAL* 3.8 19.3 - - + -
82B ILE* 4.4 6.5 - - + +
83B GLU* 3.2 33.5 + - - +
86B ALA* 3.3 33.0 - - + -
91B TYR* 4.0 3.1 + - + -
92B ASN* 1.3 96.2 - - - +
94B ILE* 1.3 79.7 + - - +
95B LEU* 4.2 11.2 - - + +
302B MET* 4.3 2.7 - - + -
95I LEU 4.8 2.0 - - - +
96I SER* 4.0 19.5 - - - -
108I LEU* 5.6 1.7 - - - +
115I LYS* 4.5 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR* 3.9 19.5 - - + -
63B VAL 3.2 5.9 + - - -
64B GLY* 3.3 6.9 - - - -
65B VAL 2.7 34.3 + - - +
93B ILE* 1.3 81.0 - - - +
95B LEU* 1.3 59.2 + - - +
96B SER* 5.7 0.2 - - - -
112B MET* 3.2 33.4 - - + +
115B LYS* 5.8 4.0 - - + -
117B VAL* 4.6 4.3 - - + -
94I ILE* 3.6 40.4 - - + -
95I LEU 4.2 0.9 - - - -
112I MET* 3.8 5.8 - - + -
115I LYS* 3.3 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.1 44.6 - - + +
67B ILE* 3.4 34.5 - - + -
70B ILE* 5.4 1.6 - - + -
79B ALA* 4.3 18.8 - - + +
83B GLU* 5.8 0.7 - - - +
93B ILE* 4.5 9.6 - - + -
94B ILE* 1.3 75.3 - - - +
96B SER* 1.3 86.3 + - - +
97B ASN* 4.7 3.4 - - - +
70I ILE* 4.1 21.1 - - + -
94I ILE* 3.6 2.9 - - - +
95I LEU* 2.8 52.0 + - + +
96I SER* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL 3.2 3.2 + - - -
66B ILE* 3.2 45.2 - - - +
67B ILE 3.2 6.4 + - - +
95B LEU* 1.3 82.7 - - - +
97B ASN* 1.3 66.8 + - - +
108B LEU* 3.8 21.5 - - - +
112B MET* 4.2 10.6 - - - +
93I ILE* 3.6 22.0 - - - -
94I ILE* 5.7 0.4 - - - -
95I LEU* 4.9 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.1 12.2 - - - +
68B PRO 3.2 3.8 + - - +
69B ASP 3.4 1.0 - - - -
70B ILE* 2.5 55.4 - - - +
95B LEU* 4.7 1.0 - - - +
96B SER* 1.3 78.2 - - - +
98B SER* 1.3 59.5 + - - +
99B ASP* 4.1 1.1 - - + +
104B LYS* 3.3 17.7 - - - -
108B LEU* 3.1 15.0 - - - +
80I ARG* 3.0 23.6 - - - +
83I GLU* 2.8 29.5 + - - +
93I ILE* 5.4 1.8 - - - +
95I LEU* 4.0 8.7 - - - +
----------------------------------------------------------
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